Package: LymphoSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LymphoSeq_1.8.0.tar.gz

StartedAt: 2018-10-16 22:18:10 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:21:43 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 212.9 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 --install=check:LymphoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LymphoSeq_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.8.0’
* 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 ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cloneTrack    30.592  2.238  32.928
productiveSeq 22.886  1.259  24.408
phyloTree      6.307  0.035   6.406
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/LymphoSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LymphoSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘LymphoSeq’ ...
** R
** 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
* DONE (LymphoSeq)

name	user	system	elapsed
alignSeq	1.602	0.017	1.644
bhattacharyyaCoefficient	0.231	0.011	0.257
bhattacharyyaMatrix	0.281	0.018	0.300
chordDiagramVDJ	1.068	0.076	1.155
clonalRelatedness	1.247	0.248	0.266
clonality	0.394	0.463	0.124
cloneTrack	30.592	2.238	32.928
commonSeqs	0.280	0.035	0.316
commonSeqsBar	2.797	0.152	2.967
commonSeqsPlot	0.618	0.006	0.630
commonSeqsVenn	1.023	0.071	1.067
differentialAbundance	2.962	0.097	3.086
exportFasta	1.708	0.021	1.756
geneFreq	2.444	0.026	2.492
lorenzCurve	1.765	0.024	1.806
mergeFiles	0.094	0.004	0.098
pairwisePlot	2.467	0.019	2.505
phyloTree	6.307	0.035	6.406
productive	0.095	0.004	0.100
productiveSeq	22.886	1.259	24.408
readImmunoSeq	0.069	0.004	0.073
removeSeq	0.089	0.003	0.093
searchPublished	0.205	0.004	0.209
searchSeq	0.523	0.007	0.533
seqMatrix	3.914	0.466	4.414
similarityMatrix	0.223	0.007	0.233
similarityScore	0.207	0.005	0.213
topFreq	1.541	0.120	1.672
topSeqs	0.218	0.005	0.224
topSeqsPlot	0.512	0.027	0.542
uniqueSeqs	0.249	0.012	0.262