BioC 3.4: CHECK report for LymphoSeq on morelia

Package: LymphoSeq

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.2.0.tar.gz

StartedAt: 2017-04-15 04:19:51 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 04:22:03 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 132.1 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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 ‘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    44.672  1.222  46.633
productiveSeq 19.171  0.829  20.006
* 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	0.295	0.011	0.306
bhattacharyyaMatrix	0.270	0.006	0.275
chordDiagramVDJ	1.673	0.018	1.910
clonality	0.086	0.005	0.091
cloneTrack	44.672	1.222	46.633
commonSeqs	0.204	0.006	0.210
commonSeqsPlot	1.408	0.006	1.456
commonSeqsVenn	4.061	0.068	4.659
geneFreq	2.251	0.033	2.435
lorenzCurve	2.120	0.026	2.153
mergeFiles	0.103	0.005	0.109
pairwisePlot	1.551	0.009	3.196
productive	0.080	0.003	0.082
productiveSeq	19.171	0.829	20.006
readImmunoSeq	0.062	0.003	0.065
removeSeq	0.074	0.003	0.078
searchPublished	0.212	0.006	0.224
searchSeq	0.907	0.008	0.915
seqMatrix	3.227	0.121	3.349
similarityMatrix	0.206	0.004	0.210
similarityScore	0.178	0.004	0.181
topFreq	1.918	0.097	2.017
topSeqs	0.236	0.006	0.254
topSeqsPlot	1.572	0.102	1.677
uniqueSeqs	0.297	0.005	0.301