Package: LymphoSeq

Version: 1.8.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings LymphoSeq_1.8.0.tar.gz

StartedAt: 2018-10-16 01:34:13 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:36:57 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 164.1 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings LymphoSeq_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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
cloneTrack    24.880  1.036  26.375
productiveSeq 20.696  0.632  21.351
phyloTree      5.156  0.008   5.169
* 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-3.7-bioc/meat/LymphoSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL LymphoSeq
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘LymphoSeq’ ...
** 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
* DONE (LymphoSeq)

name	user	system	elapsed
alignSeq	0.852	0.036	0.951
bhattacharyyaCoefficient	0.472	0.032	0.529
bhattacharyyaMatrix	0.172	0.004	0.173
chordDiagramVDJ	0.620	0.048	0.669
clonalRelatedness	1.472	0.004	0.267
clonality	0.088	0.000	0.087
cloneTrack	24.880	1.036	26.375
commonSeqs	0.148	0.028	0.173
commonSeqsBar	1.772	0.020	1.795
commonSeqsPlot	0.396	0.008	0.401
commonSeqsVenn	0.732	0.020	0.751
differentialAbundance	2.744	0.048	2.794
exportFasta	0.224	0.000	0.223
geneFreq	1.664	0.008	1.670
lorenzCurve	1.248	0.004	1.253
mergeFiles	0.076	0.000	0.075
pairwisePlot	1.476	0.008	1.485
phyloTree	5.156	0.008	5.169
productive	0.060	0.000	0.061
productiveSeq	20.696	0.632	21.351
readImmunoSeq	0.052	0.000	0.053
removeSeq	0.064	0.000	0.062
searchPublished	0.160	0.004	0.166
searchSeq	0.872	0.008	0.883
seqMatrix	2.804	0.064	2.871
similarityMatrix	0.180	0.000	0.182
similarityScore	0.156	0.004	0.161
topFreq	3.740	0.044	3.791
topSeqs	0.156	0.000	0.158
topSeqsPlot	0.384	0.000	0.385
uniqueSeqs	0.208	0.000	0.210