Stian Lågstad
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/chimeraviz |
| Branch: master |
| Last Commit: 0899406 |
| Last Changed Date: 2019-12-09 13:44:29 -0500 (Mon, 09 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:46:47 -0500 (Thu, 16 Jan 2020).
| Package 269/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chimeraviz 1.13.0 Stian Lågstad
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: chimeraviz |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chimeraviz_1.13.0.tar.gz |
| StartedAt: 2020-01-16 02:44:03 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:00:31 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 987.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chimeraviz_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/chimeraviz.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.13.0’
* 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', 'data.table'
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 ... 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
* 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 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
plot_fusion_transcript_with_protein_domain: 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_transcripts 39.081 1.472 40.896
plot_fusion 38.309 0.494 40.044
plot_fusion_transcript 36.828 0.389 38.694
plot_fusion_transcript_with_protein_domain 21.314 0.424 19.953
plot_fusion_transcripts_graph 20.814 0.188 21.027
get_transcripts_ensembl_db 13.218 0.369 13.601
select_transcript 11.117 0.030 11.147
plot_fusion_reads 5.775 0.227 6.374
create_fusion_report 5.246 0.504 6.490
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘chimeraviz’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chimeraviz)
chimeraviz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
>
> test_check("chimeraviz")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 171 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
214.720 5.496 226.141
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 1.174 | 0.056 | 1.244 | |
| create_fusion_report | 5.246 | 0.504 | 6.490 | |
| decide_transcript_category | 0.414 | 0.007 | 0.424 | |
| down_shift | 0.113 | 0.000 | 0.114 | |
| downstream_partner_gene | 0.143 | 0.002 | 0.144 | |
| fetch_reads_from_fastq | 0.001 | 0.001 | 0.001 | |
| fusion_spanning_reads_count | 0.080 | 0.001 | 0.082 | |
| fusion_split_reads_count | 0.075 | 0.001 | 0.076 | |
| fusion_to_data_frame | 0.081 | 0.001 | 0.082 | |
| get_ensembl_ids | 0.784 | 0.037 | 0.843 | |
| get_fusion_by_chromosome | 0.097 | 0.011 | 0.109 | |
| get_fusion_by_gene_name | 0.095 | 0.016 | 0.111 | |
| get_fusion_by_id | 0.086 | 0.009 | 0.096 | |
| get_transcripts_ensembl_db | 13.218 | 0.369 | 13.601 | |
| import_defuse | 0.225 | 0.002 | 0.226 | |
| import_ericscript | 0.187 | 0.002 | 0.190 | |
| import_fusioncatcher | 0.197 | 0.001 | 0.200 | |
| import_fusionmap | 0.215 | 0.001 | 0.218 | |
| import_infusion | 0.220 | 0.001 | 0.222 | |
| import_jaffa | 0.213 | 0.002 | 0.215 | |
| import_oncofuse | 0.235 | 0.002 | 0.237 | |
| import_prada | 0.233 | 0.001 | 0.236 | |
| import_soapfuse | 0.208 | 0.001 | 0.209 | |
| import_starfusion | 0.231 | 0.001 | 0.232 | |
| partner_gene_ensembl_id | 0.135 | 0.001 | 0.136 | |
| partner_gene_junction_sequence | 0.07 | 0.00 | 0.07 | |
| plot_circle | 1.388 | 0.116 | 1.479 | |
| plot_fusion | 38.309 | 0.494 | 40.044 | |
| plot_fusion_reads | 5.775 | 0.227 | 6.374 | |
| plot_fusion_transcript | 36.828 | 0.389 | 38.694 | |
| plot_fusion_transcript_with_protein_domain | 21.314 | 0.424 | 19.953 | |
| plot_fusion_transcripts_graph | 20.814 | 0.188 | 21.027 | |
| plot_transcripts | 39.081 | 1.472 | 40.896 | |
| select_transcript | 11.117 | 0.030 | 11.147 | |
| split_on_utr_and_add_feature | 0.766 | 0.005 | 0.772 | |
| upstream_partner_gene | 0.139 | 0.001 | 0.141 | |
| write_fusion_reference | 0.089 | 0.001 | 0.090 | |