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CHECK report for chimeraviz on tokay1

This page was generated on 2018-04-12 13:29:06 -0400 (Thu, 12 Apr 2018).

Package 214/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.4.3
Stian Lågstad
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/chimeraviz
Branch: RELEASE_3_6
Last Commit: ffca582
Last Changed Date: 2018-03-10 19:22:02 -0400 (Sat, 10 Mar 2018)
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: 1.4.3
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_1.4.3.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_1.4.3.tar.gz
StartedAt: 2018-04-11 22:50:02 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:03:21 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 798.7 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_1.4.3.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_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chimeraviz.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.4.3'
* 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                            20.35   0.80   21.17
plotTranscripts                       10.94   0.45   11.40
plotFusionTranscript                   9.43   0.07    9.50
plotFusionTranscriptsGraph             6.33   0.05    6.39
plotFusionTranscriptWithProteinDomain  6.21   0.04    6.25
createFusionReport                     4.09   0.53    9.33
addFusionReadsAlignment                1.58   0.03   14.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
plotFusion                            25.72   0.74   26.45
plotTranscripts                       17.97   0.61   18.58
plotFusionTranscript                  14.68   0.07   14.80
plotFusionTranscriptsGraph            12.25   0.04   12.34
plotFusionTranscriptWithProteinDomain 10.02   0.03   10.05
selectTranscript                       6.17   0.00    6.17
createFusionReport                     5.47   0.69    6.72
getTranscriptsEnsembldb                5.31   0.00    5.31
* 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.



Installation output

chimeraviz.Rcheck/00install.out


install for i386

* installing *source* package 'chimeraviz' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'chimeraviz'
    finding HTML links ... done
    Fusion-class                            html  
    PartnerGene-class                       html  
    addFusionReadsAlignment                 html  
    chimeraviz-internals-fusionsToGeneLabelData
                                            html  
    chimeraviz-internals-fusionsToLinkData
                                            html  
    chimeraviz-internals-scaleListToInterval
                                            html  
    chimeraviz                              html  
    createFusionReport                      html  
    decideTranscriptCategory                html  
    downShift                               html  
    downstreamPartnerGene                   html  
    fetchReadsFromFastq                     html  
    fusionSpanningReadsCount                html  
    fusionSplitReadsCount                   html  
    fusionToDataFrame                       html  
    getEnsemblIds                           html  
    getFusionByChromosome                   html  
    getFusionByGeneName                     html  
    getFusionById                           html  
    getTranscriptsEnsembldb                 html  
    importDefuse                            html  
    importEricscript                        html  
    importFunctionNonUCSC                   html  
    importFusioncatcher                     html  
    importFusionmap                         html  
    importInfusion                          html  
    importJaffa                             html  
    importPrada                             html  
    importSoapfuse                          html  
    importStarfusion                        html  
    partnerGeneEnsemblId                    html  
    partnerGeneJunctionSequence             html  
    plotCircle                              html  
    plotFusion                              html  
    plotFusionReads                         html  
    plotFusionTranscript                    html  
    plotFusionTranscriptWithProteinDomain   html  
    plotFusionTranscriptsGraph              html  
    plotTranscripts                         html  
    raw_Homo_sapiens.GRCh37.74              html  
    raw_cytobandhg19                        html  
    raw_cytobandhg38                        html  
    raw_defuse                              html  
    raw_ericscript                          html  
    raw_fusion5267proteindomains            html  
    raw_fusion5267reads                     html  
    raw_fusion5267readsBedGraph             html  
    raw_fusioncatcher                       html  
    raw_fusionmap                           html  
    raw_infusion                            html  
    raw_jaffa                               html  
    raw_prada                               html  
    raw_soapfuse                            html  
    raw_starfusion                          html  
    selectTranscript                        html  
    show-Fusion-method                      html  
    show-PartnerGene-method                 html  
    splitOnUtrAndAddFeature                 html  
    upstreamPartnerGene                     html  
    writeFusionReference                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chimeraviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chimeraviz' as chimeraviz_1.4.3.zip
* DONE (chimeraviz)
In R CMD INSTALL
In R CMD INSTALL

