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BioC 3.5: CHECK report for R453Plus1Toolbox on toluca2

This page was generated on 2017-04-23 14:35:26 -0400 (Sun, 23 Apr 2017).

Package 1049/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.25.1
Hans-Ulrich Klein
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 128391 / Revision: 129046
Last Changed Date: 2017-04-08 16:51:55 -0400 (Sat, 08 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: R453Plus1Toolbox
Version: 1.25.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.25.1.tar.gz
StartedAt: 2017-04-23 08:32:03 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 08:38:37 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 394.0 seconds
RetCode: 0
Status:  OK 
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.25.1’
* 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 loading without being on the library search path ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 7.205  0.166   7.444
htmlReport       5.389  0.226   5.829
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.


R453Plus1Toolbox.Rcheck/00install.out:

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c readSFF.c -o readSFF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 /Users/biocbuild/bbs-3.5-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.4990.0350.544
AVASet0.6250.0200.671
AnnotatedVariants-class0.0030.0000.003
MapperSet-class0.0350.0100.045
MapperSet0.0070.0020.009
SFFContainer-class0.0020.0000.002
SFFRead-class0.0020.0000.002
alignShortReads2.3010.0122.325
annotateVariants0.0030.0000.003
assayDataAmp0.0070.0010.007
ava2vcf0.4720.0350.508
avaSetExample0.0160.0030.020
avaSetFiltered0.0220.0030.026
avaSetFiltered_annot0.0020.0010.003
breakpoints0.0060.0010.008
calculateTiTv0.0130.0020.016
captureArray0.0020.0010.003
coverageOnTarget0.3840.0350.422
demultiplexReads0.3170.0030.322
detectBreakpoints1.8600.0211.893
fDataAmp0.0190.0020.022
featureDataAmp0.0180.0020.019
filterChimericReads2.4750.0382.546
genomeSequencerMIDs0.0240.0010.024
getAlignedReads0.1080.0030.111
getVariantPercentages0.0620.0020.065
htmlReport5.3890.2265.829
mapperSetExample0.0070.0010.009
mergeBreakpoints7.2050.1667.444
mutationInfo0.0040.0010.004
plotAmpliconCoverage000
plotChimericReads3.3310.0113.364
plotVariants0.0070.0010.008
plotVariationFrequency0.0000.0000.001
qualityReportSFF0.0010.0000.001
readSFF0.0750.0010.078
readsOnTarget0.3460.0120.369
referenceSequences0.0100.0020.012
regions0.0040.0010.005
removeLinker0.0270.0010.029
sequenceCaptureLinkers0.0050.0010.005
setVariantFilter0.1410.0030.152
variants0.0030.0010.005
writeSFF0.1100.0010.112