Multiple platform build/check report for BioC 3.19 - CHECK results for miaViz on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for miaViz on nebbiolo1

To the developers/maintainers of the miaViz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miaViz.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: miaViz

Version: 1.12.0

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings miaViz_1.12.0.tar.gz

StartedAt: 2024-10-17 02:23:32 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 02:43:03 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 1171.2 seconds

RetCode: 1

Status: ERROR

CheckDir: miaViz.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings miaViz_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/miaViz.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘miaViz/DESCRIPTION’ ... OK
* this is package ‘miaViz’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘miaViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.add_signif_to_vector_labels : <anonymous>: no visible global function
  definition for ‘italic’
.clean_tree_data: no visible global function definition for ‘all_of’
.get_prevalence_plot_matrix: no visible binding for global variable
  ‘ID’
.rda_plotter: no visible binding for global variable ‘color’
Undefined global functions or variables:
  ID all_of color italic
* checking Rd files ... NOTE
checkRd: (-1) plotAbundanceDensity.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:33-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:52-53: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘miaViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotAbundanceDensity
> ### Title: Plot abundance density
> ### Aliases: plotAbundanceDensity
> ###   plotAbundanceDensity,SummarizedExperiment-method
> 
> ### ** Examples
> 
> tse <- microbiomeDataSets::atlas1006()
Error: 'atlas1006' is not an exported object from 'namespace:microbiomeDataSets'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/miaViz.Rcheck/00check.log’
for details.

Installation output

miaViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL miaViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘miaViz’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miaViz)

Tests output

miaViz.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(miaViz)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: TreeSummarizedExperiment
Loading required package: SingleCellExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: mia
Loading required package: MultiAssayExperiment
Loading required package: ggplot2
Loading required package: ggraph
> 
> test_check("miaViz")
trying URL 'https://cloud.r-project.org/src/contrib/credentials_2.0.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/xtable_1.8-4.tar.gz'
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* installing *source* package ‘credentials’ ...
** package ‘credentials’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (credentials)
* installing *source* package ‘zip’ ...
** package ‘zip’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -g -O2  -Wall miniz.c zip.c unixutils.c tools/cmdzip.c -o tools/cmdzip
gcc -g -O2  -Wall miniz.c zip.c unixutils.c tools/cmdunzip.c -o tools/cmdunzip
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c miniz.c -o miniz.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rzip.c -o rzip.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c zip.c -o zip.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c unixutils.c -o unixutils.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o zip.so init.o miniz.o rzip.o zip.o unixutils.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing via 'install.libs.R' to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-zip/00new/zip
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (zip)
* installing *source* package ‘gitcreds’ ...
** package ‘gitcreds’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gitcreds)
* installing *source* package ‘ini’ ...
** package ‘ini’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ini)
* installing *source* package ‘xtable’ ...
** package ‘xtable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xtable)
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall  -c Reader.cpp -o Reader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall  -c Tokenizer.cpp -o Tokenizer.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall -c sourcetools-init.c -o sourcetools-init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-sourcetools/00new/sourcetools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sourcetools)
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag not needed.
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c callback_registry.cpp -o callback_registry.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c debug.cpp -o debug.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c later.cpp -o later.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c later_posix.cpp -o later_posix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c later_win32.cpp -o later_win32.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c timer_posix.cpp -o timer_posix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c timestamp_unix.cpp -o timestamp_unix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c timestamp_win32.cpp -o timestamp_win32.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c tinycthread.c -o tinycthread.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-later/00new/later/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (later)
* installing *source* package ‘clipr’ ...
** package ‘clipr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clipr)
* installing *source* package ‘rstudioapi’ ...
** package ‘rstudioapi’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rstudioapi)
* installing *source* package ‘whisker’ ...
** package ‘whisker’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (whisker)
* installing *source* package ‘downlit’ ...
** package ‘downlit’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (downlit)
* installing *source* package ‘httr2’ ...
** package ‘httr2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httr2)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-lxml2
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c connection.cpp -o connection.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_doc.cpp -o xml2_doc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_init.cpp -o xml2_init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_namespace.cpp -o xml2_namespace.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_node.cpp -o xml2_node.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_output.cpp -o xml2_output.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_schema.cpp -o xml2_schema.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_url.cpp -o xml2_url.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall  -c xml2_xpath.cpp -o xml2_xpath.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -lxml2 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-xml2/00new/xml2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xml2)
* installing *source* package ‘htmlwidgets’ ...
** package ‘htmlwidgets’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (htmlwidgets)
* installing *source* package ‘prettyunits’ ...
** package ‘prettyunits’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (prettyunits)
* installing *source* package ‘xopen’ ...
** package ‘xopen’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xopen)
* installing *source* package ‘brew’ ...
** package ‘brew’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (brew)
* installing *source* package ‘commonmark’ ...
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o extensions.o init.o wrapper.o commonmark.so cmark/libstatcmark.a
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions.c -o extensions.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c wrapper.c -o wrapper.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/cmark.c -o cmark/cmark.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/node.c -o cmark/node.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/iterator.c -o cmark/iterator.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/blocks.c -o cmark/blocks.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/inlines.c -o cmark/inlines.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/scanners.c -o cmark/scanners.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/utf8.c -o cmark/utf8.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/buffer.c -o cmark/buffer.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/references.c -o cmark/references.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/render.c -o cmark/render.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/man.c -o cmark/man.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/xml.c -o cmark/xml.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/html.c -o cmark/html.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/commonmark.c -o cmark/commonmark.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/latex.c -o cmark/latex.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/houdini_href_e.c -o cmark/houdini_href_e.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/houdini_html_e.c -o cmark/houdini_html_e.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/houdini_html_u.c -o cmark/houdini_html_u.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/cmark_ctype.c -o cmark/cmark_ctype.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/arena.c -o cmark/arena.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/linked_list.c -o cmark/linked_list.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/plugin.c -o cmark/plugin.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/registry.c -o cmark/registry.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/syntax_extension.c -o cmark/syntax_extension.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/plaintext.c -o cmark/plaintext.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/footnotes.c -o cmark/footnotes.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cmark/map.c -o cmark/map.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/autolink.c -o extensions/autolink.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/core-extensions.c -o extensions/core-extensions.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/ext_scanners.c -o extensions/ext_scanners.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/strikethrough.c -o extensions/strikethrough.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/table.c -o extensions/table.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/tagfilter.c -o extensions/tagfilter.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c extensions/tasklist.c -o extensions/tasklist.o
ar rcs cmark/libstatcmark.a cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o commonmark.so extensions.o init.o wrapper.o -Lcmark -lstatcmark -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-commonmark/00new/commonmark/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (commonmark)
* installing *source* package ‘ellipsis’ ...
** package ‘ellipsis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dots.c -o dots.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o ellipsis.so dots.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-ellipsis/00new/ellipsis/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ellipsis)
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
* installing *source* package ‘sessioninfo’ ...
** package ‘sessioninfo’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sessioninfo)
* installing *source* package ‘promises’ ...
** package ‘promises’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c promise_task.cpp -o promise_task.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o promises.so RcppExports.o promise_task.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-promises/00new/promises/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (promises)
* installing *source* package ‘gert’ ...
** package ‘gert’ successfully unpacked and MD5 sums checked
** using staged installation
Found OpenSSL3
Using static libgit2 for Linux x86_64
Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include
Using PKG_LIBS=-L/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl
Configuration OK!
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c branch.c -o branch.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c commit.c -o commit.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c config.c -o config.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c conflicts.c -o conflicts.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c files.c -o files.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ignore.c -o ignore.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rebase.c -o rebase.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c stash.c -o stash.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c submodules.c -o submodules.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c tag.c -o tag.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o -L/tmp/RtmpPur0OB/R.INSTALL1b082cbef7496/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-gert/00new/gert/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gert)
* installing *source* package ‘gh’ ...
** package ‘gh’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gh)
* installing *source* package ‘pkgdown’ ...
** package ‘pkgdown’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgdown)
* installing *source* package ‘profvis’ ...
** package ‘profvis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c pause.c -o pause.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c profvis-init.c -o profvis-init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o profvis.so pause.o profvis-init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-profvis/00new/profvis/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (profvis)
* installing *source* package ‘rcmdcheck’ ...
** package ‘rcmdcheck’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rcmdcheck)
* installing *source* package ‘roxygen2’ ...
** package ‘roxygen2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c escapeExamples.cpp -o escapeExamples.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c isComplete.cpp -o isComplete.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c leadingSpaces.cpp -o leadingSpaces.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c parser2.cpp -o parser2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c wrapUsage.cpp -o wrapUsage.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o roxygen2.so cpp11.o escapeExamples.o isComplete.o leadingSpaces.o parser2.o wrapUsage.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-roxygen2/00new/roxygen2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (roxygen2)
* installing *source* package ‘rversions’ ...
** package ‘rversions’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rversions)
* installing *source* package ‘urlchecker’ ...
** package ‘urlchecker’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (urlchecker)
* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** using staged installation
** Using libuv found by pkg-config in /usr
** PKG_CFLAGS=
** PKG_LIBS=-luv -lpthread -ldl -lrt
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c callback.cpp -o callback.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c callbackqueue.cpp -o callbackqueue.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c filedatasource-unix.cpp -o filedatasource-unix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c filedatasource-win.cpp -o filedatasource-win.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c fs.cpp -o fs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c gzipdatasource.cpp -o gzipdatasource.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c http.cpp -o http.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c httprequest.cpp -o httprequest.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c httpresponse.cpp -o httpresponse.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c httpuv.cpp -o httpuv.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall -c md5.c -o md5.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c mime.cpp -o mime.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c socket.cpp -o socket.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c staticpath.cpp -o staticpath.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c thread.cpp -o thread.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c timegm.cpp -o timegm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c uvutil.cpp -o uvutil.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c webapplication.cpp -o webapplication.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c websockets-base.cpp -o websockets-base.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c websockets-hixie76.cpp -o websockets-hixie76.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c websockets-hybi03.cpp -o websockets-hybi03.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c websockets-ietf.cpp -o websockets-ietf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c websockets.cpp -o websockets.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c winutils.cpp -o winutils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall -c http-parser/http_parser.c -o http-parser/http_parser.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall -c sha1/sha1.c -o sha1/sha1.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/later/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c base64/base64.cpp -o base64/base64.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o -luv -lpthread -ldl -lrt ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-httpuv/00new/httpuv/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httpuv)
* installing *source* package ‘usethis’ ...
** package ‘usethis’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (usethis)
* installing *source* package ‘shiny’ ...
** package ‘shiny’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (shiny)
* installing *source* package ‘miniUI’ ...
** package ‘miniUI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miniUI)
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (devtools)

