Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:48:00 -0400 (Wed, 16 Oct 2019).
Package 680/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
girafe 1.36.0 J. Toedling
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: girafe |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings girafe_1.36.0.tar.gz |
StartedAt: 2019-10-16 03:15:59 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 03:22:34 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 395.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: girafe.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings girafe_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/girafe.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘girafe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘girafe’ version ‘1.36.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘girafe’ can be installed ... OK * 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 * 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 :: no visible global function definition for ‘IRangesList’ agiFromBam : : no visible global function definition for ‘scanBamFlag’ agiFromBam : : 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 : : 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 is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed perWindow 23.398 0.099 24.721 negbinomsig 20.329 0.522 20.851 AlignedGenomeIntervals-class 11.194 1.100 9.312 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/girafe.Rcheck/00check.log’ for details.
girafe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL girafe ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘girafe’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c coverage.cpp -o coverage.o coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c girafe_init.c -o girafe_init.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-girafe/00new/girafe/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘girafe’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’ ** testing if installed package keeps a record of temporary installation path * DONE (girafe)
girafe.Rcheck/girafe-Ex.timings
name | user | system | elapsed | |
AlignedGenomeIntervals-class | 11.194 | 1.100 | 9.312 | |
agiFromBam | 0.565 | 0.381 | 0.602 | |
countReadsAnnotated | 0.240 | 0.103 | 0.316 | |
fracOverlap | 0.325 | 0.062 | 0.387 | |
intPhred | 0.185 | 0.140 | 0.294 | |
medianByPosition | 0.898 | 0.396 | 1.180 | |
negbinomsig | 20.329 | 0.522 | 20.851 | |
perWindow | 23.398 | 0.099 | 24.721 | |
plotAligned | 0.049 | 0.001 | 0.049 | |
trimAdapter | 0.119 | 0.006 | 0.131 | |
weightedConsensusMatrix | 0.008 | 0.001 | 0.009 | |
whichNearestMethods | 0.437 | 0.014 | 0.502 | |