Hans-Ulrich Klein
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/R453Plus1Toolbox |
| Branch: RELEASE_3_9 |
| Last Commit: d7102b3 |
| Last Changed Date: 2019-05-02 11:53:19 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:48:25 -0400 (Wed, 16 Oct 2019).
| Package 1303/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| R453Plus1Toolbox 1.34.0 Hans-Ulrich Klein
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: R453Plus1Toolbox |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.34.0.tar.gz |
| StartedAt: 2019-10-16 05:58:24 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:07:11 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 527.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: R453Plus1Toolbox.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.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 ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.34.0’
* 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 ... 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
* 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 or elapsed time > 5s
user system elapsed
mergeBreakpoints 10.310 0.343 10.652
filterChimericReads 5.892 0.117 6.012
htmlReport 5.066 0.736 5.934
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.
R453Plus1Toolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL R453Plus1Toolbox ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘R453Plus1Toolbox’ ... ** using staged installation ** libs 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 readSFF.c -o readSFF.o 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 writeSFF.c -o writeSFF.o clang -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/3.6/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 | 0.401 | 0.018 | 0.423 | |
| AVASet | 0.342 | 0.023 | 0.364 | |
| AnnotatedVariants-class | 0.004 | 0.000 | 0.004 | |
| MapperSet-class | 0.068 | 0.034 | 0.102 | |
| MapperSet | 0.011 | 0.007 | 0.018 | |
| SFFContainer-class | 0.002 | 0.002 | 0.004 | |
| SFFRead-class | 0.002 | 0.001 | 0.003 | |
| alignShortReads | 3.584 | 0.029 | 3.626 | |
| annotateVariants | 0.002 | 0.001 | 0.003 | |
| assayDataAmp | 0.008 | 0.005 | 0.013 | |
| ava2vcf | 0.415 | 0.018 | 0.434 | |
| avaSetExample | 0.024 | 0.006 | 0.031 | |
| avaSetFiltered | 0.037 | 0.005 | 0.042 | |
| avaSetFiltered_annot | 0.004 | 0.005 | 0.009 | |
| breakpoints | 0.009 | 0.004 | 0.012 | |
| calculateTiTv | 0.016 | 0.004 | 0.021 | |
| captureArray | 0.003 | 0.004 | 0.007 | |
| coverageOnTarget | 0.330 | 0.015 | 0.348 | |
| demultiplexReads | 0.141 | 0.014 | 0.156 | |
| detectBreakpoints | 1.507 | 0.264 | 1.773 | |
| fDataAmp | 0.022 | 0.007 | 0.029 | |
| featureDataAmp | 0.022 | 0.006 | 0.029 | |
| filterChimericReads | 5.892 | 0.117 | 6.012 | |
| genomeSequencerMIDs | 0.042 | 0.004 | 0.046 | |
| getAlignedReads | 0.133 | 0.013 | 0.148 | |
| getVariantPercentages | 0.052 | 0.008 | 0.060 | |
| htmlReport | 5.066 | 0.736 | 5.934 | |
| mapperSetExample | 0.010 | 0.005 | 0.014 | |
| mergeBreakpoints | 10.310 | 0.343 | 10.652 | |
| mutationInfo | 0.006 | 0.006 | 0.012 | |
| plotAmpliconCoverage | 0.000 | 0.000 | 0.001 | |
| plotChimericReads | 3.490 | 0.070 | 3.581 | |
| plotVariants | 0.007 | 0.001 | 0.009 | |
| plotVariationFrequency | 0.000 | 0.000 | 0.001 | |
| qualityReportSFF | 0.001 | 0.000 | 0.001 | |
| readSFF | 0.191 | 0.004 | 0.197 | |
| readsOnTarget | 0.073 | 0.005 | 0.077 | |
| referenceSequences | 0.010 | 0.005 | 0.015 | |
| regions | 0.004 | 0.002 | 0.006 | |
| removeLinker | 0.029 | 0.001 | 0.030 | |
| sequenceCaptureLinkers | 0.004 | 0.001 | 0.005 | |
| setVariantFilter | 0.054 | 0.005 | 0.059 | |
| variants | 0.003 | 0.003 | 0.006 | |
| writeSFF | 0.036 | 0.000 | 0.037 | |