BioC 3.4: CHECK report for LymphoSeq on zin1

Package: LymphoSeq

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.1.2.tar.gz

StartedAt: 2016-09-20 08:42:48 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:44:30 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 101.7 seconds

RetCode: 0

Status:  OK

CheckDir: LymphoSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LymphoSeq_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/LymphoSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.2’
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... 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    41.900  0.832  42.970
productiveSeq 13.932  0.264  14.197
* 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: OK

* 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
bhattacharyyaCoefficient	0.192	0.008	0.201
bhattacharyyaMatrix	0.176	0.004	0.178
chordDiagramVDJ	1.196	0.008	1.205
clonality	0.044	0.000	0.044
cloneTrack	41.900	0.832	42.970
commonSeqs	0.148	0.000	0.148
commonSeqsPlot	0.376	0.000	0.375
commonSeqsVenn	4.208	0.008	4.221
geneFreq	1.924	0.028	1.961
lorenzCurve	1.824	0.008	1.832
mergeFiles	0.064	0.000	0.064
pairwisePlot	0.676	0.004	0.680
productive	0.044	0.000	0.043
productiveSeq	13.932	0.264	14.197
readImmunoSeq	0.024	0.004	0.027
removeSeq	0.044	0.000	0.044
searchPublished	0.160	0.000	0.162
searchSeq	0.676	0.004	0.683
seqMatrix	2.516	0.032	2.544
similarityMatrix	0.172	0.000	0.173
similarityScore	0.152	0.000	0.152
topFreq	1.132	0.032	1.166
topSeqs	0.160	0.008	0.166
topSeqsPlot	0.340	0.004	0.345
uniqueSeqs	1.096	0.004	1.103