Package: LymphoSeq

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.6.0.tar.gz

StartedAt: 2018-04-12 00:41:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:44:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 190.7 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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  8.2Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    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    45.720  0.752  46.753
productiveSeq 12.928  0.736  13.679
phyloTree      5.024  0.004   5.048
* 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
  ‘/home/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	1.184	0.020	1.269
bhattacharyyaCoefficient	0.204	0.004	0.208
bhattacharyyaMatrix	0.452	0.008	0.460
chordDiagramVDJ	2.928	0.000	2.938
clonalRelatedness	1.516	0.020	0.278
clonality	0.14	0.00	0.14
cloneTrack	45.720	0.752	46.753
commonSeqs	0.188	0.004	0.192
commonSeqsBar	1.948	0.020	1.968
commonSeqsPlot	1.324	0.004	1.330
commonSeqsVenn	2.412	0.020	2.516
differentialAbundance	3.724	0.028	3.754
exportFasta	0.272	0.000	0.274
geneFreq	2.216	0.012	2.328
lorenzCurve	1.1	0.0	1.1
mergeFiles	0.084	0.000	0.084
pairwisePlot	1.860	0.004	1.863
phyloTree	5.024	0.004	5.048
productive	0.064	0.000	0.065
productiveSeq	12.928	0.736	13.679
readImmunoSeq	0.052	0.000	0.051
removeSeq	0.12	0.00	0.12
searchPublished	0.172	0.004	0.175
searchSeq	0.660	0.004	0.663
seqMatrix	1.772	0.064	1.837
similarityMatrix	0.224	0.004	0.229
similarityScore	1.092	0.020	1.112
topFreq	1.144	0.068	1.211
topSeqs	0.168	0.000	0.166
topSeqsPlot	0.428	0.000	0.430
uniqueSeqs	0.216	0.000	0.216