Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:15 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE ChIPseqR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 286/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ChIPseqR 1.42.0 Peter Humburg
| malbec2 | Linux (Ubuntu 18.04.4 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: ChIPseqR |
Version: 1.42.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPseqR_1.42.0.tar.gz |
StartedAt: 2020-10-17 02:31:53 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 02:38:41 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 408.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPseqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPseqR_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChIPseqR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChIPseqR' version '1.42.0' * 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 'ChIPseqR' 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 .fixCounts: no visible global function definition for 'runLength' .fixCounts: no visible global function definition for 'runValue' getBindLen: no visible global function definition for 'window' pickPeak: no visible global function definition for 'start' pickPeak: no visible global function definition for 'runLength' pickPeak : <anonymous>: no visible global function definition for 'window' [[,BindScore-ANY-numeric: no visible global function definition for 'window' decompress,Rle: no visible global function definition for 'runValue' decompress,RleList : <anonymous>: no visible global function definition for 'runValue' initialize,RLEBindScore : <anonymous>: no visible global function definition for 'Rle' initialize,RLEBindScore : <anonymous>: no visible global function definition for 'runValue' initialize,RLEBindScore : <anonymous>: no visible global function definition for 'runValue<-' plot,RLEReadCounts-missing : <anonymous>: no visible global function definition for 'window' Undefined global functions or variables: Rle runLength runValue runValue<- start window Consider adding importFrom("stats", "start", "window") to your NAMESPACE file. * 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-3.11-bioc/R/library/ChIPseqR/libs/i386/ChIPseqR.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/ChIPseqR/libs/x64/ChIPseqR.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 alignFeature 12.46 3.68 16.12 BindScore 7.75 0.27 8.02 RLEBindScore-class 6.89 0.34 7.24 simpleNucCall 6.45 0.24 6.69 callBindingSites 5.36 0.21 5.58 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed alignFeature 12.30 3.41 15.70 BindScore 7.11 0.33 7.44 RLEBindScore-class 6.70 0.30 7.00 simpleNucCall 5.32 0.27 5.58 * 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-3.11-bioc/meat/ChIPseqR.Rcheck/00check.log' for details.
ChIPseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ChIPseqR_1.42.0.tar.gz && rm -rf ChIPseqR.buildbin-libdir && mkdir ChIPseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseqR.buildbin-libdir ChIPseqR_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ChIPseqR_1.42.0.zip && rm ChIPseqR_1.42.0.tar.gz ChIPseqR_1.42.0.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 42513 100 42513 0 0 730k 0 --:--:-- --:--:-- --:--:-- 814k install for i386 * installing *source* package 'ChIPseqR' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c startScore.c -o startScore.o startScore.c: In function '_ratioStat_pois': startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable] double stat, tmp_stat; ^~~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.buildbin-libdir/00LOCK-ChIPseqR/00new/ChIPseqR/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ChIPseqR' finding HTML links ... done BindScore html ChIPseqR-package html RLEBindScore-class html finding level-2 HTML links ... done RLEReadCounts-class html ReadCounts html accessors html alignFeature html callBindingSites html compress-BindScore html compress-ReadCounts html compress-methods html decompress-methods html decompress html exportBindSequence html getBindCor html getBindLen html getCutoff html internal html pickPeak html plot-BindScore html plot-ReadCounts html plotReads html plotWindow html pos2gff html simpleNucCall html startScore html strandPileup html windowCounts 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 'ChIPseqR' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c startScore.c -o startScore.o startScore.c: In function '_ratioStat_pois': startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable] double stat, tmp_stat; ^~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ChIPseqR' as ChIPseqR_1.42.0.zip * DONE (ChIPseqR) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'ChIPseqR' successfully unpacked and MD5 sums checked
ChIPseqR.Rcheck/examples_i386/ChIPseqR-Ex.timings
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ChIPseqR.Rcheck/examples_x64/ChIPseqR-Ex.timings
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