Tests output

chimeraviz.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(chimeraviz)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

The following object is masked from 'package:Gviz':

    feature

The following object is masked from 'package:testthat':

    not


Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter


> 
> test_check("chimeraviz")
== testthat results  ===========================================================
OK: 142 SKIPPED: 2 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  77.84    3.17   83.65 

chimeraviz.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(chimeraviz)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

The following object is masked from 'package:Gviz':

    feature

The following object is masked from 'package:testthat':

    not


Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter


> 
> test_check("chimeraviz")
== testthat results  ===========================================================
OK: 142 SKIPPED: 2 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  88.20    2.48   91.98 

Example timings

chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings

nameusersystemelapsed
addFusionReadsAlignment 1.58 0.0314.62
createFusionReport4.090.539.33
decideTranscriptCategory0.370.060.44
downShift0.060.000.06
downstreamPartnerGene0.080.000.08
fetchReadsFromFastq000
fusionSpanningReadsCount0.030.000.03
fusionSplitReadsCount0.030.000.03
fusionToDataFrame0.030.000.03
getEnsemblIds0.520.040.56
getFusionByChromosome0.030.000.03
getFusionByGeneName0.030.000.03
getFusionById0.050.000.05
getTranscriptsEnsembldb4.010.044.05
importDefuse0.160.000.15
importEricscript0.120.000.13
importFusioncatcher0.140.000.14
importFusionmap0.130.000.12
importInfusion0.190.000.19
importJaffa0.170.000.17
importPrada0.170.000.17
importSoapfuse0.200.000.21
importStarfusion0.210.000.20
partnerGeneEnsemblId0.140.000.14
partnerGeneJunctionSequence0.070.000.08
plotCircle2.220.342.56
plotFusion20.35 0.8021.17
plotFusionReads0.710.070.78
plotFusionTranscript9.430.079.50
plotFusionTranscriptWithProteinDomain6.210.046.25
plotFusionTranscriptsGraph6.330.056.39
plotTranscripts10.94 0.4511.40
selectTranscript3.280.003.28
splitOnUtrAndAddFeature0.330.000.33
upstreamPartnerGene0.090.000.10
writeFusionReference0.050.000.04

chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings

nameusersystemelapsed
addFusionReadsAlignment2.970.033.02
createFusionReport5.470.696.72
decideTranscriptCategory0.720.010.74
downShift0.110.000.11
downstreamPartnerGene0.200.030.23
fetchReadsFromFastq000
fusionSpanningReadsCount0.080.000.08
fusionSplitReadsCount0.080.000.07
fusionToDataFrame0.090.000.10
getEnsemblIds0.70.00.7
getFusionByChromosome0.050.000.05
getFusionByGeneName0.060.000.06
getFusionById0.080.000.08
getTranscriptsEnsembldb5.310.005.31
importDefuse0.140.000.14
importEricscript0.130.000.13
importFusioncatcher0.190.000.18
importFusionmap0.200.000.21
importInfusion0.210.000.21
importJaffa0.220.000.22
importPrada0.140.000.14
importSoapfuse0.150.000.15
importStarfusion0.130.020.14
partnerGeneEnsemblId0.090.000.10
partnerGeneJunctionSequence0.060.020.07
plotCircle1.930.212.15
plotFusion25.72 0.7426.45
plotFusionReads1.270.121.39
plotFusionTranscript14.68 0.0714.80
plotFusionTranscriptWithProteinDomain10.02 0.0310.05
plotFusionTranscriptsGraph12.25 0.0412.34
plotTranscripts17.97 0.6118.58
selectTranscript6.170.006.17
splitOnUtrAndAddFeature0.340.000.35
upstreamPartnerGene0.110.000.11
writeFusionReference0.070.000.06