Package: LymphoSeq

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2020-01-16 05:59:00 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:05:17 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 377.2 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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.15.0’
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
cloneTrack     54.273  3.767  57.903
productiveSeq  53.343  3.207  58.225
phyloTree      11.670  0.082  12.214
seqMatrix       8.407  0.321   8.728
geneFreq        6.624  0.226   6.848
commonSeqsVenn  5.236  0.223   5.424
* 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-3.11-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/4.0/Resources/library’
* installing *source* package ‘LymphoSeq’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LymphoSeq)

name	user	system	elapsed
alignSeq	2.385	0.044	2.452
bhattacharyyaCoefficient	0.306	0.042	0.378
bhattacharyyaMatrix	0.353	0.048	0.401
chordDiagramVDJ	1.698	0.200	1.898
clonalRelatedness	1.164	0.131	0.240
clonality	0.322	0.231	0.117
cloneTrack	54.273	3.767	57.903
commonSeqs	0.363	0.057	0.420
commonSeqsBar	1.752	0.384	2.136
commonSeqsPlot	0.919	0.160	1.079
commonSeqsVenn	5.236	0.223	5.424
differentialAbundance	4.448	0.184	4.632
exportFasta	0.377	0.023	0.400
geneFreq	6.624	0.226	6.848
lorenzCurve	2.563	0.050	2.763
mergeFiles	0.141	0.010	0.151
pairwisePlot	1.414	0.040	1.568
phyloTree	11.670	0.082	12.214
productive	0.105	0.007	0.115
productiveSeq	53.343	3.207	58.225
readImmunoSeq	0.078	0.007	0.085
removeSeq	0.097	0.006	0.103
searchPublished	0.302	0.012	0.313
searchSeq	0.709	0.013	0.721
seqMatrix	8.407	0.321	8.728
similarityMatrix	0.309	0.009	0.317
similarityScore	0.196	0.007	0.203
topFreq	3.416	0.146	3.563
topSeqs	3.797	0.116	3.913
topSeqsPlot	0.655	0.008	0.665
uniqueSeqs	0.380	0.014	0.394