Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:36 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the R453Plus1Toolbox package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R453Plus1Toolbox.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1517/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
R453Plus1Toolbox 1.44.0 (landing page) Hans-Ulrich Klein
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: R453Plus1Toolbox |
Version: 1.44.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.44.0.tar.gz |
StartedAt: 2022-04-12 17:16:33 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 17:25:22 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 528.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: R453Plus1Toolbox.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/R453Plus1Toolbox.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘R453Plus1Toolbox’ version ‘1.44.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘R453Plus1Toolbox’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: R 3.0Mb extdata 2.6Mb * 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 * 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 ‘BSgenome.Hsapiens.UCSC.hg19’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .annotateVariants_MapperSet: no visible binding for global variable ‘Hsapiens’ .ava2vcf: no visible binding for global variable ‘Hsapiens’ .detectBreakpoints: no visible binding for global variable ‘Hsapiens’ .getEnsemblInfo: no visible binding for global variable ‘cds_length’ .getEnsemblInfo: no visible binding for global variable ‘ensembl_transcript_id’ .getMutations: no visible binding for global variable ‘PatternStart’ .getMutations: no visible binding for global variable ‘PatternEnd’ .htmlReport: no visible binding for global variable ‘VarFreqForward’ .htmlReport: no visible binding for global variable ‘VarFreqReverse’ .plotVariants: no visible binding for global variable ‘mutation’ qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’ annotateVariants,MapperSet-BSgenome: no visible binding for global variable ‘Hsapiens’ annotateVariants,MapperSet-missing: no visible binding for global variable ‘Hsapiens’ ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’ detectBreakpoints,list: no visible binding for global variable ‘Hsapiens’ subset,AVASet: no visible binding for global variable ‘referenceSeqID’ Undefined global functions or variables: Hsapiens PatternEnd PatternStart VarFreqForward VarFreqReverse cds_length ensembl_transcript_id mutation referenceSeqID * 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 is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mergeBreakpoints 9.678 0.150 9.839 filterChimericReads 6.426 0.041 6.479 * 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 ‘/Users/biocbuild/bbs-3.14-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’ for details.
R453Plus1Toolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL R453Plus1Toolbox ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘R453Plus1Toolbox’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c readSFF.c -o readSFF.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c writeSFF.c -o writeSFF.o clang -mmacosx-version-min=10.13 -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 R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-R453Plus1Toolbox/00new/R453Plus1Toolbox/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R453Plus1Toolbox)
R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings
name | user | system | elapsed | |
AVASet-class | 0.351 | 0.017 | 0.402 | |
AVASet | 0.229 | 0.009 | 0.237 | |
AnnotatedVariants-class | 0.002 | 0.001 | 0.002 | |
MapperSet-class | 0.037 | 0.028 | 0.064 | |
MapperSet | 0.007 | 0.004 | 0.010 | |
SFFContainer-class | 0.002 | 0.001 | 0.002 | |
SFFRead-class | 0.001 | 0.001 | 0.002 | |
alignShortReads | 2.393 | 0.011 | 2.411 | |
annotateVariants | 0.002 | 0.001 | 0.003 | |
assayDataAmp | 0.007 | 0.003 | 0.010 | |
ava2vcf | 0.457 | 0.010 | 0.470 | |
avaSetExample | 0.021 | 0.005 | 0.025 | |
avaSetFiltered | 0.027 | 0.005 | 0.031 | |
avaSetFiltered_annot | 0.002 | 0.003 | 0.005 | |
breakpoints | 0.007 | 0.003 | 0.009 | |
calculateTiTv | 0.016 | 0.004 | 0.019 | |
captureArray | 0.002 | 0.003 | 0.005 | |
coverageOnTarget | 0.358 | 0.037 | 0.397 | |
demultiplexReads | 0.138 | 0.015 | 0.154 | |
detectBreakpoints | 1.175 | 0.093 | 1.273 | |
fDataAmp | 0.020 | 0.003 | 0.024 | |
featureDataAmp | 0.019 | 0.005 | 0.025 | |
filterChimericReads | 6.426 | 0.041 | 6.479 | |
genomeSequencerMIDs | 0.037 | 0.002 | 0.039 | |
getAlignedReads | 0.100 | 0.008 | 0.109 | |
getVariantPercentages | 0.040 | 0.007 | 0.047 | |
htmlReport | 3.779 | 0.265 | 4.331 | |
mapperSetExample | 0.009 | 0.004 | 0.012 | |
mergeBreakpoints | 9.678 | 0.150 | 9.839 | |
mutationInfo | 0.004 | 0.003 | 0.007 | |
plotAmpliconCoverage | 0.000 | 0.001 | 0.001 | |
plotChimericReads | 3.561 | 0.018 | 3.581 | |
plotVariants | 0.005 | 0.002 | 0.006 | |
plotVariationFrequency | 0 | 0 | 0 | |
qualityReportSFF | 0 | 0 | 0 | |
readSFF | 0.137 | 0.005 | 0.142 | |
readsOnTarget | 0.084 | 0.003 | 0.086 | |
referenceSequences | 0.008 | 0.003 | 0.009 | |
regions | 0.004 | 0.004 | 0.006 | |
removeLinker | 0.034 | 0.002 | 0.036 | |
sequenceCaptureLinkers | 0.008 | 0.001 | 0.009 | |
setVariantFilter | 0.090 | 0.010 | 0.101 | |
variants | 0.004 | 0.003 | 0.008 | |
writeSFF | 0.050 | 0.001 | 0.051 | |