The downloaded source packages are in
	'/tmp/Rtmpt2ldmm/downloaded_packages'
mia    (1.12.0 -> c76bc909b...) [GitHub]
bitops (NA     -> 1.0-9       ) [CRAN]
RCurl  (NA     -> 1.98-1.16   ) [CRAN]
trying URL 'https://cloud.r-project.org/src/contrib/bitops_1.0-9.tar.gz'
Content type 'application/x-gzip' length 10941 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.16.tar.gz'
Content type 'application/x-gzip' length 728943 bytes (711 KB)
==================================================
downloaded 711 KB

* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit-ops.c -o bit-ops.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cksum.c -o cksum.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-bitops/00new/bitops/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bitops)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... /usr/bin/curl-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
Version has a libidn field
Version has CURLOPT_URL
Version has CURLINFO_EFFECTIVE_URL
Version has CURLINFO_RESPONSE_CODE
Version has CURLINFO_TOTAL_TIME
Version has CURLINFO_NAMELOOKUP_TIME
Version has CURLINFO_CONNECT_TIME
Version has CURLINFO_PRETRANSFER_TIME
Version has CURLINFO_SIZE_UPLOAD
Version has CURLINFO_SIZE_DOWNLOAD
Version has CURLINFO_SPEED_DOWNLOAD
Version has CURLINFO_SPEED_UPLOAD
Version has CURLINFO_HEADER_SIZE
Version has CURLINFO_REQUEST_SIZE
Version has CURLINFO_SSL_VERIFYRESULT
Version has CURLINFO_FILETIME
Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
Version has CURLINFO_CONTENT_LENGTH_UPLOAD
Version has CURLINFO_STARTTRANSFER_TIME
Version has CURLINFO_CONTENT_TYPE
Version has CURLINFO_REDIRECT_TIME
Version has CURLINFO_REDIRECT_COUNT
Version has CURLINFO_PRIVATE
Version has CURLINFO_HTTP_CONNECTCODE
Version has CURLINFO_HTTPAUTH_AVAIL
Version has CURLINFO_PROXYAUTH_AVAIL
Version has CURLINFO_OS_ERRNO
Version has CURLINFO_NUM_CONNECTS
Version has CURLINFO_SSL_ENGINES
Version has CURLINFO_COOKIELIST
Version has CURLINFO_LASTSOCKET
Version has CURLINFO_FTP_ENTRY_PATH
Version has CURLINFO_REDIRECT_URL
Version has CURLINFO_PRIMARY_IP
Version has CURLINFO_APPCONNECT_TIME
Version has CURLINFO_CERTINFO
Version has CURLINFO_CONDITION_UNMET
Version has CURLOPT_WRITEDATA
Version has CURLOPT_KEYPASSWD
Version has CURLOPT_DIRLISTONLY
Version has CURLOPT_APPEND
Version has CURLOPT_KRBLEVEL
Version has CURLOPT_USE_SSL
Version has CURLOPT_TIMEOUT_MS
Version has CURLOPT_CONNECTTIMEOUT_MS
Version has CURLOPT_HTTP_TRANSFER_DECODING
Version has CURLOPT_HTTP_CONTENT_DECODING
Version has CURLOPT_NEW_FILE_PERMS
Version has CURLOPT_NEW_DIRECTORY_PERMS
Version has CURLOPT_POSTREDIR
Version has CURLOPT_OPENSOCKETFUNCTION
Version has CURLOPT_OPENSOCKETDATA
Version has CURLOPT_COPYPOSTFIELDS
Version has CURLOPT_PROXY_TRANSFER_MODE
Version has CURLOPT_SEEKFUNCTION
Version has CURLOPT_SEEKDATA
Version has CURLOPT_CRLFILE
Version has CURLOPT_ISSUERCERT
Version has CURLOPT_ADDRESS_SCOPE
Version has CURLOPT_CERTINFO
Version has CURLOPT_USERNAME
Version has CURLOPT_PASSWORD
Version has CURLOPT_PROXYUSERNAME
Version has CURLOPT_PROXYPASSWORD
Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5
Version has CURLOPT_NOPROXY
Version has CURLOPT_TFTP_BLKSIZE
Version has CURLOPT_SOCKS5_GSSAPI_SERVICE
Version has CURLOPT_SOCKS5_GSSAPI_NEC
Version has CURLOPT_PROTOCOLS
Version has CURLOPT_REDIR_PROTOCOLS
Version has CURLOPT_SSH_AUTH_TYPES
Version has CURLOPT_SSH_PUBLIC_KEYFILE
Version has CURLOPT_SSH_PRIVATE_KEYFILE
Version has CURLOPT_FTP_SSL_CCC
Version has CURLOPT_COOKIELIST
Version has CURLOPT_IGNORE_CONTENT_LENGTH
Version has CURLOPT_FTP_SKIP_PASV_IP
Version has CURLOPT_FTP_FILEMETHOD
Version has CURLOPT_LOCALPORT
Version has CURLOPT_LOCALPORTRANGE
Version has CURLOPT_CONNECT_ONLY
Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION
Version has CURLOPT_CONV_TO_NETWORK_FUNCTION
Version has CURLOPT_CONV_FROM_UTF8_FUNCTION
Version has CURLOPT_MAX_SEND_SPEED_LARGE
Version has CURLOPT_MAX_RECV_SPEED_LARGE
Version has CURLOPT_FTP_ALTERNATIVE_TO_USER
Version has CURLOPT_SOCKOPTFUNCTION
Version has CURLOPT_SOCKOPTDATA
Version has CURLOPT_SSL_SESSIONID_CACHE
libcurl version: libcurl 7.81.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curlInit.c -o curlInit.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl_base64.c -o curl_base64.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c enums.c -o enums.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c json.c -o json.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c memoryManagement.c -o memoryManagement.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c myUTF8.c -o myUTF8.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-RCurl/00new/RCurl/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCurl)

