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 03:08:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:14:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 353.8 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) (2019-03-18 r76245)
* 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
productiveSeq 62.356  2.819  65.655
cloneTrack    48.783  3.929  52.681
topFreq       11.514  0.325  12.345
phyloTree     10.383  0.105  10.491
seqMatrix      8.637  0.301   9.199
geneFreq       6.498  0.182   6.675
commonSeqsBar  5.871  0.375   6.246
* 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	1.420	0.037	1.489
bhattacharyyaCoefficient	0.280	0.026	0.333
bhattacharyyaMatrix	0.575	0.025	0.599
chordDiagramVDJ	1.471	0.223	1.695
clonalRelatedness	1.212	0.202	0.250
clonality	0.534	0.520	0.131
cloneTrack	48.783	3.929	52.681
commonSeqs	0.286	0.053	0.340
commonSeqsBar	5.871	0.375	6.246
commonSeqsPlot	0.737	0.022	0.760
commonSeqsVenn	1.285	0.177	1.384
differentialAbundance	3.194	0.214	3.407
exportFasta	0.431	0.050	0.481
geneFreq	6.498	0.182	6.675
lorenzCurve	2.046	0.049	2.096
mergeFiles	0.119	0.007	0.125
pairwisePlot	1.249	0.025	1.275
phyloTree	10.383	0.105	10.491
productive	0.098	0.006	0.103
productiveSeq	62.356	2.819	65.655
readImmunoSeq	0.079	0.006	0.085
removeSeq	0.099	0.006	0.105
searchPublished	0.347	0.016	0.375
searchSeq	0.696	0.013	0.789
seqMatrix	8.637	0.301	9.199
similarityMatrix	0.342	0.015	0.360
similarityScore	0.323	0.013	0.336
topFreq	11.514	0.325	12.345
topSeqs	0.246	0.007	0.254
topSeqsPlot	0.720	0.009	0.740
uniqueSeqs	0.410	0.027	0.518