BioC 3.5: CHECK report for LymphoSeq on toluca2

Package: LymphoSeq

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.3.1.tar.gz

StartedAt: 2017-04-23 05:59:39 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 06:04:06 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 267.0 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LymphoSeq_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.3.1’
* 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            49.872  1.427  52.080
productiveSeq         21.951  1.005  23.636
phyloTree              6.977  0.022   7.140
differentialAbundance  5.686  0.070   5.943
* 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	1.911	0.040	2.003
bhattacharyyaCoefficient	0.326	0.015	0.346
bhattacharyyaMatrix	0.308	0.009	0.320
chordDiagramVDJ	4.112	0.037	4.156
clonalRelatedness	0.638	0.004	0.644
clonality	0.123	0.003	0.126
cloneTrack	49.872	1.427	52.080
commonSeqs	0.295	0.012	0.309
commonSeqsBar	2.816	0.076	2.922
commonSeqsPlot	0.804	0.005	0.834
commonSeqsVenn	3.437	0.045	3.518
differentialAbundance	5.686	0.070	5.943
exportFasta	0.428	0.010	0.453
geneFreq	3.009	0.027	3.112
lorenzCurve	2.659	0.023	2.728
mergeFiles	0.132	0.003	0.135
pairwisePlot	2.497	0.009	2.563
phyloTree	6.977	0.022	7.140
productive	0.096	0.002	0.098
productiveSeq	21.951	1.005	23.636
readImmunoSeq	0.072	0.003	0.075
removeSeq	0.183	0.004	0.187
searchPublished	0.250	0.004	0.255
searchSeq	1.043	0.006	1.091
seqMatrix	2.798	0.064	2.916
similarityMatrix	0.304	0.006	0.313
similarityScore	1.312	0.092	1.439
topFreq	2.092	0.099	2.232
topSeqs	0.264	0.003	0.272
topSeqsPlot	0.695	0.005	0.724
uniqueSeqs	0.328	0.003	0.344