BioC 3.3: CHECK report for LymphoSeq on oaxaca

Package: LymphoSeq

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.0.2.tar.gz

StartedAt: 2016-10-13 03:13:43 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:16:09 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 146.0 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.0.2’
* 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 ‘LymphoSeq’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
cloneTrack     54.138  1.385  56.528
productiveSeq  19.911  0.969  20.894
commonSeqsVenn  5.744  0.069   6.271
* 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: OK

* installing *source* package ‘LymphoSeq’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LymphoSeq)

name	user	system	elapsed
bhattacharyyaCoefficient	0.304	0.008	0.313
bhattacharyyaMatrix	0.292	0.006	0.298
chordDiagramVDJ	1.76	0.03	2.33
clonality	0.060	0.004	0.064
cloneTrack	54.138	1.385	56.528
commonSeqs	0.220	0.007	0.227
commonSeqsPlot	0.537	0.013	0.657
commonSeqsVenn	5.744	0.069	6.271
geneFreq	2.947	0.048	3.842
lorenzCurve	2.517	0.029	2.759
mergeFiles	0.084	0.002	0.087
pairwisePlot	0.942	0.006	1.113
productive	0.059	0.002	0.062
productiveSeq	19.911	0.969	20.894
readImmunoSeq	0.032	0.002	0.034
removeSeq	0.042	0.001	0.045
searchPublished	0.222	0.004	0.225
searchSeq	0.935	0.008	0.943
seqMatrix	3.190	0.170	3.362
similarityMatrix	0.177	0.002	0.179
similarityScore	0.190	0.003	0.192
topFreq	1.641	0.085	1.728
topSeqs	0.179	0.006	0.208
topSeqsPlot	0.440	0.004	0.476
uniqueSeqs	1.395	0.124	1.521