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 13:44:05 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_1.4.3.tar.gz |
| StartedAt: 2018-04-12 01:30:09 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:38:44 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 514.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chimeraviz_1.4.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chimeraviz.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘chimeraviz’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
doc 4.0Mb
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 24.521 0.789 25.894
plotTranscripts 14.226 0.511 15.023
plotFusionTranscript 12.756 0.179 13.163
plotFusionTranscriptsGraph 8.890 0.048 9.147
plotFusionTranscriptWithProteinDomain 7.903 0.036 8.125
getTranscriptsEnsembldb 5.604 0.026 5.768
createFusionReport 5.197 0.175 5.505
* 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/tests/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-apple-darwin15.6.0 (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: 147 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
103.399 2.653 108.788
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| addFusionReadsAlignment | 1.552 | 0.057 | 1.653 | |
| createFusionReport | 5.197 | 0.175 | 5.505 | |
| decideTranscriptCategory | 0.579 | 0.029 | 0.619 | |
| downShift | 0.086 | 0.001 | 0.090 | |
| downstreamPartnerGene | 0.103 | 0.001 | 0.104 | |
| fetchReadsFromFastq | 0.001 | 0.000 | 0.001 | |
| fusionSpanningReadsCount | 0.056 | 0.001 | 0.057 | |
| fusionSplitReadsCount | 0.052 | 0.000 | 0.052 | |
| fusionToDataFrame | 0.056 | 0.001 | 0.056 | |
| getEnsemblIds | 0.722 | 0.014 | 0.741 | |
| getFusionByChromosome | 0.618 | 0.004 | 0.627 | |
| getFusionByGeneName | 0.056 | 0.001 | 0.056 | |
| getFusionById | 0.058 | 0.001 | 0.058 | |
| getTranscriptsEnsembldb | 5.604 | 0.026 | 5.768 | |
| importDefuse | 0.154 | 0.001 | 0.160 | |
| importEricscript | 0.144 | 0.000 | 0.149 | |
| importFusioncatcher | 0.144 | 0.001 | 0.150 | |
| importFusionmap | 0.151 | 0.002 | 0.156 | |
| importInfusion | 0.131 | 0.001 | 0.132 | |
| importJaffa | 0.132 | 0.001 | 0.132 | |
| importPrada | 0.130 | 0.000 | 0.134 | |
| importSoapfuse | 0.158 | 0.001 | 0.163 | |
| importStarfusion | 0.161 | 0.002 | 0.170 | |
| partnerGeneEnsemblId | 0.109 | 0.002 | 0.111 | |
| partnerGeneJunctionSequence | 0.065 | 0.001 | 0.069 | |
| plotCircle | 1.445 | 0.028 | 1.500 | |
| plotFusion | 24.521 | 0.789 | 25.894 | |
| plotFusionReads | 1.052 | 0.054 | 1.151 | |
| plotFusionTranscript | 12.756 | 0.179 | 13.163 | |
| plotFusionTranscriptWithProteinDomain | 7.903 | 0.036 | 8.125 | |
| plotFusionTranscriptsGraph | 8.890 | 0.048 | 9.147 | |
| plotTranscripts | 14.226 | 0.511 | 15.023 | |
| selectTranscript | 4.247 | 0.010 | 4.350 | |
| splitOnUtrAndAddFeature | 0.355 | 0.002 | 0.367 | |
| upstreamPartnerGene | 0.101 | 0.001 | 0.102 | |
| writeFusionReference | 0.056 | 0.001 | 0.057 | |