BioC 3.5: CHECK report for LymphoSeq on malbec2

Package: LymphoSeq

Version: 1.4.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.4.1.tar.gz

StartedAt: 2017-10-18 00:25:44 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:29:12 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 208.1 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_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.4.1’
* 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    45.008  2.728  48.280
productiveSeq 12.756  6.104  18.882
phyloTree      5.068  0.004   5.209
* 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	1.576	0.052	1.652
bhattacharyyaCoefficient	0.212	0.000	0.212
bhattacharyyaMatrix	0.208	0.000	0.207
chordDiagramVDJ	2.796	0.016	2.833
clonalRelatedness	1.720	0.004	0.316
clonality	0.088	0.000	0.091
cloneTrack	45.008	2.728	48.280
commonSeqs	0.180	0.000	0.178
commonSeqsBar	2.296	0.012	2.310
commonSeqsPlot	0.544	0.000	0.541
commonSeqsVenn	2.420	0.016	2.475
differentialAbundance	3.804	0.004	3.811
exportFasta	0.268	0.000	0.270
geneFreq	2.148	0.020	2.267
lorenzCurve	1.888	0.012	1.901
mergeFiles	0.076	0.004	0.084
pairwisePlot	1.772	0.008	1.782
phyloTree	5.068	0.004	5.209
productive	0.076	0.000	0.074
productiveSeq	12.756	6.104	18.882
readImmunoSeq	0.052	0.000	0.053
removeSeq	0.124	0.000	0.126
searchPublished	0.176	0.000	0.175
searchSeq	0.660	0.004	0.665
seqMatrix	1.700	0.132	1.836
similarityMatrix	1.120	0.012	1.135
similarityScore	0.16	0.00	0.16
topFreq	1.060	0.016	1.079
topSeqs	0.176	0.000	0.175
topSeqsPlot	0.552	0.000	0.552
uniqueSeqs	0.216	0.000	0.214