Package: LymphoSeq

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2019-10-16 04:09:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:16:05 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 373.3 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 71.797  3.015  75.970
cloneTrack    51.256  3.882  55.154
phyloTree     10.094  0.100  10.196
topFreq        7.645  0.347   8.221
geneFreq       6.782  0.206   6.986
commonSeqsBar  5.427  0.395   5.823
* 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’ ...
** 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	1.564	0.033	1.625
bhattacharyyaCoefficient	0.814	0.050	0.891
bhattacharyyaMatrix	0.376	0.031	0.407
chordDiagramVDJ	1.539	0.226	1.765
clonalRelatedness	1.190	0.153	0.320
clonality	0.894	0.343	0.677
cloneTrack	51.256	3.882	55.154
commonSeqs	0.370	0.071	0.441
commonSeqsBar	5.427	0.395	5.823
commonSeqsPlot	0.666	0.016	0.682
commonSeqsVenn	1.117	0.141	1.205
differentialAbundance	4.329	0.176	4.504
exportFasta	0.403	0.052	0.455
geneFreq	6.782	0.206	6.986
lorenzCurve	2.225	0.056	2.282
mergeFiles	0.138	0.006	0.145
pairwisePlot	1.234	0.015	1.250
phyloTree	10.094	0.100	10.196
productive	0.100	0.006	0.105
productiveSeq	71.797	3.015	75.970
readImmunoSeq	0.074	0.006	0.084
removeSeq	0.088	0.006	0.094
searchPublished	0.348	0.020	0.367
searchSeq	0.705	0.014	0.800
seqMatrix	4.447	0.245	4.836
similarityMatrix	0.338	0.014	0.359
similarityScore	0.297	0.015	0.320
topFreq	7.645	0.347	8.221
topSeqs	0.248	0.019	0.268
topSeqsPlot	0.645	0.009	0.655
uniqueSeqs	0.387	0.012	0.398