BioC 3.5: CHECK report for LymphoSeq on malbec2

Package: LymphoSeq

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.4.0.tar.gz

StartedAt: 2017-08-16 00:14:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:18:11 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 213.8 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.4.0’
* 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  8.3Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    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    46.028  5.284  51.762
productiveSeq 13.744  4.064  17.836
phyloTree      5.056  0.008   5.077
* 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-3.5-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	1.176	0.052	1.280
bhattacharyyaCoefficient	0.212	0.008	0.220
bhattacharyyaMatrix	0.272	0.000	0.269
chordDiagramVDJ	3.096	0.004	3.129
clonalRelatedness	1.564	0.000	0.277
clonality	0.096	0.004	0.099
cloneTrack	46.028	5.284	51.762
commonSeqs	0.204	0.000	0.206
commonSeqsBar	2.024	0.040	2.063
commonSeqsPlot	0.508	0.000	0.509
commonSeqsVenn	2.720	0.012	2.737
differentialAbundance	3.788	0.008	3.797
exportFasta	0.284	0.000	0.284
geneFreq	2.092	0.008	2.179
lorenzCurve	2.016	0.004	2.022
mergeFiles	0.084	0.000	0.085
pairwisePlot	1.824	0.004	1.830
phyloTree	5.056	0.008	5.077
productive	0.064	0.000	0.066
productiveSeq	13.744	4.064	17.836
readImmunoSeq	0.052	0.000	0.051
removeSeq	0.108	0.004	0.115
searchPublished	0.268	0.004	0.274
searchSeq	0.676	0.004	0.680
seqMatrix	2.032	0.408	2.449
similarityMatrix	1.164	0.024	1.188
similarityScore	0.172	0.000	0.170
topFreq	1.148	0.376	1.525
topSeqs	0.168	0.000	0.169
topSeqsPlot	0.448	0.000	0.453
uniqueSeqs	0.228	0.004	0.233