Package: LymphoSeq

Version: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2020-04-15 03:29:03 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:33:04 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 240.6 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.0’
* 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    30.128  1.987  31.037
productiveSeq 24.460  1.282  26.153
phyloTree      7.121  0.032   7.230
* 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-3.10-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	1.866	0.018	1.914
bhattacharyyaCoefficient	0.540	0.015	0.599
bhattacharyyaMatrix	0.289	0.012	0.302
chordDiagramVDJ	1.193	0.097	1.304
clonalRelatedness	0.852	0.126	0.186
clonality	0.829	0.233	0.105
cloneTrack	30.128	1.987	31.037
commonSeqs	0.253	0.029	0.281
commonSeqsBar	1.370	0.212	1.600
commonSeqsPlot	1.974	0.084	2.071
commonSeqsVenn	1.090	0.063	1.126
differentialAbundance	3.288	0.070	3.395
exportFasta	0.358	0.023	0.382
geneFreq	3.922	0.098	4.070
lorenzCurve	1.920	0.020	1.956
mergeFiles	0.111	0.003	0.116
pairwisePlot	0.993	0.007	1.006
phyloTree	7.121	0.032	7.230
productive	0.088	0.003	0.092
productiveSeq	24.460	1.282	26.153
readImmunoSeq	0.048	0.002	0.051
removeSeq	0.085	0.004	0.088
searchPublished	0.309	0.008	0.319
searchSeq	0.707	0.009	0.728
seqMatrix	4.518	0.159	4.817
similarityMatrix	0.301	0.004	0.306
similarityScore	0.278	0.008	0.287
topFreq	2.343	0.103	2.525
topSeqs	1.695	0.059	1.787
topSeqsPlot	0.645	0.005	0.654
uniqueSeqs	0.343	0.005	0.348