The downloaded source packages are in
	'/tmp/Rtmpt2ldmm/downloaded_packages'
R.methodsS3  (NA -> 1.8.2   ) [CRAN]
R.oo         (NA -> 1.26.0  ) [CRAN]
nloptr       (NA -> 2.1.1   ) [CRAN]
minqa        (NA -> 1.2.8   ) [CRAN]
backports    (NA -> 1.5.0   ) [CRAN]
checkmate    (NA -> 2.3.2   ) [CRAN]
Formula      (NA -> 1.2-5   ) [CRAN]
htmlTable    (NA -> 2.4.3   ) [CRAN]
data.table   (NA -> 1.16.2  ) [CRAN]
zoo          (NA -> 1.8-12  ) [CRAN]
openxlsx     (NA -> 4.2.7.1 ) [CRAN]
slam         (NA -> 0.1-54  ) [CRAN]
R.utils      (NA -> 2.12.3  ) [CRAN]
rjson        (NA -> 0.2.23  ) [CRAN]
RcppParallel (NA -> 5.1.9   ) [CRAN]
lme4         (NA -> 1.1-35.5) [CRAN]
Hmisc        (NA -> 5.1-3   ) [CRAN]
lpSolve      (NA -> 5.6.21  ) [CRAN]
sandwich     (NA -> 3.1-1   ) [CRAN]
mvtnorm      (NA -> 1.3-1   ) [CRAN]
rbiom        (NA -> 1.0.3   ) [CRAN]
mediation    (NA -> 4.5.0   ) [CRAN]
trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz'
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* installing *source* package ‘R.methodsS3’ ...
** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.methodsS3)
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... /usr/bin/cmake
using NLopt via local cmake build on x86_64 
set CMAKE_BIN=/usr/bin/cmake
set CC=gcc
set CFLAGS=-I/usr/local/include -fpic -g -O2 -Wall
set CXX=g++
set CXXFLAGS=-std=gnu++11 -I/usr/local/include -fpic -g -O2 -Wall
set LDFLAGS=-L/usr/local/lib
-- The C compiler identification is GNU 11.4.0
-- The CXX compiler identification is GNU 11.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- NLopt version 2.7.1
-- Looking for getopt.h
-- Looking for getopt.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for getpid
-- Looking for getpid - found
-- Looking for syscall
-- Looking for syscall - found
-- Looking for isinf
-- Looking for isinf - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for qsort_r
-- Looking for qsort_r - found
-- Looking for time
-- Looking for time - found
-- Looking for copysign
-- Looking for copysign - found
-- Looking for getopt
-- Looking for getopt - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of uint32_t
-- Check size of uint32_t - done
-- Check size of unsigned int
-- Check size of unsigned int - done
-- Check size of unsigned long
-- Check size of unsigned long - done
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Looking for fpclassify
-- Looking for fpclassify - TRUE
-- Performing Test HAVE_THREAD_LOCAL_STORAGE
-- Performing Test HAVE_THREAD_LOCAL_STORAGE - Success
-- Performing Test HAVE_THREAD_LOCAL_STORAGE
-- Performing Test HAVE_THREAD_LOCAL_STORAGE - Failed
-- Looking for __cplusplus
-- Looking for __cplusplus - found
-- Performing Test SUPPORTS_STDCXX11
-- Performing Test SUPPORTS_STDCXX11 - Success
-- Performing Test HAS_FPIC
-- Performing Test HAS_FPIC - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-build
[  3%] Generating nlopt.hpp
[  3%] Generating nlopt.f
[  3%] Built target generate-fortran
[  3%] Built target generate-cpp
[  7%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRect.c.o
[  7%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/direct_wrap.c.o
[  9%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRserial.c.o
[ 11%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRsubrout.c.o
[ 13%] Building C object CMakeFiles/nlopt.dir/src/algs/cdirect/cdirect.c.o
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c: In function 'cdirect':
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:596:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  596 |      ret = cdirect_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n, x, minf, stop,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  597 |                             magic_eps, which_alg);
      |                             ~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:476:14: note: by argument 4 of type 'const double *' to 'cdirect_unscaled' declared here
  476 | nlopt_result cdirect_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:596:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  596 |      ret = cdirect_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n, x, minf, stop,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  597 |                             magic_eps, which_alg);
      |                             ~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:476:14: note: by argument 5 of type 'const double *' to 'cdirect_unscaled' declared here
  476 | nlopt_result cdirect_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:596:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  596 |      ret = cdirect_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n, x, minf, stop,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  597 |                             magic_eps, which_alg);
      |                             ~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:476:14: note: by argument 4 of type 'const double *' to 'cdirect_unscaled' declared here
  476 | nlopt_result cdirect_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:596:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  596 |      ret = cdirect_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n, x, minf, stop,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  597 |                             magic_eps, which_alg);
      |                             ~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c:476:14: note: by argument 5 of type 'const double *' to 'cdirect_unscaled' declared here
  476 | nlopt_result cdirect_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/cdirect.c: At top level:
cc1: note: unrecognized command-line option '-Wno-unknown-warning-option' may have been intended to silence earlier diagnostics
[ 15%] Building C object CMakeFiles/nlopt.dir/src/algs/cdirect/hybrid.c.o
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c: In function 'cdirect_hybrid':
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:337:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  337 |      ret = cdirect_hybrid_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  338 |                                    x, minf, stop, local_alg, local_maxeval,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  339 |                                    randomized_div);
      |                                    ~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:230:14: note: by argument 4 of type 'const double *' to 'cdirect_hybrid_unscaled' declared here
  230 | nlopt_result cdirect_hybrid_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:337:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  337 |      ret = cdirect_hybrid_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  338 |                                    x, minf, stop, local_alg, local_maxeval,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  339 |                                    randomized_div);
      |                                    ~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:230:14: note: by argument 5 of type 'const double *' to 'cdirect_hybrid_unscaled' declared here
  230 | nlopt_result cdirect_hybrid_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:337:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  337 |      ret = cdirect_hybrid_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  338 |                                    x, minf, stop, local_alg, local_maxeval,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  339 |                                    randomized_div);
      |                                    ~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:230:14: note: by argument 4 of type 'const double *' to 'cdirect_hybrid_unscaled' declared here
  230 | nlopt_result cdirect_hybrid_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:337:12: warning: '<unknown>' may be used uninitialized [-Wmaybe-uninitialized]
  337 |      ret = cdirect_hybrid_unscaled(n, cdirect_uf, &d, d.x+n, d.x+2*n,
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  338 |                                    x, minf, stop, local_alg, local_maxeval,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  339 |                                    randomized_div);
      |                                    ~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c:230:14: note: by argument 5 of type 'const double *' to 'cdirect_hybrid_unscaled' declared here
  230 | nlopt_result cdirect_hybrid_unscaled(int n, nlopt_func f, void *f_data,
      |              ^~~~~~~~~~~~~~~~~~~~~~~
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/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/cdirect/hybrid.c: At top level:
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/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c: In function 'bobyqa':
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c:2465:28: warning: 'cauchy' may be used uninitialized in this function [-Wmaybe-uninitialized]
 2465 |         if (denom < cauchy && cauchy > zero) {
      |             ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c:1987:20: note: 'cauchy' was declared here
 1987 |     double errbig, cauchy, fracsq, biglsq, densav;
      |                    ^~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c:885:14: warning: 'adelt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  885 |         subd = *adelt / sqrt(distsq);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c:1982:26: note: 'adelt' was declared here
 1982 |     double alpha, delta, adelt, denom, fsave, bdtol, delsq;
      |                          ^~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c:2464:37: warning: 'alpha' may be used uninitialized in this function [-Wmaybe-uninitialized]
 2464 |         denom = d__1 * d__1 + alpha * beta;
      |                               ~~~~~~^~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c:1982:12: note: 'alpha' was declared here
 1982 |     double alpha, delta, adelt, denom, fsave, bdtol, delsq;
      |            ^~~~~
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/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/slsqp/slsqp.c: In function 'lsq_':
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/slsqp/slsqp.c:1197:24: warning: 'xnorm' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1197 |     *xnrm = sqrt(*xnrm * *xnrm + t * t);
      |                  ~~~~~~^~~~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/slsqp/slsqp.c:1252:12: note: 'xnorm' was declared here
 1252 |     double xnorm;
      |            ^~~~~
/tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt-src/src/algs/bobyqa/bobyqa.c: At top level:
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-- Install configuration: "Release"
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-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/include/nlopt.h
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/include/nlopt.hpp
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/include/nlopt.f
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/lib/libnlopt.a
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends.cmake
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends-release.cmake
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfig.cmake
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfigVersion.cmake
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/share/man/man3/nlopt.3
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/share/man/man3/nlopt_minimize.3
-- Installing: /tmp/Rtmp9PrWP6/R.INSTALL1b7cfd7892d9b3/nloptr/src/nlopt/share/man/man3/nlopt_minimize_constrained.3
mv: cannot move 'nlopt/lib' to a subdirectory of itself, 'nlopt/lib/lib'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include   -I/usr/local/include    -fpic  -g -O2  -Wall  -c dummy.cpp -o dummy.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include   -I/usr/local/include    -fpic  -g -O2  -Wall -c init_nloptr.c -o init_nloptr.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include   -I/usr/local/include    -fpic  -g -O2  -Wall -c nloptr.c -o nloptr.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o nloptr.so dummy.o init_nloptr.o nloptr.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-nloptr/00new/nloptr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nloptr)
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gfortran  -fpic  -g -O2  -Wall -c altmov.f -o altmov.o
altmov.f:180:72:

