Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:23 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the snapCGH package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snapCGH.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 1796/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
snapCGH 1.62.0 (landing page) John Marioni
| 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: snapCGH |
Version: 1.62.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings snapCGH_1.62.0.tar.gz |
StartedAt: 2021-10-15 05:54:15 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 05:57:48 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 212.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: snapCGH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings snapCGH_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/snapCGH.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'snapCGH/DESCRIPTION' ... OK * this is package 'snapCGH' version '1.62.0' * 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 whether package 'snapCGH' 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE heatmapGenome: no visible binding for global variable 'floor.func' readPositionalInfo: no visible binding for global variable 'RGList' Undefined global functions or variables: RGList floor.func * 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 compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/snapCGH/libs/i386/snapCGH.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/snapCGH/libs/x64/snapCGH.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (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. 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/snapCGH.Rcheck/00check.log' for details.
snapCGH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/snapCGH_1.62.0.tar.gz && rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.62.0.zip && rm snapCGH_1.62.0.tar.gz snapCGH_1.62.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 616k 100 616k 0 0 1880k 0 --:--:-- --:--:-- --:--:-- 1884k install for i386 * installing *source* package 'snapCGH' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c optimizer.c -o optimizer.o optimizer.c: In function 'fr_two': optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c: In function 'fr_three': optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1]; ^~~~~~~~ optimizer.c: In function 'fr_four': optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1]; ^~~~~~~~ optimizer.c: In function 'fr_five': optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1]; ^~~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'snapCGH' finding HTML links ... done IDProbes html LargeDataObject html SegList html Viterbi.five html Viterbi.four html Viterbi.three html Viterbi.two html cbind html chrominfo.Mb html compareSegmentations html convert.output html dim html dimnames html filter html find.param.five html find.param.four html find.param.one html find.param.three html find.param.two html findBreakPoints html fit.model html genomePlot html heatmapGenome html imputeMissingValues html log2ratios html mergeStates html plotSegmentedGenome html processCGH html read.clonesinfo html readPositionalInfo html removeByWeights html runBioHMM html runDNAcopy html runGLAD html runHMM html runTilingArray html sim.structure html zoomChromosome html zoomGenome html ** 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 install for x64 * installing *source* package 'snapCGH' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c optimizer.c -o optimizer.o optimizer.c: In function 'fr_two': optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c: In function 'fr_three': optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1]; ^~~~~~~~ optimizer.c: In function 'fr_four': optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1]; ^~~~~~~~ optimizer.c: In function 'fr_five': optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable] double denom, temp, temp2, temp3; ^~~~~ optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable] double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1]; ^~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'snapCGH' as snapCGH_1.62.0.zip * DONE (snapCGH) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'snapCGH' successfully unpacked and MD5 sums checked
snapCGH.Rcheck/examples_i386/snapCGH-Ex.timings
|
snapCGH.Rcheck/examples_x64/snapCGH-Ex.timings
|