BioC 3.5: CHECK report for LymphoSeq on veracruz2

Package: LymphoSeq

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.4.1.tar.gz

StartedAt: 2017-10-18 05:28:50 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:32:30 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 219.7 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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.4.1’
* 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  8.9Mb
  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    44.949  1.431  47.611
productiveSeq 19.131  1.007  20.711
phyloTree      4.906  0.033   5.046
* 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-3.5-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	1.200	0.037	1.276
bhattacharyyaCoefficient	0.253	0.007	0.269
bhattacharyyaMatrix	0.245	0.006	0.253
chordDiagramVDJ	3.404	0.023	3.517
clonalRelatedness	1.130	0.109	0.313
clonality	0.386	0.109	0.134
cloneTrack	44.949	1.431	47.611
commonSeqs	0.216	0.005	0.225
commonSeqsBar	2.228	0.073	2.365
commonSeqsPlot	0.613	0.007	0.635
commonSeqsVenn	3.927	0.054	4.089
differentialAbundance	3.386	0.052	3.528
exportFasta	1.182	0.014	1.239
geneFreq	2.432	0.028	2.533
lorenzCurve	1.258	0.018	1.304
mergeFiles	0.095	0.003	0.100
pairwisePlot	2.009	0.019	2.102
phyloTree	4.906	0.033	5.046
productive	0.077	0.003	0.089
productiveSeq	19.131	1.007	20.711
readImmunoSeq	0.063	0.003	0.067
removeSeq	0.148	0.004	0.155
searchPublished	0.210	0.005	0.219
searchSeq	0.478	0.006	0.492
seqMatrix	2.456	0.080	2.598
similarityMatrix	1.461	0.078	1.573
similarityScore	0.207	0.004	0.218
topFreq	1.785	0.092	1.934
topSeqs	0.205	0.004	0.212
topSeqsPlot	0.652	0.007	0.683
uniqueSeqs	0.248	0.006	0.261