BioC 3.3: CHECK report for LymphoSeq on morelia

Package: LymphoSeq

Version: 0.99.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_0.99.3.tar.gz

StartedAt: 2016-04-21 04:28:01 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:30:22 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 140.7 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_0.99.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.3’
* 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 ... [3s/4s] 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 ... [102s/103s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cloneTrack     52.481  1.334  54.858
productiveSeq  21.631  0.981  22.636
commonSeqsVenn  5.274  0.059   5.533
* 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	0.285	0.007	0.296
bhattacharyyaMatrix	0.250	0.005	0.254
chordDiagramVDJ	1.835	0.022	1.879
clonality	0.051	0.003	0.054
cloneTrack	52.481	1.334	54.858
commonSeqs	0.199	0.010	0.209
commonSeqsPlot	0.463	0.011	0.475
commonSeqsVenn	5.274	0.059	5.533
geneFreq	2.450	0.027	2.529
lorenzCurve	2.292	0.023	2.318
mergeFiles	0.082	0.001	0.083
pairwisePlot	0.958	0.006	0.966
productive	0.052	0.002	0.055
productiveSeq	21.631	0.981	22.636
readImmunoSeq	0.035	0.002	0.036
removeSeq	0.057	0.002	0.059
searchPublished	0.235	0.005	0.239
searchSeq	0.996	0.007	1.003
seqMatrix	3.508	0.170	3.683
similarityMatrix	0.206	0.011	0.217
similarityScore	0.175	0.009	0.183
topFreq	1.833	0.096	1.930
topSeqs	0.172	0.010	0.182
topSeqsPlot	0.494	0.006	0.500
uniqueSeqs	1.361	0.059	1.421