Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the CGEN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 277/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CGEN 3.28.0 (landing page) Nilotpal Sanyal
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: CGEN |
Version: 3.28.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGEN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGEN_3.28.0.tar.gz |
StartedAt: 2021-10-14 17:15:01 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:18:26 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 205.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CGEN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGEN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGEN_3.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CGEN.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CGEN/DESCRIPTION’ ... OK * this is package ‘CGEN’ version ‘3.28.0’ * 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 ‘CGEN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: GPL-2 + file LICENSE * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed additive.test 45.430 7.802 53.274 getMatchedSets 11.685 0.195 11.887 snp.matched 10.669 0.024 10.704 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CGEN.Rcheck/00check.log’ for details.
CGEN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CGEN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘CGEN’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Additive.c -o Additive.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c CML.c -o CML.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ccl.c -o ccl.o gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c csclust.f -o csclust.o f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs] f951: Warning: Nonconforming tab character in column 2 of line 190 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs] csclust.f:222:3: 650 RETURN 1 Warning: Label 650 at (1) defined but not used [-Wunused-label] clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c fsclust.c -o fsclust.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hcl.c -o hcl.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pmatch.c -o pmatch.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c score.c -o score.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-CGEN/00new/CGEN/libs ** 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 ** 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 (CGEN)
CGEN.Rcheck/CGEN-Ex.timings
name | user | system | elapsed | |
GxE.scan | 0.002 | 0.001 | 0.002 | |
GxE.scan.combine | 0 | 0 | 0 | |
GxE.scan.partition | 0.003 | 0.002 | 0.004 | |
LocusMapData | 0.032 | 0.007 | 0.038 | |
QQ.plot | 0.018 | 0.004 | 0.022 | |
Xdata | 0.014 | 0.002 | 0.016 | |
Xdata2 | 0.047 | 0.004 | 0.051 | |
additive.test | 45.430 | 7.802 | 53.274 | |
chromosome.plot | 0.452 | 0.009 | 0.461 | |
getMatchedSets | 11.685 | 0.195 | 11.887 | |
getSummary | 0.004 | 0.002 | 0.006 | |
getWaldTest | 0.005 | 0.001 | 0.006 | |
printEffects | 0.236 | 0.013 | 0.251 | |
snp.effects | 0.224 | 0.006 | 0.230 | |
snp.effects.plot | 0.815 | 0.010 | 0.826 | |
snp.list | 0.000 | 0.000 | 0.001 | |
snp.logistic | 0.420 | 0.006 | 0.426 | |
snp.matched | 10.669 | 0.024 | 10.704 | |
snp.score | 0.024 | 0.000 | 0.026 | |