Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 212/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.33.0  (landing page)
Jitao David Zhang
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BioQC
git_branch: devel
git_last_commit: 9aef270
git_last_commit_date: 2024-04-30 10:47:01 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BioQC on palomino4

To the developers/maintainers of the BioQC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.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: BioQC
Version: 1.33.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioQC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BioQC_1.33.0.tar.gz
StartedAt: 2024-06-10 00:22:33 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:24:16 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 102.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BioQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioQC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BioQC_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BioQC.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BioQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioQC' version '1.33.0'
* 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 whether package 'BioQC' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
* 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) readCurrentSignatures.Rd:13: Lost braces
    13 | \item{namespace}{Character, namespace of the gene-set, or code{NULL}, passed
       |                                                               ^
checkRd: (-1) wmwTest.Rd:282: Lost braces
   282 | code{wilcox.test} in the \code{stats} package, and \code{rankSumTestWithCorrelation} in
       |     ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/BioQC/libs/x64/BioQC.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/BioQC.Rcheck/00check.log'
for details.


Installation output

BioQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BioQC
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BioQC' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG `F:/biocbuild/bbs-3.20-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gini.c -o gini.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG `F:/biocbuild/bbs-3.20-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG `F:/biocbuild/bbs-3.20-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_gmt.cpp -o read_gmt.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG `F:/biocbuild/bbs-3.20-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stat_rank.c -o stat_rank.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG `F:/biocbuild/bbs-3.20-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:118: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  118 | #pragma omp parallel for
      | 
wmw_test.c: In function 'wmw_test':
wmw_test.c:168: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  168 | #pragma omp parallel for
      | 
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:201: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  201 | #pragma omp parallel for
      | 
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:270: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  270 | #pragma omp parallel for
      | 
g++ -std=gnu++17 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BioQC/00new/BioQC/libs/x64
** 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 (BioQC)

Tests output

BioQC.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(BioQC)
Loading required package: Biobase
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

Welcome to Bioconductor

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

> 
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
   8.29    0.60    8.85 

Example timings

BioQC.Rcheck/BioQC-Ex.timings

nameusersystemelapsed
GmtList000
IndexList000
SignedGenesets000
SignedIndexList000
absLog10p000
appendGmtList0.010.000.01
as.GmtList000
entropy000
entropyDiversity0.020.000.02
entropySpecificity000
filterPmat000
getLeadingEdgeIndexFromVector000
gini000
gmtlist2signedGenesets0.010.000.01
matchGenes0.070.000.06
offset-set000
offset000
prettySigNames0.060.000.06
readCurrentSignatures0.050.010.07
readGmt0.090.000.10
readSignedGmt0.020.000.02
sampleSpecialization000
setNamespace0.010.000.02
simplifyMatrix000
sub-.GmtList000
sub-sub-.GmtList000
uniqGenesetsByNamespace0.020.000.01
wmwLeadingEdge000
wmwTest0.290.000.30
wmwTestInR000