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BioC 3.5: CHECK report for chimeraviz on malbec2

This page was generated on 2017-08-16 13:18:04 -0400 (Wed, 16 Aug 2017).

Package 204/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.0.2
Stian Lågstad
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/chimeraviz
Last Changed Rev: 130080 / Revision: 131943
Last Changed Date: 2017-06-02 10:51:57 -0400 (Fri, 02 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


chimeraviz.Rcheck/00install.out:

* 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)

chimeraviz.Rcheck/chimeraviz-Ex.timings:

nameusersystemelapsed
addFusionReadsAlignment1.0960.0121.302
createFusionReport5.0480.2565.469
decideTranscriptCategory0.3960.0280.427
downstreamPartnerGene0.0800.0080.089
fetchReadsFromFastq0.0000.0000.001
fusionSpanningReadsCount0.0400.0000.041
fusionSplitReadsCount0.0440.0000.042
fusionToDataFrame0.0360.0080.046
getEnsemblIds0.6800.0200.703
getFusionByChromosome0.0640.0040.069
getFusionByGeneName0.0720.0000.071
getFusionById0.1080.0000.108
getTranscriptsEnsembldb4.3160.0164.334
importDefuse0.1080.0000.110
importEricscript0.1080.0000.111
importFusioncatcher0.1080.0000.108
importFusionmap0.1280.0000.127
importInfusion0.1480.0000.148
importJaffa0.1640.0000.166
importPrada0.1680.0000.172
importSoapfuse0.1680.0000.167
importStarfusion0.1440.0000.143
partnerGeneEnsemblId0.0800.0040.082
partnerGeneJunctionSequence0.0400.0000.042
plotCircle1.0920.0001.094
plotFusion14.892 1.69216.606
plotFusionReads0.7400.0080.745
plotFusionTranscript5.3880.0005.390
plotFusionTranscriptsGraph7.3200.0007.328
plotTranscripts7.5321.0408.589
selectTranscript3.3120.0003.316
splitOnUtrAndAddFeature0.2760.0000.277
upstreamPartnerGene0.0840.0040.088
writeFusionReference0.0480.0000.051