Package: LymphoSeq

Version: 1.11.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings LymphoSeq_1.11.0.tar.gz

StartedAt: 2019-04-09 01:38:13 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:41:52 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 219.1 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings LymphoSeq_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.11.0’
* 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  5.7Mb
  sub-directories of 1Mb or more:
    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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
productiveSeq 33.240  1.008  34.263
cloneTrack    28.206  1.176  29.795
topFreq        6.131  0.128   6.324
phyloTree      5.947  0.000   5.947
* 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-3.9-bioc/meat/LymphoSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL LymphoSeq
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘LymphoSeq’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LymphoSeq)

name	user	system	elapsed
alignSeq	1.373	0.045	1.448
bhattacharyyaCoefficient	0.227	0.016	0.286
bhattacharyyaMatrix	0.702	0.020	0.723
chordDiagramVDJ	0.825	0.060	0.886
clonalRelatedness	1.436	0.020	0.342
clonality	0.051	0.004	0.055
cloneTrack	28.206	1.176	29.795
commonSeqs	0.167	0.012	0.179
commonSeqsBar	2.037	0.076	2.113
commonSeqsPlot	0.509	0.004	0.517
commonSeqsVenn	0.977	0.019	1.005
differentialAbundance	3.053	0.047	3.108
exportFasta	0.338	0.032	0.370
geneFreq	3.390	0.024	3.427
lorenzCurve	1.188	0.000	1.188
mergeFiles	0.101	0.000	0.100
pairwisePlot	0.751	0.004	0.755
phyloTree	5.947	0.000	5.947
productive	0.083	0.004	0.087
productiveSeq	33.240	1.008	34.263
readImmunoSeq	0.060	0.008	0.068
removeSeq	0.074	0.008	0.082
searchPublished	0.265	0.000	0.268
searchSeq	1.167	0.004	1.182
seqMatrix	4.268	0.107	4.379
similarityMatrix	0.251	0.012	0.263
similarityScore	0.255	0.008	0.263
topFreq	6.131	0.128	6.324
topSeqs	0.24	0.00	0.24
topSeqsPlot	0.494	0.000	0.494
uniqueSeqs	0.323	0.000	0.324