Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:22:36 -0400 (Sat, 13 Apr 2019).
Package 203/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
casper 2.16.1 David Rossell
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: casper |
Version: 2.16.1 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:casper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings casper_2.16.1.tar.gz |
StartedAt: 2019-04-13 00:59:03 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 01:06:09 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 425.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: casper.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:casper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings casper_2.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/casper.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'casper/DESCRIPTION' ... OK * this is package 'casper' version '2.16.1' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 'casper' can be installed ... WARNING Found the following significant warnings: Warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp23zEY8/R.INSTALL261c28d24220/casper/man/getDistrs.Rd:47: unknown macro '\item' Warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp23zEY8/R.INSTALL261c28d24220/casper/man/getDistrs.Rd:54: unknown macro '\item' Warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp23zEY8/R.INSTALL261c28d24220/casper/man/getDistrs.Rd:58: unknown macro '\item' See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/casper.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: data 1.8Mb libs 1.9Mb * 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 .mergeFramesViaRanges: no visible global function definition for 'queryHits' .mergeFramesViaRanges: no visible global function definition for 'subjectHits' assignExons2GeneF: no visible global function definition for 'queryHits' assignExons2GeneF: no visible global function definition for 'subjectHits' findNewExonsF: no visible global function definition for 'queryHits' generateNOexons: no visible global function definition for 'queryHits' generateNOexons: no visible global function definition for 'subjectHits' getDistrsFromBam: no visible global function definition for 'subjectHits' getDistrsFromBam: no visible global function definition for 'queryHits' getDistrsFrompBam: no visible global function definition for 'subjectHits' getDistrsFrompBam: no visible global function definition for 'queryHits' procPaths: no visible global function definition for 'queryHits' procPaths: no visible global function definition for 'subjectHits' Undefined global functions or variables: queryHits subjectHits * checking Rd files ... WARNING prepare_Rd: getDistrs.Rd:47: unknown macro '\item' prepare_Rd: getDistrs.Rd:54: unknown macro '\item' prepare_Rd: getDistrs.Rd:58: unknown macro '\item' * 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 ... OK * checking installed files from 'inst/doc' ... OK * 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 WARNINGs, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/casper.Rcheck/00check.log' for details.
casper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/casper_2.16.1.tar.gz && rm -rf casper.buildbin-libdir && mkdir casper.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=casper.buildbin-libdir casper_2.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL casper_2.16.1.zip && rm casper_2.16.1.tar.gz casper_2.16.1.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 2378k 100 2378k 0 0 26.0M 0 --:--:-- --:--:-- --:--:-- 27.3M install for i386 * installing *source* package 'casper' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c casper.cpp -o casper.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cstat.cpp -o cstat.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dataframe.cpp -o dataframe.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c discretedf.cpp -o discretedf.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dropVariant.cpp -o dropVariant.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c exon.cpp -o exon.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c fragFunc.c -o fragFunc.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c fragment.cpp -o fragment.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c functions.c -o functions.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hash.c -o hash.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c join_exons.c -o join_exons.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c makeIslands.c -o makeIslands.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c model.cpp -o model.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c model_cmp.cpp -o model_cmp.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c pathCounts.c -o pathCounts.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c procBam.c -o procBam.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c rcasper.cpp -o rcasper.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c seppel.cpp -o seppel.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c simReads.c -o simReads.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c simReadsfunc.c -o simReadsfunc.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c smartmodeldist.cpp -o smartmodeldist.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c uniqQname.c -o uniqQname.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c variant.cpp -o variant.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c variant_cmp.cpp -o variant_cmp.o C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/casper.buildbin-libdir/casper/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'transcripts' in package 'casper' ** help Warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp23zEY8/R.INSTALL261c28d24220/casper/man/getDistrs.Rd:47: unknown macro '\item' Warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp23zEY8/R.INSTALL261c28d24220/casper/man/getDistrs.Rd:54: unknown macro '\item' Warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp23zEY8/R.INSTALL261c28d24220/casper/man/getDistrs.Rd:58: unknown macro '\item' *** installing help indices converting help for package 'casper' finding HTML links ... done K562.r1l1 html annotatedGenome-class html asymmetryCheck html calcDenovo html calcExp html denovoExpr html denovoGeneExpr-class html denovoGenomeExpr-class html distrsGSE37704 html genePlot html getDistrs html getIsland html getNreads html getReads html getRoc html hg19DB html mergeBatches html mergeExp html modelPrior html modelPriorAS-class html pathCounts-class html pathCounts html plot-methods html plotExpr html plotPriorAS html probNonEquiv html procBam-class html procBam html procGenome html qqnormGenomeWide html quantileNorm html relexprByGene html rmShortInserts html simMAE html simMAEcheck html simMultSamples html simReads html simulatedSamples-class html splitGenomeByLength html subsetGenome html transcripts html txLength-methods html wrapDenovo html wrapKnown html ** building package indices ** installing vignettes 'casper.Rnw' ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'casper' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c casper.cpp -o casper.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cstat.cpp -o cstat.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dataframe.cpp -o dataframe.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c discretedf.cpp -o discretedf.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dropVariant.cpp -o dropVariant.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c exon.cpp -o exon.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c fragFunc.c -o fragFunc.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c fragment.cpp -o fragment.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c functions.c -o functions.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hash.c -o hash.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c join_exons.c -o join_exons.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c makeIslands.c -o makeIslands.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c model.cpp -o model.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c model_cmp.cpp -o model_cmp.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c pathCounts.c -o pathCounts.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c procBam.c -o procBam.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c rcasper.cpp -o rcasper.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c seppel.cpp -o seppel.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c simReads.c -o simReads.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c simReadsfunc.c -o simReadsfunc.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c smartmodeldist.cpp -o smartmodeldist.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c uniqQname.c -o uniqQname.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c variant.cpp -o variant.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c variant_cmp.cpp -o variant_cmp.o C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/casper.buildbin-libdir/casper/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'casper' as casper_2.16.1.zip * DONE (casper) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'casper' successfully unpacked and MD5 sums checked In R CMD INSTALL
casper.Rcheck/examples_i386/casper-Ex.timings
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casper.Rcheck/examples_x64/casper-Ex.timings
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