Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the genoCN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genoCN.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 733/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genoCN 1.44.0 (landing page) Wei Sun
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: genoCN |
Version: 1.44.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings genoCN_1.44.0.tar.gz |
StartedAt: 2021-10-14 23:34:39 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:36:09 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 89.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: genoCN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings genoCN_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/genoCN.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 'genoCN/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'genoCN' version '1.44.0' * 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 'genoCN' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 genoCNA: no visible binding for global variable 'init.Para.CNA' genoCNV: no visible binding for global variable 'init.Para.CNV' Undefined global functions or variables: init.Para.CNA init.Para.CNV * 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 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/genoCN/libs/i386/genoCN.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/genoCN/libs/x64/genoCN.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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed genoCNA 13.07 0.75 13.81 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genoCNA 14.64 0.8 15.5 * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/genoCN.Rcheck/00check.log' for details.
genoCN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/genoCN_1.44.0.tar.gz && rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoCN.buildbin-libdir genoCN_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genoCN_1.44.0.zip && rm genoCN_1.44.0.tar.gz genoCN_1.44.0.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 22 740k 22 169k 0 0 620k 0 0:00:01 --:--:-- 0:00:01 619k 100 740k 100 740k 0 0 1894k 0 --:--:-- --:--:-- --:--:-- 1894k install for i386 * installing *source* package 'genoCN' ... ** 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 tnorm_mle.c -o tnorm_mle.o "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 utility.c -o utility.o "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 xCNV.c -o xCNV.o xCNV.c: In function 'emiss': xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable] int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR; ^ xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable] int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR; ^ xCNV.c: In function 'baum_welch': xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable] double mu_b_tmp, sd_b_tmp; ^~~~~~~~ xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable] double mu_b_tmp, sd_b_tmp; ^~~~~~~~ xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable] int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA, ^~ xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized] weights(ws, pbf, z, CNA, contam, nGtp, *geno_error); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized] C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.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/genoCN.buildbin-libdir/00LOCK-genoCN/00new/genoCN/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'genoCN' finding HTML links ... done code.genotype html genoCNA html genoCNV html init.Para.CNA html init.Para.CNV html plotCN html snpData html snpInfo 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 'genoCN' ... ** 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 tnorm_mle.c -o tnorm_mle.o "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 utility.c -o utility.o "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 xCNV.c -o xCNV.o xCNV.c: In function 'emiss': xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable] int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR; ^ xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable] int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR; ^ xCNV.c: In function 'baum_welch': xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable] double mu_b_tmp, sd_b_tmp; ^~~~~~~~ xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable] double mu_b_tmp, sd_b_tmp; ^~~~~~~~ xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable] int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA, ^~ xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized] weights(ws, pbf, z, CNA, contam, nGtp, *geno_error); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized] C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.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/genoCN.buildbin-libdir/genoCN/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'genoCN' as genoCN_1.44.0.zip * DONE (genoCN) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'genoCN' successfully unpacked and MD5 sums checked
genoCN.Rcheck/examples_i386/genoCN-Ex.timings
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genoCN.Rcheck/examples_x64/genoCN-Ex.timings
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