BioC 3.6: CHECK report for chimeraviz on malbec1

Package: chimeraviz

Version: 1.2.2

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.2.2.tar.gz

StartedAt: 2017-08-15 21:52:14 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:59:48 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 454.5 seconds

RetCode: 0

Status:  OK

CheckDir: chimeraviz.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.2.2’
* 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  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   2.3Mb
* 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 ... NOTE
plotFusionTranscriptWithProteinDomain: no visible binding for global
  variable 'protein_domain_location'
Undefined global functions or variables:
  protein_domain_location
* 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                            21.040  2.332  23.416
plotTranscripts                       11.328  1.308  12.648
plotFusionTranscript                  10.384  0.072  10.471
plotFusionTranscriptsGraph             7.016  0.012   7.034
plotFusionTranscriptWithProteinDomain  6.780  0.004   6.802
getTranscriptsEnsembldb                5.616  0.048   5.668
createFusionReport                     4.992  0.224   5.246
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-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	0.892	0.008	0.936
createFusionReport	4.992	0.224	5.246
decideTranscriptCategory	0.592	0.044	0.634
downShift	0.100	0.004	0.104
downstreamPartnerGene	0.152	0.004	0.158
fetchReadsFromFastq	0.004	0.000	0.001
fusionSpanningReadsCount	0.060	0.004	0.066
fusionSplitReadsCount	0.064	0.000	0.067
fusionToDataFrame	0.064	0.000	0.066
getEnsemblIds	0.796	0.008	0.807
getFusionByChromosome	0.068	0.000	0.070
getFusionByGeneName	0.068	0.004	0.073
getFusionById	0.076	0.000	0.074
getTranscriptsEnsembldb	5.616	0.048	5.668
importDefuse	0.100	0.000	0.104
importEricscript	0.108	0.000	0.109
importFusioncatcher	0.116	0.000	0.114
importFusionmap	0.12	0.00	0.12
importInfusion	0.116	0.000	0.116
importJaffa	0.108	0.000	0.110
importPrada	0.104	0.000	0.103
importSoapfuse	0.104	0.000	0.104
importStarfusion	0.124	0.000	0.127
partnerGeneEnsemblId	0.080	0.000	0.078
partnerGeneJunctionSequence	0.044	0.000	0.043
plotCircle	1.064	0.012	1.077
plotFusion	21.040	2.332	23.416
plotFusionReads	0.760	0.080	0.841
plotFusionTranscript	10.384	0.072	10.471
plotFusionTranscriptWithProteinDomain	6.780	0.004	6.802
plotFusionTranscriptsGraph	7.016	0.012	7.034
plotTranscripts	11.328	1.308	12.648
selectTranscript	3.460	0.000	3.461
splitOnUtrAndAddFeature	0.296	0.004	0.299
upstreamPartnerGene	0.080	0.000	0.081
writeFusionReference	0.044	0.000	0.047