Package: LymphoSeq

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2019-10-16 02:47:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:51:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 225.0 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_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 33.335  0.990  34.620
cloneTrack    30.192  1.211  31.750
phyloTree      6.281  0.000   6.283
topFreq        5.501  0.107   5.658
* 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	0.960	0.049	1.081
bhattacharyyaCoefficient	0.232	0.007	0.284
bhattacharyyaMatrix	0.267	0.016	0.283
chordDiagramVDJ	1.154	0.076	1.230
clonalRelatedness	1.415	0.001	0.265
clonality	0.059	0.004	0.063
cloneTrack	30.192	1.211	31.750
commonSeqs	0.229	0.016	0.245
commonSeqsBar	1.671	0.080	1.750
commonSeqsPlot	0.379	0.000	0.379
commonSeqsVenn	0.739	0.016	0.755
differentialAbundance	2.966	0.028	2.994
exportFasta	0.197	0.036	0.232
geneFreq	2.995	0.056	3.051
lorenzCurve	1.739	0.004	1.743
mergeFiles	0.077	0.000	0.077
pairwisePlot	0.659	0.000	0.659
phyloTree	6.281	0.000	6.283
productive	0.093	0.000	0.092
productiveSeq	33.335	0.990	34.620
readImmunoSeq	0.064	0.000	0.064
removeSeq	0.08	0.00	0.08
searchPublished	0.257	0.007	0.265
searchSeq	1.084	0.007	1.096
seqMatrix	4.110	0.091	4.216
similarityMatrix	0.240	0.004	0.246
similarityScore	0.208	0.000	0.212
topFreq	5.501	0.107	5.658
topSeqs	0.249	0.004	0.252
topSeqsPlot	0.519	0.000	0.519
uniqueSeqs	0.241	0.000	0.241