  180 |          TEMP=XOPT(I)+STPSAV*(XPT(KSAV,I)-XOPT(I))
      |                                                                        ^
Warning: ‘stpsav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
altmov.f:170:15:

  170 |            KSAV=K
      |               ^
Warning: ‘ksav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
altmov.f:238:72:

  238 |           W(I)=-STEP*GLAG(I)
      |                                                                        ^
Warning: ‘step’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c bigden.f -o bigden.o
bigden.f:51:3:

   51 |  20         W(N+K)=W(N+K)+TEMP*ZMAT(K,J)
      |   1
Warning: Label 20 at (1) defined but not used [-Wunused-label]
gfortran  -fpic  -g -O2  -Wall -c biglag.f -o biglag.o
biglag.f:173:72:

  173 |           TEMPB=TEMPB-TAUMAX
      |                                                                        ^
Warning: ‘tempb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c bobyqa.f -o bobyqa.o
gfortran  -fpic  -g -O2  -Wall -c bobyqb.f -o bobyqb.o
bobyqb.f:712:10:

  712 |       IF (RATIO .GT. ZERO) GOTO 60
      |          ^
Warning: ‘ratio’ may be used uninitialized in this function [-Wmaybe-uninitialized]
bobyqb.f:139:72:

  139 |           ERRBIG=DMAX1(DIFFA,DIFFB,DIFFC)
      |                                                                        ^
Warning: ‘diffc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c lagmax.f -o lagmax.o
lagmax.f:40:13:

   40 |             K=I
      |             ^
Warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c minqa.cpp -o minqa.o
gfortran  -fpic  -g -O2  -Wall -c newuoa.f -o newuoa.o
gfortran  -fpic  -g -O2  -Wall -c newuob.f -o newuob.o
newuob.f:195:10:

  195 |   120 IF (DSQ .LE. 1.0D-3*XOPTSQ) THEN
      |          ^
Warning: ‘xoptsq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:146:14:

  146 |           IF (XJPT .LT. ZERO) JPT=JPT+N
      |              ^
Warning: ‘xjpt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:145:14:

  145 |           IF (XIPT .LT. ZERO) IPT=IPT+N
      |              ^
Warning: ‘xipt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:495:13:

  495 |          IF (DABS(RATIO) .GT. 1.0D-2) THEN
      |             ^
Warning: ‘ratio’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:186:14:

  186 |           IF (NF .LE. NFSAV+2) GOTO 460
      |              ^
Warning: ‘nfsav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:146:72:

  146 |           IF (XJPT .LT. ZERO) JPT=JPT+N
      |                                                                        ^
Warning: ‘jpt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:514:72:

  514 |               ITEST=ITEST+1
      |                                                                        ^
Warning: ‘itest’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:144:72:

  144 |           IH=(IPT*(IPT-1))/2+JPT
      |                                                                        ^
Warning: ‘ipt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:135:72:

  135 |               TEMP=(FBEG-F)/RHOBEG
      |                                                                        ^
Warning: ‘fbeg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:422:72:

  422 |           DELTA=DMAX1(HALF*DELTA,DNORM)
      |                                                                        ^
Warning: ‘dnorm’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:188:14:

  188 |           IF (TEMP .LE. DMAX1(DIFFA,DIFFB,DIFFC)) GOTO 460
      |              ^
Warning: ‘diffc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
newuob.f:188:14: Warning: ‘diffa’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c prelim.f -o prelim.o
prelim.f:128:72:

  128 |               DIFF=STEPB-STEPA
      |                                                                        ^
Warning: ‘stepb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
prelim.f:128:72: Warning: ‘stepa’ may be used uninitialized in this function [-Wmaybe-uninitialized]
prelim.f:152:72:

  152 |           IH=(IPT*(IPT-1))/2+JPT
      |                                                                        ^
Warning: ‘jpt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
prelim.f:152:72: Warning: ‘ipt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
prelim.f:119:72:

