Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the fabia package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fabia.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 612/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fabia 2.38.0 (landing page) Andreas Mitterecker
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: fabia |
Version: 2.38.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fabia_2.38.0.tar.gz |
StartedAt: 2021-10-14 23:01:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:02:31 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 74.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fabia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fabia_2.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.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 'fabia/DESCRIPTION' ... OK * this is package 'fabia' version '2.38.0' * 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 'fabia' 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 File 'fabia/R/zzz.R': .onLoad calls: packageStartupMessage("+----------------------------+ \n", "|............................| \n", "|............................| \n", "|..............########......| ####### # ###### ### # \n", "|..............########......| # # # # # # # # \n", "|.....####.....########......| # # # # # # # # \n", "|.....####.....########......| ##### # # ###### # # # \n", "|.....####...................| # ####### # # # ####### \n", "|.....####...........###.....| # # # # # # # # \n", "|....................###.....| # # # ###### ### # # \n", "|....................###.....| \n", "|............................| \n", "+----------------------------+ \n") packageStartupMessage("Citation: S. Hochreiter et al.,", "\n", "FABIA: Factor Analysis for Bicluster Acquisition,", "\n", "Bioinformatics 26(12):1520-1527, 2010.", "\n", "BibTex: enter 'toBibtex(citation(\"fabia\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html", "\n\n", "FABIA Package Version ", version, "\n") See section 'Good practice' in '?.onAttach'. plot,Factorization-missing: warning in symbols(ll[isel, 1], ll[isel, 2], circle = sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg = colors[2]): partial argument match of 'circle' to 'circles' plot,Factorization-missing: warning in symbols(zz[ii, 1], zz[ii, 2], square = sqs, inches = FALSE, lwd = 3, add = TRUE, fg = colors[2 + iGroup[i]]): partial argument match of 'square' to 'squares' .onLoad: no visible global function definition for 'winMenuNames' .onLoad: no visible global function definition for 'winMenuAdd' .onLoad: no visible global function definition for 'winMenuAddItem' plot,Factorization-missing: no visible global function definition for 'dev.new' Undefined global functions or variables: dev.new winMenuAdd winMenuAddItem winMenuNames Consider adding importFrom("grDevices", "dev.new") importFrom("utils", "winMenuAdd", "winMenuAddItem", "winMenuNames") 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... NOTE Found the following Makefile(s) with an include directive with a pathname using R_HOME: src/Makefile.win Even though not recommended, variable R_HOME may contain spaces. Makefile directives use space as a separator and there is no portable way to quote/escape the space in Make rules and directives. However, one can and should quote pathnames when passed from Makefile to the shell, and this can be done specifically when invoking Make recursively. It is therefore recommended to use the Make '-f' option to include files in directories specified using R_HOME. This option can be specified multiple times to include multiple Makefiles. Note that 'Makeconf' is included automatically into top-level makefile of a package. More information can be found in 'Writing R Extensions'. * 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/fabia/libs/i386/fabia.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/fabia/libs/x64/fabia.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 ** 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.Rcheck/00check.log' for details.
fabia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/fabia_2.38.0.tar.gz && rm -rf fabia.buildbin-libdir && mkdir fabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fabia.buildbin-libdir fabia_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL fabia_2.38.0.zip && rm fabia_2.38.0.tar.gz fabia_2.38.0.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 203k 100 203k 0 0 849k 0 --:--:-- --:--:-- --:--:-- 851k install for i386 * installing *source* package 'fabia' ... ** using staged installation ** libs running 'src/Makefile.win' ... rm -f fabia.o fabia.dll *.a *.o *.so *.dll "C:/rtools40/mingw32/bin/"gcc -c fabiac.c -o fabia.o -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -Wall -O3 "C:/rtools40/mingw32/bin/"gcc -shared -s -static-libgcc fabia.o -L"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386" -lR -o fabia.dll rm -f fabia.o *.a *.o *.so installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/libs/i386 ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'fabia' finding HTML links ... done Factorization-class html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/help/L.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/help/L+2CFactorization-method.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/help/L+3C-.html estimateMode html extractBic html extractPlot html fabi html fabia html fabiaDemo html fabiaVersion html fabiap html fabias html fabiasp html makeFabiaData html makeFabiaDataBlocks html makeFabiaDataBlocksPos html makeFabiaDataPos html matrixImagePlot html mfsc html nmfdiv html nmfeu html nmfsc html plotBicluster html projFunc html projFuncPos html readSamplesSpfabia html readSpfabiaResult html samplesPerFeature html spfabia 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 'fabia' ... ** libs running 'src/Makefile.win' ... rm -f fabia.o fabia.dll *.a *.o *.so *.dll "C:/rtools40/mingw64/bin/"gcc -c fabiac.c -o fabia.o -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -Wall -O3 "C:/rtools40/mingw64/bin/"gcc -shared -s -static-libgcc fabia.o -L"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64" -lR -o fabia.dll rm -f fabia.o *.a *.o *.so installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/fabia.buildbin-libdir/fabia/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'fabia' as fabia_2.38.0.zip * DONE (fabia) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'fabia' successfully unpacked and MD5 sums checked
fabia.Rcheck/examples_i386/fabia-Ex.timings
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fabia.Rcheck/examples_x64/fabia-Ex.timings
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