Package: LymphoSeq

Version: 1.11.0

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_1.11.0.tar.gz

StartedAt: 2019-04-09 01:53:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:57:02 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 236.3 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_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.11.0’
* 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    28.962  2.158  31.120
productiveSeq 27.643  1.493  29.331
phyloTree      6.932  0.036   7.031
topFreq        6.018  0.179   6.253
* 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-3.9-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/3.6/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	1.323	0.014	1.368
bhattacharyyaCoefficient	0.210	0.013	0.241
bhattacharyyaMatrix	0.605	0.014	0.622
chordDiagramVDJ	1.226	0.099	1.341
clonalRelatedness	1.270	0.194	0.227
clonality	0.490	0.511	0.129
cloneTrack	28.962	2.158	31.120
commonSeqs	0.283	0.035	0.321
commonSeqsBar	2.686	0.177	2.894
commonSeqsPlot	0.582	0.007	0.595
commonSeqsVenn	1.105	0.067	1.163
differentialAbundance	3.189	0.100	3.322
exportFasta	0.314	0.028	0.345
geneFreq	3.780	0.038	3.860
lorenzCurve	1.853	0.018	1.897
mergeFiles	0.133	0.004	0.137
pairwisePlot	1.007	0.008	1.031
phyloTree	6.932	0.036	7.031
productive	0.086	0.003	0.089
productiveSeq	27.643	1.493	29.331
readImmunoSeq	0.057	0.003	0.059
removeSeq	0.076	0.003	0.080
searchPublished	0.294	0.006	0.303
searchSeq	0.608	0.007	0.622
seqMatrix	4.000	0.130	4.166
similarityMatrix	0.270	0.005	0.279
similarityScore	0.240	0.005	0.245
topFreq	6.018	0.179	6.253
topSeqs	0.286	0.004	0.294
topSeqsPlot	0.655	0.005	0.668
uniqueSeqs	0.377	0.009	0.389