  119 |               GOPT(NFM)=(F-FBEG)/STEPA
      |                                                                        ^
Warning: ‘fbeg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c rescue.f -o rescue.o
rescue.f:144:15:

  144 |             IW=(DBLE(K-NP)-HALF)/DBLE(N)
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:224:15:

  224 |             IP=PTSID(K)
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:226:15:

  226 |             IQ=DBLE(NP)*PTSID(K)-DBLE(IP*NP)
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:328:12:

  328 |          IP=PTSID(KPT)
      |            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:329:12:

  329 |          IQ=DBLE(NP)*PTSID(KPT)-DBLE(IP*NP)
      |            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:398:15:

  398 |             IP=PTSID(K)
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:399:15:

  399 |             IQ=DBLE(NP)*PTSID(K)-DBLE(IP*NP)
      |               1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
rescue.f:358:72:

  358 |             IF (IQ .GT. 0) TEMP=TEMP+XQ*XPT(K,IQ)
      |                                                                        ^
Warning: ‘xq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
rescue.f:352:72:

  352 |                VQUAD=VQUAD+XP*XQ*HQ(IW)
      |                                                                        ^
Warning: ‘xp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
rescue.f:351:72:

  351 |                IW=MAX0(IHP,IHQ)-IABS(IP-IQ)
      |                                                                        ^
Warning: ‘ihp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c trsapp.f -o trsapp.o
trsapp.f:171:72:

  171 |           TEMPB=TEMPB-QMIN
      |                                                                        ^
Warning: ‘tempb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:145:72:

  145 |       CF=HALF*(SHS-DHD)
      |                                                                        ^
Warning: ‘shs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:156:72:

  156 |          QNEW=(SG+CF*CTH)*CTH+(DG+DHS*CTH)*STH
      |                                                                        ^
Warning: ‘sg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:187:72:

  187 |       QRED=QRED+REDUC
      |                                                                        ^
Warning: ‘qred’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:112:10:

  112 |    90 IF (GG .LE. 1.0D-4*GGBEG) GOTO 160
      |          ^
Warning: ‘ggbeg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:94:72:

   94 |           TEMP=GG/GGSAV
      |                                                                        ^
Warning: ‘gg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:70:72:

   70 |           TEMP=DHD/DD
      |                                                                        ^
Warning: ‘dd’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsapp.f:73:72:

   73 |           ALPHA=DMIN1(ALPHA,GG/DHD)
      |                                                                        ^
Warning: ‘bstep’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c trsbox.f -o trsbox.o
trsbox.f:294:9:

  294 |       IU=17.0D0*ANGBD+3.1D0
      |         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
trsbox.f:342:72:

  342 |          XBDI(IACT)=XSAV
      |                                                                        ^
Warning: ‘xsav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:321:72:

  321 |       SDEC=STH*(ANGT*DREDG-SREDG-HALF*STH*TEMP)
      |                                                                        ^
Warning: ‘sredg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:315:72:

  315 |           TEMP=(RDNEXT-RDPREV)/(REDMAX+REDMAX-RDPREV-RDNEXT)
      |                                                                        ^
Warning: ‘rdnext’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:186:13:

  186 |          IF (ITERC .EQ. ITERMAX) GOTO 190
      |             ^
Warning: ‘itermax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:387:10:

  387 |       IF (ITERC .GT. ITCSAV) GOTO 150
      |          ^
Warning: ‘itcsav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:134:10:

  134 |       IACT=0
      |          ^
Warning: ‘iact’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:100:10:

  100 |       IF (GREDSQ*DELSQ .LE. 1.0D-4*QRED*QRED) GO TO 190
      |          ^
Warning: ‘gredsq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:188:72:

  188 |           BETA=GREDSQ/GGSAV
      |                                                                        ^
Warning: ‘ggsav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:223:72:

  223 |             S(I)=(DREDG*D(I)-DREDSQ*GNEW(I))/TEMP
      |                                                                        ^
Warning: ‘dredsq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:299:72:

  299 |          REDNEW=STH*(ANGT*DREDG-SREDG-HALF*STH*TEMP)
      |                                                                        ^
Warning: ‘dredg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trsbox.f:294:72:

  294 |       IU=17.0D0*ANGBD+3.1D0
      |                                                                        ^
Warning: ‘angbd’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c trstep.f -o trstep.o
trstep.f:373:18:

  373 |               IF (PIV(K)-TEMP .LT. TEMP-PIVKSV) THEN
      |                  ^
Warning: ‘pivksv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trstep.f:280:72:

  280 |           IF (PARU .GT. ZERO) SLOPE=(PHIU-PHI)/(PARU-PAR)
      |                                                                        ^
Warning: ‘phiu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trstep.f:336:72:

  336 |           SLOPE=(PHI-PHIL)/(PAR-PARL)
      |                                                                        ^
Warning: ‘phil’ may be used uninitialized in this function [-Wmaybe-uninitialized]
trstep.f:216:72:

  216 |           SCALE=-DSIGN(DELTA/DSQRT(DSQ),DTG)
      |                                                                        ^
Warning: ‘dsq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c uobyqa.f -o uobyqa.o
gfortran  -fpic  -g -O2  -Wall -c uobyqb.f -o uobyqb.o
uobyqb.f:419:18:

  419 |               IF (WMULT*VMAX .LE. ERRTOL) GOTO 310
      |                  ^
Warning: ‘wmult’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:356:10:

  356 |       IF (DDKNEW .GT. TWORSQ) GOTO 70
      |          ^
Warning: ‘tworsq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:268:72:

  268 |       SIXTHM=DMAX1(SIXTHM,DABS(DIFF)/SUM)
      |                                                                        ^
Warning: ‘sixthm’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:70:13:

   70 |          KOPT=NF
      |             ^
Warning: ‘kopt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:332:72:

  332 |       TEMP=ONE/VLAG(KNEW)
      |                                                                        ^
Warning: ‘knew’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:86:72:

   86 |           JSWITCH=-JSWITCH
      |                                                                        ^
Warning: ‘jswitch’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:156:72:

  156 |           IQ=IQ+1
      |                                                                        ^
Warning: ‘iq’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:151:72:

  151 |           IP=IP+1
      |                                                                        ^
Warning: ‘ip’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:89:72:

   89 |                   IH=IH+J
      |                                                                        ^
Warning: ‘ih’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:92:72:

   92 |                       PQ(J)=(FSAVE-F)/(TWO*RHO)
      |                                                                        ^
Warning: ‘fsave’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:91:72:

   91 |                       D(J)=(FSAVE+F-TWO*FBASE)/RHOSQ
      |                                                                        ^
Warning: ‘fbase’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:402:14:

  402 |           IF (ERRTOL .GT. ZERO) THEN
      |              ^
Warning: ‘errtol’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:297:72:

  297 |           DELTA=DMAX1(HALF*DELTA,DNORM)
      |                                                                        ^
Warning: ‘dnorm’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:356:10:

  356 |       IF (DDKNEW .GT. TWORSQ) GOTO 70
      |          ^
Warning: ‘ddknew’ may be used uninitialized in this function [-Wmaybe-uninitialized]
uobyqb.f:89:72:

