BioC 3.5: CHECK report for LymphoSeq on veracruz2

Package: LymphoSeq

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.4.0.tar.gz

StartedAt: 2017-08-16 04:42:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:46:02 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 231.9 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.4.0’
* 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  8.9Mb
  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    46.383  1.304  48.980
productiveSeq 18.088  0.916  19.516
phyloTree      5.379  0.020   5.550
* 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	1.282	0.037	1.360
bhattacharyyaCoefficient	0.285	0.008	0.296
bhattacharyyaMatrix	0.286	0.007	0.301
chordDiagramVDJ	3.429	0.015	3.575
clonalRelatedness	0.978	0.047	0.316
clonality	0.314	0.086	0.134
cloneTrack	46.383	1.304	48.980
commonSeqs	0.256	0.009	0.272
commonSeqsBar	2.265	0.070	2.389
commonSeqsPlot	0.649	0.009	0.661
commonSeqsVenn	4.132	0.038	4.296
differentialAbundance	3.827	0.047	4.007
exportFasta	1.635	0.012	1.698
geneFreq	2.789	0.057	2.922
lorenzCurve	1.335	0.018	1.411
mergeFiles	0.113	0.005	0.122
pairwisePlot	2.309	0.018	2.400
phyloTree	5.379	0.020	5.550
productive	0.088	0.003	0.098
productiveSeq	18.088	0.916	19.516
readImmunoSeq	0.063	0.003	0.067
removeSeq	0.159	0.003	0.170
searchPublished	0.241	0.004	0.245
searchSeq	0.492	0.005	0.521
seqMatrix	2.461	0.081	2.582
similarityMatrix	1.295	0.089	1.423
similarityScore	0.223	0.003	0.237
topFreq	1.754	0.084	1.867
topSeqs	0.224	0.002	0.237
topSeqsPlot	0.607	0.004	0.633
uniqueSeqs	0.250	0.004	0.260