Aaron Lun
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/beachmat |
| Branch: RELEASE_3_6 |
| Last Commit: 6bd57b9 |
| Last Changed Date: 2017-11-25 11:15:16 -0400 (Sat, 25 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:16:28 -0400 (Thu, 12 Apr 2018).
| Package 101/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| beachmat 1.0.2 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: beachmat |
| Version: 1.0.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings beachmat_1.0.2.tar.gz |
| StartedAt: 2018-04-11 21:41:56 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:44:05 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 128.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beachmat.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings beachmat_1.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘1.0.2’
* 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 ‘beachmat’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 54.5Mb
sub-directories of 1Mb or more:
lib 35.5Mb
libs 18.5Mb
* 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 R 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 ... OK
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck/00check.log’
for details.
beachmat.Rcheck/00install.out
* installing *source* package ‘beachmat’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c HDF5_utils.cpp -o HDF5_utils.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c any_matrix.cpp -o any_matrix.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c character_matrix.cpp -o character_matrix.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c character_output.cpp -o character_output.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c find_chunks.cpp -o find_chunks.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c functions.cpp -o functions.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c integer_matrix.cpp -o integer_matrix.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c logical_matrix.cpp -o logical_matrix.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c numeric_matrix.cpp -o numeric_matrix.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c output_param.cpp -o output_param.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c repacker.cpp -o repacker.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o beachmat.so HDF5_utils.o any_matrix.o character_matrix.o character_output.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o /home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/lib/libsz.a -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
ar rc libbeachmat.a any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o libbeachmat.so any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o `echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "/home/biocbuild/bbs-3.6-bioc/R/bin/R" --vanilla --slave`
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck/beachmat/lib" "/home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck/beachmat/include/beachmat"
cp any_matrix.h utils.h beachmat.h HDF5_utils.h output_param.h Psymm_matrix.h HDF5_matrix.h Csparse_matrix.h dense_matrix.h simple_matrix.h Rle_matrix.h Input_matrix.h simple_output.h Csparse_output.h HDF5_output.h Output_matrix.h LIN_matrix.h LIN_methods.h LIN_output.h LIN_outfun.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h "/home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck/beachmat/include/beachmat"
mv libbeachmat.* "/home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck/beachmat/lib"
installing to /home/biocbuild/bbs-3.6-bioc/meat/beachmat.Rcheck/beachmat/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beachmat)
beachmat.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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(beachmat)
> test_check("beachmat")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 25 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.300 0.068 4.401
beachmat.Rcheck/beachmat-Ex.timings
| name | user | system | elapsed | |
| getBestChunkDims | 0 | 0 | 0 | |
| pkgconfig | 0.012 | 0.004 | 0.015 | |
| rechunkByMargins | 0.468 | 0.004 | 0.620 | |