   89 |                   IH=IH+J
      |                                                                        ^
Warning: ‘j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c update.f -o update.o
gfortran  -fpic  -g -O2  -Wall -c updatebobyqa.f -o updatebobyqa.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o minqa.so altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-minqa/00new/minqa/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (minqa)
* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dotsElt.c -o dotsElt.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dotsLength.c -o dotsLength.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dotsNames.c -o dotsNames.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o backports.so dotsElt.o dotsLength.o dotsNames.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-backports/00new/backports/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (backports)
* installing *source* package ‘Formula’ ...
** package ‘Formula’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Formula)
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
gcc 11.4.0
zlib 1.2.11 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c assign.c -o assign.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c between.c -o between.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c bmerge.c -o bmerge.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c chmatch.c -o chmatch.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c cj.c -o cj.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c coalesce.c -o coalesce.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c dogroups.c -o dogroups.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fastmean.c -o fastmean.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fcast.c -o fcast.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fifelse.c -o fifelse.o
fifelse.c: In function ‘fcaseR’:
fifelse.c:280:10: warning: ‘ans_is_factor’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  280 |       if (!naout && ans_is_factor) {
      |          ^
fifelse.c:281:14: warning: ‘ans_levels’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  281 |         if (!R_compute_identical(ans_levels,  PROTECT(getAttrib(thens, R_LevelsSymbol)), 0)) {
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fmelt.c -o fmelt.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c forder.c -o forder.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c frank.c -o frank.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fread.c -o fread.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c freadR.c -o freadR.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c froll.c -o froll.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c frollR.c -o frollR.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c frolladaptive.c -o frolladaptive.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fsort.c -o fsort.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fwrite.c -o fwrite.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c fwriteR.c -o fwriteR.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c gsumm.c -o gsumm.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c idatetime.c -o idatetime.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c ijoin.c -o ijoin.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c inrange.c -o inrange.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c nafill.c -o nafill.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c negate.c -o negate.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c nqrecreateindices.c -o nqrecreateindices.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c openmp-utils.c -o openmp-utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c programming.c -o programming.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c quickselect.c -o quickselect.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c rbindlist.c -o rbindlist.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c shift.c -o shift.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c snprintf.c -o snprintf.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c subset.c -o subset.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c transpose.c -o transpose.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c types.c -o types.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c uniqlist.c -o uniqlist.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c vecseq.c -o vecseq.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -c wrappers.c -o wrappers.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
PKG_CFLAGS = -fopenmp
PKG_LIBS = -fopenmp -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
* installing *source* package ‘zoo’ ...
** package ‘zoo’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall -c coredata.c -o coredata.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall -c lag.c -o lag.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o zoo.so coredata.o init.o lag.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-zoo/00new/zoo/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (zoo)
* installing *source* package ‘openxlsx’ ...
** package ‘openxlsx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c helper_functions.cpp -o helper_functions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c load_workbook.cpp -o load_workbook.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c read_workbook.cpp -o read_workbook.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c write_data.cpp -o write_data.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c write_file.cpp -o write_file.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c write_file_2.cpp -o write_file_2.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o openxlsx.so RcppExports.o helper_functions.o load_workbook.o read_workbook.o write_data.o write_file.o write_file_2.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-openxlsx/00new/openxlsx/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openxlsx)
* installing *source* package ‘slam’ ...
** package ‘slam’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c apply.c -o apply.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dll.c -o dll.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c grouped.c -o grouped.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sparse.c -o sparse.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o slam.so apply.o dll.o grouped.o sparse.o util.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-slam/00new/slam/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (slam)
* installing *source* package ‘rjson’ ...
** package ‘rjson’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c dump.cpp -o dump.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c parser.c -o parser.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c register.c -o register.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o rjson.so dump.o parser.o register.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-rjson/00new/rjson/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rjson)
* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'R/tbb-autodetected.R.in' => 'R/tbb-autodetected.R'
*** configured file: 'src/Makevars.in' => 'src/Makevars'
*** configured file: 'src/install.libs.R.in' => 'src/install.libs.R'
** finished configure for package 'RcppParallel'
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
(tbb) Building TBB using bundled sources ...
make[1]: Entering directory '/tmp/RtmpsJvkiN/R.INSTALL1bd35b7ffad958/RcppParallel/src/tbb/src'
OS: linux
arch=intel64
compiler=gcc
runtime=cc11.4.0_libc2.35_kernel5.15.0
tbb_build_prefix=linux_intel64_gcc_cc11.4.0_libc2.35_kernel5.15.0
work_dir=/tmp/RtmpsJvkiN/R.INSTALL1bd35b7ffad958/RcppParallel/src/build/linux_intel64_gcc_cc11.4.0_libc2.35_kernel5.15.0_release
make[1]: Leaving directory '/tmp/RtmpsJvkiN/R.INSTALL1bd35b7ffad958/RcppParallel/src/tbb/src'
(tbb) TBB compilation finished successfully.
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include   -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -Wall  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include   -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -Wall  -c options.cpp -o options.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o RcppParallel.so init.o options.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
(tbb) Building TBB using bundled sources ...
make[1]: Entering directory '/tmp/RtmpsJvkiN/R.INSTALL1bd35b7ffad958/RcppParallel/src/tbb/src'
OS: linux
arch=intel64
compiler=gcc
runtime=cc11.4.0_libc2.35_kernel5.15.0
tbb_build_prefix=linux_intel64_gcc_cc11.4.0_libc2.35_kernel5.15.0
work_dir=/tmp/RtmpsJvkiN/R.INSTALL1bd35b7ffad958/RcppParallel/src/build/linux_intel64_gcc_cc11.4.0_libc2.35_kernel5.15.0_release
make[1]: Leaving directory '/tmp/RtmpsJvkiN/R.INSTALL1bd35b7ffad958/RcppParallel/src/tbb/src'
(tbb) TBB compilation finished successfully.
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include   -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -Wall  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include   -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -Wall  -c options.cpp -o options.o
installing via 'install.libs.R' to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-RcppParallel/00new/RcppParallel
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)
* installing *source* package ‘lpSolve’ ...
