Stian Lågstad
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/chimeraviz |
| Branch: RELEASE_3_10 |
| Last Commit: 18940b3 |
| Last Changed Date: 2020-03-02 07:41:55 -0400 (Mon, 02 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:12:08 -0400 (Wed, 15 Apr 2020).
| Package 269/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chimeraviz 1.12.3 Stian Lågstad
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: chimeraviz |
| Version: 1.12.3 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chimeraviz_1.12.3.tar.gz |
| StartedAt: 2020-04-15 04:23:37 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:35:17 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 699.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chimeraviz.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chimeraviz_1.12.3.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/chimeraviz.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.3’
* 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', '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 ... NOTE
Namespace in Imports field not imported from: 'magick'
All declared Imports should be used.
* 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 or elapsed time > 5s
user system elapsed
plot_fusion 36.464 0.700 44.045
plot_transcripts 22.936 0.372 25.663
plot_fusion_transcript 20.456 0.000 23.756
plot_fusion_transcript_with_protein_domain 17.812 0.016 18.121
plot_fusion_transcripts_graph 13.056 0.044 15.493
get_transcripts_ensembl_db 8.960 0.152 9.537
select_transcript 7.536 0.008 8.803
create_fusion_report 3.856 0.380 5.620
* 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-3.10-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
157.332 3.004 165.160
chimeraviz.Rcheck/chimeraviz-Ex.timings
| name | user | system | elapsed | |
| add_fusion_reads_alignment | 1.524 | 0.028 | 1.862 | |
| create_fusion_report | 3.856 | 0.380 | 5.620 | |
| decide_transcript_category | 0.236 | 0.012 | 0.381 | |
| down_shift | 0.088 | 0.004 | 0.089 | |
| downstream_partner_gene | 0.084 | 0.004 | 0.087 | |
| fetch_reads_from_fastq | 0 | 0 | 0 | |
| fusion_spanning_reads_count | 0.036 | 0.008 | 0.042 | |
| fusion_split_reads_count | 0.036 | 0.008 | 0.043 | |
| fusion_to_data_frame | 0.040 | 0.004 | 0.044 | |
| get_ensembl_ids | 0.512 | 0.016 | 0.721 | |
| get_fusion_by_chromosome | 0.124 | 0.000 | 0.145 | |
| get_fusion_by_gene_name | 0.052 | 0.000 | 0.054 | |
| get_fusion_by_id | 0.048 | 0.004 | 0.054 | |
| get_transcripts_ensembl_db | 8.960 | 0.152 | 9.537 | |
| import_defuse | 0.144 | 0.000 | 0.142 | |
| import_ericscript | 0.188 | 0.000 | 0.332 | |
| import_fusioncatcher | 0.120 | 0.004 | 0.191 | |
| import_fusionmap | 0.148 | 0.000 | 0.202 | |
| import_infusion | 0.140 | 0.000 | 0.224 | |
| import_jaffa | 0.140 | 0.000 | 0.256 | |
| import_oncofuse | 0.120 | 0.000 | 0.135 | |
| import_prada | 0.132 | 0.000 | 0.272 | |
| import_soapfuse | 0.136 | 0.000 | 0.133 | |
| import_starfusion | 0.128 | 0.000 | 0.132 | |
| partner_gene_ensembl_id | 0.096 | 0.000 | 0.094 | |
| partner_gene_junction_sequence | 0.056 | 0.000 | 0.054 | |
| plot_circle | 1.072 | 0.016 | 1.136 | |
| plot_fusion | 36.464 | 0.700 | 44.045 | |
| plot_fusion_reads | 2.484 | 0.032 | 2.876 | |
| plot_fusion_transcript | 20.456 | 0.000 | 23.756 | |
| plot_fusion_transcript_with_protein_domain | 17.812 | 0.016 | 18.121 | |
| plot_fusion_transcripts_graph | 13.056 | 0.044 | 15.493 | |
| plot_transcripts | 22.936 | 0.372 | 25.663 | |
| select_transcript | 7.536 | 0.008 | 8.803 | |
| split_on_utr_and_add_feature | 0.440 | 0.000 | 0.439 | |
| upstream_partner_gene | 0.076 | 0.000 | 0.078 | |
| write_fusion_reference | 0.048 | 0.000 | 0.049 | |