BioC 3.5: CHECK report for chimeraviz on toluca2

Package: chimeraviz

Version: 0.99.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_0.99.7.tar.gz

StartedAt: 2017-04-23 01:34:54 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:43:46 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 532.9 seconds

RetCode: 0

Status:  OK

CheckDir: chimeraviz.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chimeraviz.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 ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘0.99.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Gviz’ ‘S4Vectors’ ‘ensembldb’
  ‘AnnotationFilter’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘chimeraviz’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.0Mb
* 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
plotFusion                 18.303  0.733  19.274
plotFusionTranscriptsGraph 10.515  0.038  10.674
plotTranscripts             8.088  0.464   8.692
plotFusionTranscript        8.128  0.035   8.246
createFusionReport          6.756  0.181   7.017
getTranscriptsEnsembldb     6.393  0.036   6.484
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.

* installing *source* package ‘chimeraviz’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chimeraviz)

name	user	system	elapsed
addFusionReadsAlignment	1.103	0.023	1.137
createFusionReport	6.756	0.181	7.017
decideTranscriptCategory	0.528	0.015	0.547
downstreamPartnerGene	0.130	0.003	0.134
fetchReadsFromFastq	0.001	0.001	0.001
fusionSpanningReadsCount	0.059	0.000	0.060
fusionSplitReadsCount	0.060	0.001	0.061
fusionToDataFrame	0.061	0.001	0.062
getEnsemblIds	1.020	0.021	1.044
getFusionByChromosome	0.059	0.001	0.060
getFusionByGeneName	0.061	0.001	0.062
getFusionById	0.067	0.002	0.069
getTranscriptsEnsembldb	6.393	0.036	6.484
importDefuse	0.146	0.000	0.147
importEricscript	0.147	0.000	0.148
importFusioncatcher	0.162	0.000	0.163
importFusionmap	0.173	0.001	0.176
importInfusion	0.189	0.001	0.191
importJaffa	0.168	0.001	0.172
importPrada	0.162	0.001	0.166
importSoapfuse	0.163	0.001	0.166
importStarfusion	0.164	0.001	0.167
partnerGeneEnsemblId	0.130	0.002	0.132
partnerGeneJunctionSequence	0.060	0.001	0.061
plotCircle	1.680	0.024	1.718
plotFusion	18.303	0.733	19.274
plotFusionReads	1.965	0.229	2.250
plotFusionTranscript	8.128	0.035	8.246
plotFusionTranscriptsGraph	10.515	0.038	10.674
plotTranscripts	8.088	0.464	8.692
selectTranscript	4.650	0.009	4.706
splitOnUtrAndAddFeature	0.345	0.002	0.348
upstreamPartnerGene	0.104	0.001	0.105
writeFusionReference	0.068	0.001	0.069