** package ‘lpSolve’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c colamd.c -o colamd.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c commonlib.c -o commonlib.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c hbio.c -o hbio.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c ini.c -o ini.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c isfixedvar.c -o isfixedvar.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_Hash.c -o lp_Hash.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_LUSOL.c -o lp_LUSOL.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_MDO.c -o lp_MDO.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_MPS.c -o lp_MPS.o
lp_MPS.c: In function ‘MPS_getnameidx.constprop’:
lp_MPS.c:1532:9: warning: ‘in’ may be used uninitialized [-Wmaybe-uninitialized]
 1532 |   return( in );
      |         ^
lp_MPS.c:1502:7: note: ‘in’ declared here
 1502 |   int in;
      |       ^~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_SOS.c -o lp_SOS.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_crash.c -o lp_crash.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_lib.c -o lp_lib.o
lp_lib.c: In function ‘set_outputfile’:
lp_lib.c:201:5: warning: ‘output’ may be used uninitialized [-Wmaybe-uninitialized]
  201 |     set_outputstream(lp, output);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_matrix.c -o lp_matrix.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_mipbb.c -o lp_mipbb.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_params.c -o lp_params.o
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
  266 | {
      | ^
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
lp_params.c:266:1: warning: missing braces around initializer [-Wmissing-braces]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_presolve.c -o lp_presolve.o
lp_presolve.c: In function ‘presolve_debugmap’:
lp_presolve.c:486:51: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
  486 |   int    colnr, ix, ie, nx, jx, je, *cols, *rows, n;
      |                                                   ^
lp_presolve.c: In function ‘presolve_colfixdual’:
lp_presolve.c:2016:18: warning: variable ‘isMI’ set but not used [-Wunused-but-set-variable]
 2016 |   MYBOOL  hasOF, isMI, isDualFREE = TRUE;
      |                  ^~~~
lp_presolve.c: In function ‘presolve_coldominance01’:
lp_presolve.c:3849:34: warning: variable ‘je’ set but not used [-Wunused-but-set-variable]
 3849 |   int      i, ii, ib, ie, n, jb, je, jx, jj, item, item2,
      |                                  ^~
lp_presolve.c: In function ‘presolve_columns’:
lp_presolve.c:4622:46: warning: variable ‘item’ set but not used [-Wunused-but-set-variable]
 4622 |            status = RUNNING, ix, j, countNZ, item;
      |                                              ^~~~
lp_presolve.c:4615:31: warning: variable ‘unbounded’ set but not used [-Wunused-but-set-variable]
 4615 |   MYBOOL   candelete, isOFNZ, unbounded,
      |                               ^~~~~~~~~
lp_presolve.c: In function ‘presolve_rows’:
lp_presolve.c:5060:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 5060 |             if(!presolve_fixSOS1(psdata, j, Value1, &iConRemove, &iVarFixed))
      |             ^~
lp_presolve.c:5062:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 5062 |               psdata->forceupdate = TRUE;
      |               ^~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_price.c -o lp_price.o
lp_price.c: In function ‘compareImprovementVar’:
lp_price.c:49:7: warning: variable ‘candidatecolno’ set but not used [-Wunused-but-set-variable]
   49 |       candidatecolno, candidatevarno = candidate->varno;
      |       ^~~~~~~~~~~~~~
lp_price.c:48:7: warning: variable ‘currentcolno’ set but not used [-Wunused-but-set-variable]
   48 |   int currentcolno, currentvarno = current->varno,
      |       ^~~~~~~~~~~~
lp_price.c: In function ‘compareSubstitutionVar’:
lp_price.c:162:10: warning: variable ‘candidatecolno’ set but not used [-Wunused-but-set-variable]
  162 |          candidatecolno, candidatevarno = candidate->varno;
      |          ^~~~~~~~~~~~~~
lp_price.c:161:10: warning: variable ‘currentcolno’ set but not used [-Wunused-but-set-variable]
  161 |   int    currentcolno, currentvarno = current->varno,
      |          ^~~~~~~~~~~~
lp_price.c: In function ‘partial_findBlocks’:
lp_price.c:1560:15: warning: variable ‘blockdata’ set but not used [-Wunused-but-set-variable]
 1560 |   partialrec *blockdata;
      |               ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_pricePSE.c -o lp_pricePSE.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_report.c -o lp_report.o
lp_report.c: In function ‘REPORT_mat_mmsave’:
lp_report.c:790:3: warning: ‘output’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  790 |   fclose(output);
      |   ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_rlp.c -o lp_rlp.o
In file included from lp_rlp.c:97:
lp_rlp.h:1871:14: warning: ‘lp_yy_flex_realloc’ defined but not used [-Wunused-function]
 1871 | static void *lp_yy_flex_realloc( void *ptr, lp_yy_size_t size )
      |              ^~~~~~~~~~~~~~~~~~
lp_rlp.h:1845:12: warning: ‘lp_yy_flex_strlen’ defined but not used [-Wunused-function]
 1845 | static int lp_yy_flex_strlen( lp_yyconst char *s )
      |            ^~~~~~~~~~~~~~~~~
lp_rlp.h:1797:13: warning: ‘lp_yy_fatal_error’ defined but not used [-Wunused-function]
 1797 | static void lp_yy_fatal_error( lp_yyconst char msg[] )
      |             ^~~~~~~~~~~~~~~~~
lp_rlp.h:1353:13: warning: ‘lp_yyunput’ defined but not used [-Wunused-function]
 1353 | static void lp_yyunput( int c, register char *lp_yy_bp )
      |             ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_scale.c -o lp_scale.o
lp_scale.c: In function ‘CurtisReidScales’:
lp_scale.c:150:24: warning: variable ‘ekm2’ set but not used [-Wunused-but-set-variable]
  150 |          qkm2, qkqkm1, ekm2, ekekm1,
      |                        ^~~~
lp_scale.c:150:10: warning: variable ‘qkm2’ set but not used [-Wunused-but-set-variable]
  150 |          qkm2, qkqkm1, ekm2, ekekm1,
      |          ^~~~
lp_scale.c: In function ‘scale_columns’:
lp_scale.c:632:16: warning: variable ‘colMax’ set but not used [-Wunused-but-set-variable]
  632 |   int     i,j, colMax, nz;
      |                ^~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_simplex.c -o lp_simplex.o
lp_simplex.c: In function ‘dualloop’:
lp_simplex.c:983:10: warning: variable ‘epsvalue’ set but not used [-Wunused-but-set-variable]
  983 |   REAL   epsvalue, xviolated, cviolated,
      |          ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_utils.c -o lp_utils.o
lp_utils.c: In function ‘searchFor’:
lp_utils.c:546:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  546 |     if(absolute)
      |     ^~
lp_utils.c:548:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  548 |       while((beginPos < endPos) && (match != target)) {
      |       ^~~~~
lp_utils.c: In function ‘compareLink’:
lp_utils.c:947:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  947 |   if(test == 0)
      |   ^~
lp_utils.c:949:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  949 |     if(test == 0)
      |     ^~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lp_wlp.c -o lp_wlp.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lpslink56.c -o lpslink56.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lusol.c -o lusol.o
In file included from lusol.c:748:
lusol1.h: In function ‘LU1FAC’:
lusol1.h:3359:34: warning: variable ‘TSP’ set but not used [-Wunused-but-set-variable]
 3359 |   MYBOOL  KEEPLU, TCP, TPP, TRP, TSP;
      |                                  ^~~
lusol1.h:3359:29: warning: variable ‘TRP’ set but not used [-Wunused-but-set-variable]
 3359 |   MYBOOL  KEEPLU, TCP, TPP, TRP, TSP;
      |                             ^~~
lusol1.h:3359:19: warning: variable ‘TCP’ set but not used [-Wunused-but-set-variable]
 3359 |   MYBOOL  KEEPLU, TCP, TPP, TRP, TSP;
      |                   ^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c lusolio.c -o lusolio.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c mmio.c -o mmio.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c myblas.c -o myblas.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c sparselib.c -o sparselib.o
sparselib.c: In function ‘dswapVector1’:
sparselib.c:823:10: warning: variable ‘d’ set but not used [-Wunused-but-set-variable]
  823 |   int i, d, n;
      |          ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia  -I/usr/local/include    -fpic  -g -O2  -Wall -c yacc_read.c -o yacc_read.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o lpSolve.so colamd.o commonlib.o hbio.o ini.o init.o isfixedvar.o lp_Hash.o lp_LUSOL.o lp_MDO.o lp_MPS.o lp_SOS.o lp_crash.o lp_lib.o lp_matrix.o lp_mipbb.o lp_params.o lp_presolve.o lp_price.o lp_pricePSE.o lp_report.o lp_rlp.o lp_scale.o lp_simplex.o lp_utils.o lp_wlp.o lpslink56.o lusol.o lusolio.o mmio.o myblas.o sparselib.o yacc_read.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-lpSolve/00new/lpSolve/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lpSolve)
* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c lpmvnorm.c -o lpmvnorm.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ltMatrices.c -o ltMatrices.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c miwa.c -o miwa.o
gfortran  -fpic  -g -O2  -Wall -c mvt.f -o mvt.o
mvt.f:868:11:

