BioC 3.6: CHECK report for LymphoSeq on veracruz1

Package: LymphoSeq

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.5.0.tar.gz

StartedAt: 2017-08-16 04:59:52 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:03:44 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 231.5 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.0’
* 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  8.9Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    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    47.005  1.347  50.109
productiveSeq 19.634  0.888  21.111
* 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	1.196	0.033	1.275
bhattacharyyaCoefficient	0.256	0.009	0.265
bhattacharyyaMatrix	0.262	0.006	0.268
chordDiagramVDJ	3.143	0.013	3.235
clonalRelatedness	1.073	0.100	0.299
clonality	0.314	0.084	0.135
cloneTrack	47.005	1.347	50.109
commonSeqs	0.222	0.006	0.235
commonSeqsBar	2.474	0.068	2.634
commonSeqsPlot	0.623	0.005	0.643
commonSeqsVenn	3.108	0.037	3.231
differentialAbundance	4.633	0.032	4.819
exportFasta	0.338	0.010	0.359
geneFreq	2.581	0.027	2.714
lorenzCurve	4.137	0.016	4.293
mergeFiles	0.112	0.003	0.115
pairwisePlot	1.158	0.009	1.188
phyloTree	4.282	0.085	4.513
productive	0.080	0.003	0.084
productiveSeq	19.634	0.888	21.111
readImmunoSeq	0.065	0.002	0.075
removeSeq	0.110	0.002	0.112
searchPublished	0.224	0.006	0.233
searchSeq	0.510	0.004	0.524
seqMatrix	2.598	0.076	2.760
similarityMatrix	0.248	0.008	0.269
similarityScore	0.218	0.012	0.240
topFreq	3.092	0.119	3.322
topSeqs	0.218	0.002	0.224
topSeqsPlot	0.522	0.009	0.544
uniqueSeqs	0.269	0.003	0.279