Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:42 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE girafe PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 734/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
girafe 1.40.0 J. Toedling
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: girafe |
Version: 1.40.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings girafe_1.40.0.tar.gz |
StartedAt: 2020-10-17 04:31:39 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 04:38:07 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 387.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: girafe.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings girafe_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/girafe.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 'girafe/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'girafe' version '1.40.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'Rsamtools', 'intervals', 'ShortRead', 'genomeIntervals', 'grid' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'girafe' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/fracOverlap.Rd:38: file link 'interval_overlap' in package 'genomeIntervals' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/trimAdapter.Rd:39: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/trimAdapter.Rd:41: file link 'writeFastq' in package 'ShortRead' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/weightedConsensusMatrix.Rd:23: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/whichNearestMethods.Rd:44: file link 'which_nearest' in package 'intervals' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/girafe.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'genomeIntervals' A package should be listed in only one of these fields. * 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 'library' or 'require' call to 'MASS' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: 'Rsamtools' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: 'genomeIntervals:::intervalsForOverlap' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE agiFromBam: no visible binding for global variable 'mclapply' agiFromBam: no visible global function definition for 'scanBamHeader' agiFromBam: no visible global function definition for 'ScanBamParam' agiFromBam : <anonymous>: no visible global function definition for 'IRangesList' agiFromBam : <anonymous>: no visible global function definition for 'scanBamFlag' agiFromBam : <anonymous>: no visible global function definition for 'scanBam' countReadsAnnotated: no visible binding for global variable 'mclapply' countReadsAnnotated: no visible binding for global variable 'fraction1' fracOverlap: no visible binding for global variable 'fraction1' fracOverlap: no visible binding for global variable 'fraction2' getFeatureCounts: no visible binding for global variable 'fraction1' getFeatureCounts: no visible binding for global variable 'Index1' intPhred: no visible binding for global variable 'mclapply' oldAGIoverlap: no visible binding for global variable 'mclapply' plotReads: no visible binding for global variable 'x.start' plotReads: no visible binding for global variable 'x.end' plotReads: no visible binding for global variable 'y' reduceOne: no visible binding for global variable 'fraction1' reduceOne: no visible binding for global variable 'fraction2' trimAdapter: no visible global function definition for 'DNAString' trimAdapter: no visible global function definition for 'narrow' windowCountAndGC: no visible binding for global variable 'n.reads' windowCountAndGC: no visible global function definition for 'Views' windowCountAndGC: no visible global function definition for 'unmasked' windowCountAndGC: no visible global function definition for 'alphabetFrequency' clusters,AlignedGenomeIntervals: no visible binding for global variable 'mclapply' clusters,Genome_intervals: no visible binding for global variable 'mclapply' coverage,AlignedGenomeIntervals: no visible binding for global variable 'mclapply' coverage,AlignedGenomeIntervals : <anonymous>: no visible binding for global variable 'on.minus' interval_included,AlignedGenomeIntervals-AlignedGenomeIntervals: no visible binding for global variable 'mclapply' reduce,AlignedGenomeIntervals: no visible binding for global variable 'mclapply' reduce,Genome_intervals: no visible binding for global variable 'mclapply' reduce,Genome_intervals: no visible binding for global variable 'fraction1' reduce,Genome_intervals: no visible binding for global variable 'fraction2' Undefined global functions or variables: DNAString IRangesList Index1 ScanBamParam Views alphabetFrequency fraction1 fraction2 mclapply n.reads narrow on.minus scanBam scanBamFlag scanBamHeader unmasked x.end x.start y * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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/girafe/libs/i386/girafe.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/girafe/libs/x64/girafe.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 AlignedGenomeIntervals-class 13.91 1.17 15.22 perWindow 12.72 0.41 13.13 negbinomsig 10.53 0.73 11.28 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignedGenomeIntervals-class 13.86 1.01 14.87 perWindow 11.97 0.27 12.24 negbinomsig 9.24 0.59 9.83 * 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 WARNING, 5 NOTEs See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/girafe.Rcheck/00check.log' for details.
girafe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/girafe_1.40.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL girafe_1.40.0.zip && rm girafe_1.40.0.tar.gz girafe_1.40.0.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 1062k 100 1062k 0 0 16.3M 0 --:--:-- --:--:-- --:--:-- 18.1M install for i386 * installing *source* package 'girafe' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coverage.cpp -o coverage.o "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 girafe_init.c -o girafe_init.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.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/girafe.buildbin-libdir/00LOCK-girafe/00new/girafe/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe' Creating a generic function for 'sample' from package 'base' in package 'girafe' ** help *** installing help indices converting help for package 'girafe' finding HTML links ... done AlignedGenomeIntervals-class html agiFromBam html countReadsAnnotated html fracOverlap html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/fracOverlap.Rd:38: file link 'interval_overlap' in package 'genomeIntervals' does not exist and so has been treated as a topic getFeatureCounts html girafe-internal html intPhred html medianByPosition html negbinomsig html perWindow html plotAligned html plotReads html plotnegbinomfit html reduce-extras html trimAdapter html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/trimAdapter.Rd:39: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/trimAdapter.Rd:41: file link 'writeFastq' in package 'ShortRead' does not exist and so has been treated as a topic weightedConsensusMatrix html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/weightedConsensusMatrix.Rd:23: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic whichNearestMethods html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpo7VvmF/R.INSTALL204c77391081/girafe/man/whichNearestMethods.Rd:44: file link 'which_nearest' in package 'intervals' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe' ** testing if installed package can be loaded from final location No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'girafe' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coverage.cpp -o coverage.o "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 girafe_init.c -o girafe_init.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.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/girafe.buildbin-libdir/girafe/libs/x64 ** testing if installed package can be loaded No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe' * MD5 sums packaged installation of 'girafe' as girafe_1.40.0.zip * DONE (girafe) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'girafe' successfully unpacked and MD5 sums checked
girafe.Rcheck/examples_i386/girafe-Ex.timings
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girafe.Rcheck/examples_x64/girafe-Ex.timings
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