Package: LymphoSeq

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.6.0.tar.gz

StartedAt: 2018-04-12 05:41:49 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:45:52 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 243.1 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 --no-vignettes --timings LymphoSeq_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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  8.8Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
cloneTrack            49.205  1.441  51.682
productiveSeq         21.521  1.025  22.965
phyloTree              5.733  0.025   5.890
differentialAbundance  5.074  0.060   5.282
* 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-3.6-bioc/meat/LymphoSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘LymphoSeq’ ...
** R
** inst
** preparing 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	1.629	0.027	1.687
bhattacharyyaCoefficient	0.269	0.009	0.284
bhattacharyyaMatrix	0.263	0.010	0.274
chordDiagramVDJ	3.893	0.032	4.027
clonalRelatedness	0.934	0.027	0.363
clonality	0.221	0.033	0.143
cloneTrack	49.205	1.441	51.682
commonSeqs	0.239	0.010	0.260
commonSeqsBar	2.421	0.064	2.533
commonSeqsPlot	1.775	0.009	1.820
commonSeqsVenn	3.105	0.038	3.248
differentialAbundance	5.074	0.060	5.282
exportFasta	0.358	0.011	0.378
geneFreq	2.807	0.078	2.945
lorenzCurve	1.342	0.025	1.405
mergeFiles	0.114	0.005	0.119
pairwisePlot	2.417	0.029	2.533
phyloTree	5.733	0.025	5.890
productive	0.087	0.003	0.095
productiveSeq	21.521	1.025	22.965
readImmunoSeq	0.071	0.003	0.077
removeSeq	0.157	0.004	0.161
searchPublished	0.240	0.006	0.253
searchSeq	0.521	0.006	0.558
seqMatrix	2.757	0.087	2.908
similarityMatrix	0.255	0.006	0.266
similarityScore	1.227	0.083	1.350
topFreq	2.091	0.105	2.224
topSeqs	0.207	0.004	0.212
topSeqsPlot	0.484	0.004	0.495
uniqueSeqs	0.256	0.004	0.264