BioC 3.5: CHECK report for chimeraviz on malbec2

Package: chimeraviz

Version: 1.0.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.0.2.tar.gz

StartedAt: 2017-08-15 21:49:28 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:56:27 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 418.7 seconds

RetCode: 0

Status:  OK

CheckDir: chimeraviz.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/chimeraviz.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.2’
* 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  5.1Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    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                 14.892  1.692  16.606
plotTranscripts             7.532  1.040   8.589
plotFusionTranscriptsGraph  7.320  0.000   7.328
plotFusionTranscript        5.388  0.000   5.390
createFusionReport          5.048  0.256   5.469
* 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
  ‘/home/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	1.096	0.012	1.302
createFusionReport	5.048	0.256	5.469
decideTranscriptCategory	0.396	0.028	0.427
downstreamPartnerGene	0.080	0.008	0.089
fetchReadsFromFastq	0.000	0.000	0.001
fusionSpanningReadsCount	0.040	0.000	0.041
fusionSplitReadsCount	0.044	0.000	0.042
fusionToDataFrame	0.036	0.008	0.046
getEnsemblIds	0.680	0.020	0.703
getFusionByChromosome	0.064	0.004	0.069
getFusionByGeneName	0.072	0.000	0.071
getFusionById	0.108	0.000	0.108
getTranscriptsEnsembldb	4.316	0.016	4.334
importDefuse	0.108	0.000	0.110
importEricscript	0.108	0.000	0.111
importFusioncatcher	0.108	0.000	0.108
importFusionmap	0.128	0.000	0.127
importInfusion	0.148	0.000	0.148
importJaffa	0.164	0.000	0.166
importPrada	0.168	0.000	0.172
importSoapfuse	0.168	0.000	0.167
importStarfusion	0.144	0.000	0.143
partnerGeneEnsemblId	0.080	0.004	0.082
partnerGeneJunctionSequence	0.040	0.000	0.042
plotCircle	1.092	0.000	1.094
plotFusion	14.892	1.692	16.606
plotFusionReads	0.740	0.008	0.745
plotFusionTranscript	5.388	0.000	5.390
plotFusionTranscriptsGraph	7.320	0.000	7.328
plotTranscripts	7.532	1.040	8.589
selectTranscript	3.312	0.000	3.316
splitOnUtrAndAddFeature	0.276	0.000	0.277
upstreamPartnerGene	0.084	0.004	0.088
writeFusionReference	0.048	0.000	0.051