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 13:15:43 -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: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.4.3.tar.gz |
| StartedAt: 2018-04-11 22:08:06 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:15:25 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 438.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.4.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/chimeraviz.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 5.3Mb
sub-directories of 1Mb or more:
doc 2.6Mb
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 21.612 0.396 22.074
plotTranscripts 11.572 0.236 11.822
plotFusionTranscript 10.112 0.060 10.183
plotFusionTranscriptsGraph 7.848 0.016 7.870
plotFusionTranscriptWithProteinDomain 6.536 0.000 6.555
getTranscriptsEnsembldb 5.024 0.004 5.030
* 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
‘/home/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-pc-linux-gnu (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
86.048 1.824 88.585
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| addFusionReadsAlignment | 1.176 | 0.052 | 1.242 | |
| createFusionReport | 4.740 | 0.236 | 4.997 | |
| decideTranscriptCategory | 0.396 | 0.048 | 0.443 | |
| downShift | 0.064 | 0.008 | 0.072 | |
| downstreamPartnerGene | 0.084 | 0.008 | 0.093 | |
| fetchReadsFromFastq | 0 | 0 | 0 | |
| fusionSpanningReadsCount | 0.056 | 0.008 | 0.063 | |
| fusionSplitReadsCount | 0.032 | 0.008 | 0.040 | |
| fusionToDataFrame | 0.044 | 0.000 | 0.042 | |
| getEnsemblIds | 0.540 | 0.016 | 0.558 | |
| getFusionByChromosome | 0.040 | 0.000 | 0.041 | |
| getFusionByGeneName | 0.044 | 0.000 | 0.042 | |
| getFusionById | 0.044 | 0.000 | 0.045 | |
| getTranscriptsEnsembldb | 5.024 | 0.004 | 5.030 | |
| importDefuse | 0.112 | 0.000 | 0.112 | |
| importEricscript | 0.12 | 0.00 | 0.12 | |
| importFusioncatcher | 0.112 | 0.000 | 0.115 | |
| importFusionmap | 0.124 | 0.000 | 0.127 | |
| importInfusion | 0.108 | 0.000 | 0.108 | |
| importJaffa | 0.104 | 0.000 | 0.105 | |
| importPrada | 0.116 | 0.000 | 0.112 | |
| importSoapfuse | 0.108 | 0.000 | 0.109 | |
| importStarfusion | 0.124 | 0.000 | 0.125 | |
| partnerGeneEnsemblId | 0.076 | 0.004 | 0.081 | |
| partnerGeneJunctionSequence | 0.040 | 0.004 | 0.044 | |
| plotCircle | 1.812 | 0.048 | 1.863 | |
| plotFusion | 21.612 | 0.396 | 22.074 | |
| plotFusionReads | 0.772 | 0.024 | 0.800 | |
| plotFusionTranscript | 10.112 | 0.060 | 10.183 | |
| plotFusionTranscriptWithProteinDomain | 6.536 | 0.000 | 6.555 | |
| plotFusionTranscriptsGraph | 7.848 | 0.016 | 7.870 | |
| plotTranscripts | 11.572 | 0.236 | 11.822 | |
| selectTranscript | 3.316 | 0.004 | 3.323 | |
| splitOnUtrAndAddFeature | 0.256 | 0.000 | 0.260 | |
| upstreamPartnerGene | 0.080 | 0.000 | 0.081 | |
| writeFusionReference | 0.048 | 0.000 | 0.048 | |