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BioC 3.6: CHECK report for chimeraviz on tokay1

This page was generated on 2017-08-16 13:37:15 -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: rm -rf chimeraviz.buildbin-libdir chimeraviz.Rcheck && mkdir chimeraviz.buildbin-libdir chimeraviz.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimeraviz.buildbin-libdir chimeraviz_1.2.2.tar.gz >chimeraviz.Rcheck\00install.out 2>&1 && cp chimeraviz.Rcheck\00install.out chimeraviz-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chimeraviz.buildbin-libdir --install="check:chimeraviz-install.out" --force-multiarch --no-vignettes --timings chimeraviz_1.2.2.tar.gz
StartedAt: 2017-08-15 22:18:58 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:32:07 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 788.2 seconds
RetCode: 0
Status:  OK  
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chimeraviz.buildbin-libdir chimeraviz.Rcheck && mkdir chimeraviz.buildbin-libdir chimeraviz.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimeraviz.buildbin-libdir chimeraviz_1.2.2.tar.gz >chimeraviz.Rcheck\00install.out 2>&1 && cp chimeraviz.Rcheck\00install.out chimeraviz-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chimeraviz.buildbin-libdir --install="check:chimeraviz-install.out" --force-multiarch --no-vignettes --timings chimeraviz_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimeraviz.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'chimeraviz' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
plotFusion                            18.24   0.78   23.01
plotTranscripts                       10.98   0.60   11.58
plotFusionTranscript                   9.47   0.26    9.73
plotFusionTranscriptsGraph             7.83   0.03    7.86
plotFusionTranscriptWithProteinDomain  6.89   0.08    6.97
createFusionReport                     4.20   0.68    6.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
plotFusion                            23.17   0.66   23.83
plotTranscripts                       16.79   0.66   17.48
plotFusionTranscript                  10.70   0.05   10.75
plotFusionTranscriptsGraph             8.44   0.03    8.47
plotFusionTranscriptWithProteinDomain  7.39   0.08    7.47
getTranscriptsEnsembldb                5.23   0.00    5.24
createFusionReport                     4.63   0.55    5.66
selectTranscript                       5.02   0.12    5.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimeraviz.Rcheck/00check.log'
for details.


chimeraviz.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'chimeraviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chimeraviz' as chimeraviz_1.2.2.zip
* DONE (chimeraviz)

chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings:

nameusersystemelapsed
addFusionReadsAlignment0.860.012.42
createFusionReport4.200.686.34
decideTranscriptCategory0.390.000.39
downShift0.070.000.06
downstreamPartnerGene0.120.000.12
fetchReadsFromFastq000
fusionSpanningReadsCount0.030.000.04
fusionSplitReadsCount0.050.000.04
fusionToDataFrame0.050.000.05
getEnsemblIds0.580.000.58
getFusionByChromosome0.030.000.03
getFusionByGeneName0.030.000.04
getFusionById0.050.000.04
getTranscriptsEnsembldb4.060.004.06
importDefuse0.110.000.11
importEricscript0.130.000.13
importFusioncatcher0.110.000.11
importFusionmap0.090.000.09
importInfusion0.130.000.13
importJaffa0.090.000.09
importPrada0.090.000.09
importSoapfuse0.090.000.09
importStarfusion0.10.00.1
partnerGeneEnsemblId0.070.010.09
partnerGeneJunctionSequence0.040.000.03
plotCircle0.930.284.74
plotFusion18.24 0.7823.01
plotFusionReads0.680.070.75
plotFusionTranscript9.470.269.73
plotFusionTranscriptWithProteinDomain6.890.086.97
plotFusionTranscriptsGraph7.830.037.86
plotTranscripts10.98 0.6011.58
selectTranscript3.170.003.18
splitOnUtrAndAddFeature0.340.000.34
upstreamPartnerGene0.100.000.09
writeFusionReference0.030.010.05

chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings:

nameusersystemelapsed
addFusionReadsAlignment0.870.010.89
createFusionReport4.630.555.66
decideTranscriptCategory0.50.00.5
downShift0.110.000.11
downstreamPartnerGene0.10.00.1
fetchReadsFromFastq000
fusionSpanningReadsCount0.050.000.05
fusionSplitReadsCount0.040.000.04
fusionToDataFrame0.070.000.07
getEnsemblIds0.550.020.57
getFusionByChromosome0.030.010.04
getFusionByGeneName0.050.000.05
getFusionById0.060.000.06
getTranscriptsEnsembldb5.230.005.24
importDefuse0.150.000.14
importEricscript0.140.000.14
importFusioncatcher0.120.000.12
importFusionmap0.130.000.13
importInfusion0.120.000.12
importJaffa0.160.000.16
importPrada0.150.000.15
importSoapfuse0.140.000.15
importStarfusion0.140.000.14
partnerGeneEnsemblId0.100.000.09
partnerGeneJunctionSequence0.080.000.08
plotCircle1.090.171.26
plotFusion23.17 0.6623.83
plotFusionReads0.830.090.92
plotFusionTranscript10.70 0.0510.75
plotFusionTranscriptWithProteinDomain7.390.087.47
plotFusionTranscriptsGraph8.440.038.47
plotTranscripts16.79 0.6617.48
selectTranscript5.020.125.14
splitOnUtrAndAddFeature0.340.000.35
upstreamPartnerGene0.110.000.10
writeFusionReference0.080.000.08