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) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:06 -0400 (Thu, 12 Apr 2018).
| Package 214/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chimeraviz 1.4.3 Stian Lågstad
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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
|
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
|
|
chimeraviz.Rcheck/examples_i386/chimeraviz-Ex.timings
|
chimeraviz.Rcheck/examples_x64/chimeraviz-Ex.timings
|