Package: LymphoSeq

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2019-04-16 00:56:13 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:59:56 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 223.3 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.0’
* 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
productiveSeq 29.977  1.462  31.658
cloneTrack    28.307  1.993  30.579
phyloTree      6.817  0.035   6.921
* 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-3.8-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	1.525	0.017	1.570
bhattacharyyaCoefficient	0.225	0.023	0.267
bhattacharyyaMatrix	0.249	0.017	0.324
chordDiagramVDJ	0.957	0.060	1.031
clonalRelatedness	1.416	0.169	0.267
clonality	0.486	0.810	0.177
cloneTrack	28.307	1.993	30.579
commonSeqs	0.277	0.035	0.314
commonSeqsBar	2.691	0.168	2.883
commonSeqsPlot	0.512	0.009	0.532
commonSeqsVenn	1.107	0.066	1.165
differentialAbundance	3.228	0.106	3.378
exportFasta	1.823	0.035	1.874
geneFreq	2.507	0.028	2.558
lorenzCurve	1.796	0.033	1.844
mergeFiles	0.121	0.004	0.126
pairwisePlot	1.015	0.013	1.036
phyloTree	6.817	0.035	6.921
productive	0.070	0.002	0.073
productiveSeq	29.977	1.462	31.658
readImmunoSeq	0.070	0.004	0.074
removeSeq	0.086	0.003	0.090
searchPublished	0.281	0.005	0.289
searchSeq	0.571	0.007	0.578
seqMatrix	2.327	0.113	2.447
similarityMatrix	0.262	0.010	0.274
similarityScore	0.226	0.010	0.236
topFreq	3.293	0.219	3.531
topSeqs	0.241	0.005	0.248
topSeqsPlot	0.505	0.005	0.619
uniqueSeqs	0.295	0.007	0.303