BioC 3.5: CHECK report for chimeraviz on veracruz2

Package: chimeraviz

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_1.0.4.tar.gz

StartedAt: 2017-10-18 01:31:30 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:39:39 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 489.5 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_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chimeraviz.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.4’
* 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’
  ‘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  6.5Mb
  sub-directories of 1Mb or more:
    doc       4.1Mb
    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                 17.103  0.687  18.329
plotFusionTranscriptsGraph  9.069  0.059   9.401
plotTranscripts             7.663  0.420   8.323
plotFusionTranscript        7.864  0.196   8.329
createFusionReport          5.942  0.203   6.273
getTranscriptsEnsembldb     5.685  0.034   5.894
* 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	0.980	0.029	1.040
createFusionReport	5.942	0.203	6.273
decideTranscriptCategory	0.577	0.017	0.606
downstreamPartnerGene	0.109	0.002	0.111
fetchReadsFromFastq	0.001	0.000	0.002
fusionSpanningReadsCount	0.056	0.001	0.057
fusionSplitReadsCount	0.057	0.001	0.059
fusionToDataFrame	0.059	0.001	0.061
getEnsemblIds	0.664	0.017	0.702
getFusionByChromosome	0.061	0.002	0.066
getFusionByGeneName	0.059	0.002	0.066
getFusionById	0.108	0.005	0.115
getTranscriptsEnsembldb	5.685	0.034	5.894
importDefuse	0.153	0.002	0.158
importEricscript	0.156	0.002	0.162
importFusioncatcher	0.158	0.002	0.165
importFusionmap	0.188	0.002	0.195
importInfusion	0.158	0.001	0.163
importJaffa	0.162	0.002	0.165
importPrada	0.166	0.002	0.170
importSoapfuse	0.153	0.001	0.161
importStarfusion	0.173	0.001	0.178
partnerGeneEnsemblId	0.120	0.002	0.124
partnerGeneJunctionSequence	0.056	0.001	0.059
plotCircle	1.507	0.033	1.569
plotFusion	17.103	0.687	18.329
plotFusionReads	1.136	0.060	1.277
plotFusionTranscript	7.864	0.196	8.329
plotFusionTranscriptsGraph	9.069	0.059	9.401
plotTranscripts	7.663	0.420	8.323
selectTranscript	4.264	0.022	4.382
splitOnUtrAndAddFeature	0.400	0.004	0.416
upstreamPartnerGene	0.127	0.001	0.130
writeFusionReference	0.074	0.001	0.078