Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:30:00 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the BicARE package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 145/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BicARE 1.48.0 (landing page) Pierre Gestraud
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: BicARE |
Version: 1.48.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BicARE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BicARE_1.48.0.tar.gz |
StartedAt: 2021-05-06 00:43:34 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 00:59:57 -0400 (Thu, 06 May 2021) |
EllapsedTime: 983.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BicARE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BicARE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BicARE_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BicARE.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BicARE/DESCRIPTION' ... OK * this is package 'BicARE' version '1.48.0' * 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 'BicARE' 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 ... NOTE Packages in Depends field not imported from: 'Biobase' 'GSEABase' 'multtest' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE FLOC: no visible global function definition for 'new' FLOC: no visible global function definition for 'exprs' FLOC: no visible global function definition for 'runif' FLOC: no visible binding for global variable 'var' bicluster: no visible global function definition for 'exprs' bicluster: no visible global function definition for 'featureNames' bicluster: no visible global function definition for 'sampleNames' makeReport: no visible global function definition for 'annotation' makeReport: no visible global function definition for 'png' makeReport: no visible global function definition for 'dev.off' makeReport: no visible global function definition for 'getSYMBOL' makeReport: no visible global function definition for 'setName' makeReport: no visible global function definition for 'browseURL' plot.bicluster: no visible global function definition for 'par' plot.bicluster: no visible global function definition for 'matplot' plot.bicluster: no visible global function definition for 'axis' residue: no visible global function definition for 'new' residue: no visible global function definition for 'exprs' testAnnot: no visible global function definition for 'pData' testAnnot: no visible global function definition for 'phenoData' testAnnot: no visible global function definition for 'chisq.test' testAnnot: no visible global function definition for 'mt.rawp2adjp' testSet: no visible global function definition for 'exprs' testSet: no visible global function definition for 'GeneSet' testSet: no visible global function definition for 'geneIdType' testSet: no visible global function definition for 'geneIds' testSet: no visible global function definition for 'mapIdentifiers' testSet: no visible global function definition for 'phyper' testSet: no visible global function definition for 'mt.rawp2adjp' Undefined global functions or variables: GeneSet annotation axis browseURL chisq.test dev.off exprs featureNames geneIdType geneIds getSYMBOL mapIdentifiers matplot mt.rawp2adjp new pData par phenoData phyper png runif sampleNames setName var Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "axis", "matplot", "par") importFrom("methods", "new") importFrom("stats", "chisq.test", "phyper", "runif", "var") importFrom("utils", "browseURL") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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-3.12-bioc/R/library/BicARE/libs/i386/BicARE.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BicARE/libs/x64/BicARE.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'printf', possibly from 'printf' (C) 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 testSet 349.55 0.33 349.88 FLOC 23.65 0.06 23.72 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed testSet 413.89 0.33 414.23 FLOC 24.05 0.03 24.08 makeReport 2.03 0.28 5.94 * 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BicARE.Rcheck/00check.log' for details.
BicARE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/BicARE_1.48.0.tar.gz && rm -rf BicARE.buildbin-libdir && mkdir BicARE.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BicARE.buildbin-libdir BicARE_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BicARE_1.48.0.zip && rm BicARE_1.48.0.tar.gz BicARE_1.48.0.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 200k 100 200k 0 0 1987k 0 --:--:-- --:--:-- --:--:-- 2002k install for i386 * installing *source* package 'BicARE' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BicARE.c -o BicARE.o BicARE.c: In function 'floc': BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable] double invk = 1/(double)*k; ^~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o BicARE.dll tmp.def BicARE.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BicARE.buildbin-libdir/00LOCK-BicARE/00new/BicARE/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BicARE' finding HTML links ... done BicARE-package html FLOC html bicluster html makeReport html residue html sample.bicData html sample.biclustering html testAnnot html testSet 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 'BicARE' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BicARE.c -o BicARE.o BicARE.c: In function 'floc': BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable] double invk = 1/(double)*k; ^~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o BicARE.dll tmp.def BicARE.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BicARE.buildbin-libdir/BicARE/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BicARE' as BicARE_1.48.0.zip * DONE (BicARE) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'BicARE' successfully unpacked and MD5 sums checked
BicARE.Rcheck/examples_i386/BicARE-Ex.timings
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BicARE.Rcheck/examples_x64/BicARE-Ex.timings
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