BioC 3.5: CHECK report for chimeraviz on oaxaca

Package: chimeraviz

Version: 0.99.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_0.99.4.tar.gz

StartedAt: 2017-03-04 00:20:55 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:29:33 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 517.8 seconds

RetCode: 0

Status:  OK

CheckDir: chimeraviz.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_0.99.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chimeraviz.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘0.99.4’
* 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’
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  5.8Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    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                 15.289  0.617  16.533
plotTranscripts             7.235  0.388   7.649
plotFusionTranscriptsGraph  6.784  0.020   6.813
plotFusionTranscript        6.251  0.036   6.305
getTranscriptsEnsembldb     6.040  0.013   6.057
createFusionReport          5.528  0.272  30.417
* 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	1.591	0.041	2.323
createFusionReport	5.528	0.272	30.417
decideTranscriptCategory	0.490	0.009	0.499
downstreamPartnerGene	0.101	0.001	0.103
fetchReadsFromFastq	0.001	0.000	0.001
fusionSpanningReadsCount	0.045	0.001	0.046
fusionSplitReadsCount	0.043	0.001	0.043
fusionToDataFrame	0.081	0.001	0.082
getEnsemblIds	0.794	0.021	0.815
getFusionByChromosome	0.048	0.000	0.049
getFusionByGeneName	0.055	0.000	0.056
getFusionById	0.056	0.000	0.057
getTranscriptsEnsembldb	6.040	0.013	6.057
importDefuse	0.171	0.001	0.172
importEricscript	0.111	0.001	0.112
importFusioncatcher	0.164	0.001	0.165
importFusionmap	0.161	0.001	0.162
importInfusion	0.180	0.000	0.181
importJaffa	0.163	0.000	0.163
importPrada	0.158	0.001	0.159
importSoapfuse	0.157	0.001	0.181
importStarfusion	0.148	0.001	0.149
partnerGeneEnsemblId	0.095	0.001	0.095
partnerGeneJunctionSequence	0.060	0.001	0.061
plotCircle	1.643	0.025	1.706
plotFusion	15.289	0.617	16.533
plotFusionReads	1.642	0.171	1.856
plotFusionTranscript	6.251	0.036	6.305
plotFusionTranscriptsGraph	6.784	0.020	6.813
plotTranscripts	7.235	0.388	7.649
selectTranscript	4.182	0.093	4.276
splitOnUtrAndAddFeature	0.251	0.002	0.253
upstreamPartnerGene	0.076	0.001	0.076
writeFusionReference	0.045	0.000	0.046