Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:37:03 -0400 (Wed, 17 Oct 2018).
Package 1343/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SeqArray 1.20.2 Xiuwen Zheng
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: SeqArray |
Version: 1.20.2 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SeqArray_1.20.2.tar.gz |
StartedAt: 2018-10-17 04:45:32 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 04:49:08 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 216.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SeqArray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SeqArray_1.20.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'SeqArray/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SeqArray' version '1.20.2' * 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 whether package 'SeqArray' 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 ... 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 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 ... 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-3.7-bioc/R/library/SeqArray/libs/i386/SeqArray.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'SeqArray/libs/i386/SeqArray.dll': Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection', 'R_WriteConnection', 'R_new_custom_connection' 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. Compiled code should not call non-API entry points in R. 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 or elapsed time > 5s user system elapsed seqVCF2GDS 0.64 0.04 10.65 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed seqVCF2GDS 0.76 0.05 11.94 SeqArray-package 0.60 0.12 5.97 seqParallelSetup 0.06 0.01 5.65 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test.R' OK ** running tests for arch 'x64' ... Running 'test.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 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.Rcheck/00check.log' for details.
SeqArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SeqArray_1.20.2.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.20.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.20.2.zip && rm SeqArray_1.20.2.tar.gz SeqArray_1.20.2.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 1907k 100 1907k 0 0 24.5M 0 --:--:-- --:--:-- --:--:-- 26.6M install for i386 * installing *source* package 'SeqArray' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FileMerge.cpp -o FileMerge.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GetData.cpp -o GetData.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Index.cpp -o Index.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Methods.cpp -o Methods.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadBySample.cpp -o ReadBySample.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SeqArray.cpp -o SeqArray.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pkg_test.cpp -o pkg_test.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SeqArray' finding HTML links ... done KG_P1_SampData html SeqArray-package html SeqVarGDSClass-class html finding level-2 HTML links ... done seqAlleleFreq html seqApply html seqAsVCF html seqBED2GDS html seqBlockApply html seqClose html seqDelete html seqDigest html seqExampleFileName html seqExport html seqGDS2SNP html seqGDS2VCF html seqGetData html seqGetFilter html seqMerge html seqMissing html seqNumAllele html seqOpen html seqOptimize html seqParallel html seqParallelSetup html seqSNP2GDS html seqSetFilter html seqSetFilterCond html seqStorageOption html seqSummary html seqSystem html seqTranspose html seqVCF2GDS html seqVCF_Header html seqVCF_SampID html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'SeqArray' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FileMerge.cpp -o FileMerge.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GetData.cpp -o GetData.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Index.cpp -o Index.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Methods.cpp -o Methods.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadBySample.cpp -o ReadBySample.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SeqArray.cpp -o SeqArray.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pkg_test.cpp -o pkg_test.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SeqArray' as SeqArray_1.20.2.zip * DONE (SeqArray) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'SeqArray' successfully unpacked and MD5 sums checked In R CMD INSTALL
SeqArray.Rcheck/tests_i386/test.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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. > if (Sys.info()[['sysname']] != "Windows") + { + # according to the limit of 32-bit Windows + BiocGenerics:::testPackage("SeqArray") + } > > proc.time() user system elapsed 0.23 0.09 0.31 |
SeqArray.Rcheck/tests_x64/test.Rout R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. > if (Sys.info()[['sysname']] != "Windows") + { + # according to the limit of 32-bit Windows + BiocGenerics:::testPackage("SeqArray") + } > > proc.time() user system elapsed 0.28 0.03 0.29 |
SeqArray.Rcheck/examples_i386/SeqArray-Ex.timings
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SeqArray.Rcheck/examples_x64/SeqArray-Ex.timings
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