  868 |       hs = sign( one, dh - r*dk )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:869:11:

  869 |       ks = sign( one, dk - r*dh )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:1164:16:

 1164 |             K = MOD( C(NP, MIN(NDIM-1,KLIM-1))*DBLE(K), DBLE(P(NP)) )
      |                1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:1224:17:

 1224 |             JP = 1 + J*R(J)
      |                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c mvtnorm-init.c -o mvtnorm-init.o
gfortran  -fpic  -g -O2  -Wall -c tvpack.f -o tvpack.o
tvpack.f:395:14:

  395 |          HS = SIGN( ONE, DH - R*DK )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:396:14:

  396 |          KS = SIGN( ONE, DK - R*DH )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:220:72:

  220 |       END
      |                                                                        ^
Warning: ‘fin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
tvpack.f:196:58:

  196 |       DOUBLE PRECISION EI(NL), AI(NL), BI(NL), FI(NL), FIN, ERR, KRNRDT
      |                                                          ^
note: ‘fin’ was declared here
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o mvtnorm.so C_FORTRAN_interface.o lpmvnorm.o ltMatrices.o miwa.o mvt.o mvtnorm-init.o tvpack.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-mvtnorm/00new/mvtnorm/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mvtnorm)
* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getMethods to getMethods.default, which was defined in environment R.oo.
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getClasses to getClasses.default, which was defined in environment R.oo.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.oo)
* installing *source* package ‘checkmate’ ...
** package ‘checkmate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c all_missing.c -o all_missing.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c any_infinite.c -o any_infinite.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c any_missing.c -o any_missing.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c any_nan.c -o any_nan.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c checks.c -o checks.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c find_nchar.c -o find_nchar.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c guess_type.c -o guess_type.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c helper.c -o helper.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integerish.c -o integerish.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c is_sorted.c -o is_sorted.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c qassert.c -o qassert.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c which_first.c -o which_first.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-checkmate/00new/checkmate/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (checkmate)
* installing *source* package ‘lme4’ ...
** package ‘lme4’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppEigen/include' -I'/home/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I/usr/local/include   -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -g -O2  -Wall  -c external.cpp -o external.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppEigen/include' -I'/home/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I/usr/local/include   -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -g -O2  -Wall  -c glmFamily.cpp -o glmFamily.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppEigen/include' -I'/home/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I/usr/local/include   -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -g -O2  -Wall  -c optimizer.cpp -o optimizer.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppEigen/include' -I'/home/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I/usr/local/include   -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -g -O2  -Wall  -c predModule.cpp -o predModule.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppEigen/include' -I'/home/biocbuild/bbs-3.19-bioc/R/library/Matrix/include' -I/usr/local/include   -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -g -O2  -Wall  -c respModule.cpp -o respModule.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-lme4/00new/lme4/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lme4)
* installing *source* package ‘sandwich’ ...
** package ‘sandwich’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sandwich)
* installing *source* package ‘htmlTable’ ...
** package ‘htmlTable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (htmlTable)
* installing *source* package ‘R.utils’ ...
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils.
Warning in setGenericS3.default("use") :
  Renamed the preexisting function use to use.default, which was defined in environment R.utils.
Warning in setMethodS3.default("use", "default", function(pkg = "R.utils",  :
  Method already existed and was overwritten: use.default
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.utils)
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Hmisc.c -o Hmisc.o
gfortran  -fpic  -g -O2  -Wall -c cidxcn.f -o cidxcn.o
cidxcn.f:70:5:

   70 | 23003 continue
      |     1
Warning: Label 23003 at (1) defined but not used [-Wunused-label]
cidxcn.f:77:5:

   77 | 23001 continue
      |     1
Warning: Label 23001 at (1) defined but not used [-Wunused-label]
gfortran  -fpic  -g -O2  -Wall -c cidxcp.f -o cidxcp.o
cidxcp.f:64:5:

   64 | 23003 continue
      |     1
Warning: Label 23003 at (1) defined but not used [-Wunused-label]
cidxcp.f:71:5:

   71 | 23001 continue
      |     1
Warning: Label 23001 at (1) defined but not used [-Wunused-label]
gfortran  -fpic  -g -O2  -Wall -c hoeffd.f -o hoeffd.o
hoeffd.f:50:5:

   50 | 23017 continue
      |     1
Warning: Label 23017 at (1) defined but not used [-Wunused-label]
hoeffd.f:52:5:

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hoeffd.f:28:5:

   28 | 23009 continue
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hoeffd.f:41:5:

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hoeffd.f:113:5:

  113 | 23023 continue
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hoeffd.f:118:5:

  118 | 23021 continue
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gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gfortran  -fpic  -g -O2  -Wall -c jacklins.f -o jacklins.o
jacklins.f:16:5:

   16 | 23005 continue
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Warning: Label 23005 at (1) defined but not used [-Wunused-label]
jacklins.f:19:5:

   19 | 23003 continue
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jacklins.f:21:5:

   21 | 23001 continue
      |     1
Warning: Label 23001 at (1) defined but not used [-Wunused-label]
gfortran  -fpic  -g -O2  -Wall -c largrec.f -o largrec.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c mChoice.c -o mChoice.o
gfortran  -fpic  -g -O2  -Wall -c maxempr.f -o maxempr.o
maxempr.f:54:5:

   54 | 23015 continue
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maxempr.f:33:5:

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maxempr.f:65:5:

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gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nstr.c -o nstr.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c ranksort.c -o ranksort.o
gfortran  -fpic  -g -O2  -Wall -c rcorr.f -o rcorr.o
rcorr.f:76:5:

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Warning: Label 23023 at (1) defined but not used [-Wunused-label]
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rcorr.f:101:5:

  101 | 23025 continue
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gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c string_box.c -o string_box.o
gfortran  -fpic  -g -O2  -Wall -c wclosest.f -o wclosest.o
wclosest.f:17:5:

   17 | 23003 continue
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wclosest.f:20:5:

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wclosest.f:52:5:

   52 | 23013 continue
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wclosest.f:55:5:

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gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-Hmisc/00new/Hmisc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Hmisc)
* installing *source* package ‘rbiom’ ...
** package ‘rbiom’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c par_beta_div.cpp -o par_beta_div.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c par_unifrac.cpp -o par_unifrac.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_alpha_div.cpp -o rcpp_alpha_div.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_rarefy.cpp -o rcpp_rarefy.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/Rcpp/include' -I'/tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcpp_treeIO.cpp -o rcpp_treeIO.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o rbiom.so RcppExports.o par_beta_div.o par_unifrac.o rcpp_alpha_div.o rcpp_rarefy.o rcpp_treeIO.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpPsOIEi/RLIBS_1a3ff24e0c8f57/00LOCK-rbiom/00new/rbiom/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rbiom)
* installing *source* package ‘mediation’ ...
** package ‘mediation’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mediation)

The downloaded source packages are in
	'/tmp/Rtmpt2ldmm/downloaded_packages'
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmpt2ldmm/remotes1ab80f33469dc7/microbiome-mia-c76bc90/DESCRIPTION’ ... OK
* preparing ‘mia’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘mia_1.13.46.tar.gz’

* installing *source* package ‘mia’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mia)
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmpt2ldmm/remotes1ab80f6125a6a5/microbiome-miaTime-f66d54f/DESCRIPTION’ ... OK
* preparing ‘miaTime’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘miaTime_0.1.22.tar.gz’

* installing *source* package ‘miaTime’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miaTime)
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 215 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 215 ]
> 
> proc.time()
   user  system elapsed 
781.060  61.250 851.834

Example timings

miaViz.Rcheck/miaViz-Ex.timings

name	user	system	elapsed
plotAbundance	7.370	0.367	7.739