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BioC 3.6: CHECK report for chimeraviz on veracruz1

This page was generated on 2017-08-16 13:49:46 -0400 (Wed, 16 Aug 2017).

Package 206/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.2.2
Stian Lågstad
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chimeraviz
Last Changed Rev: 130079 / Revision: 131943
Last Changed Date: 2017-06-02 10:51:30 -0400 (Fri, 02 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chimeraviz
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_1.2.2.tar.gz
StartedAt: 2017-08-16 00:58:06 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:06:35 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 508.8 seconds
RetCode: 0
Status:  OK 
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chimeraviz.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.2’
* 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  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.2Mb
    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                            24.892  0.735  26.381
plotTranscripts                       13.921  0.460  14.847
plotFusionTranscript                  11.629  0.044  11.983
plotFusionTranscriptsGraph             8.777  0.042   9.095
plotFusionTranscriptWithProteinDomain  7.903  0.030   8.215
getTranscriptsEnsembldb                5.814  0.024   5.980
createFusionReport                     5.049  0.161   5.389
* 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
  ‘/Users/biocbuild/bbs-3.6-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
addFusionReadsAlignment0.8500.0320.913
createFusionReport5.0490.1615.389
decideTranscriptCategory0.4230.0030.441
downShift0.0680.0010.075
downstreamPartnerGene0.1180.0010.123
fetchReadsFromFastq0.0020.0000.001
fusionSpanningReadsCount0.0650.0020.068
fusionSplitReadsCount0.0540.0010.063
fusionToDataFrame0.0580.0010.059
getEnsemblIds0.7060.0130.748
getFusionByChromosome0.0520.0010.059
getFusionByGeneName0.0540.0010.056
getFusionById0.0590.0010.062
getTranscriptsEnsembldb5.8140.0245.980
importDefuse0.1600.0010.165
importEricscript0.1430.0010.143
importFusioncatcher0.1450.0010.152
importFusionmap0.1550.0000.159
importInfusion0.1230.0010.128
importJaffa0.1110.0010.111
importPrada0.1520.0010.154
importSoapfuse0.1290.0010.147
importStarfusion0.1700.0010.170
partnerGeneEnsemblId0.1020.0010.104
partnerGeneJunctionSequence0.0660.0010.069
plotCircle1.3660.0261.415
plotFusion24.892 0.73526.381
plotFusionReads1.1120.0761.248
plotFusionTranscript11.629 0.04411.983
plotFusionTranscriptWithProteinDomain7.9030.0308.215
plotFusionTranscriptsGraph8.7770.0429.095
plotTranscripts13.921 0.46014.847
selectTranscript4.1540.0084.284
splitOnUtrAndAddFeature0.3330.0020.353
upstreamPartnerGene0.0980.0010.099
writeFusionReference0.0580.0010.060