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This page was generated on 2021-05-06 12:27:07 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the chimeraviz package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 281/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chimeraviz 1.16.1 (landing page) Stian Lågstad
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: chimeraviz |
Version: 1.16.1 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings chimeraviz_1.16.1.tar.gz |
StartedAt: 2021-05-05 23:57:03 -0400 (Wed, 05 May 2021) |
EndedAt: 2021-05-06 00:09:39 -0400 (Thu, 06 May 2021) |
EllapsedTime: 756.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chimeraviz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings chimeraviz_1.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/chimeraviz.Rcheck’ * using R version 4.0.5 (2021-03-31) * 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 ‘1.16.1’ * 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 (user + system) or elapsed time > 5s user system elapsed plot_fusion 36.552 0.704 38.861 plot_transcripts 24.156 0.312 24.509 plot_fusion_transcript 19.092 0.008 19.128 plot_fusion_transcript_with_protein_domain 12.096 0.004 12.121 plot_fusion_transcripts_graph 11.500 0.028 11.543 get_transcripts_ensembl_db 8.868 0.152 9.038 select_transcript 7.456 0.000 7.466 * 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-3.12-bioc/meat/chimeraviz.Rcheck/00check.log’ for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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.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") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 213.400 3.372 221.160
chimeraviz.Rcheck/chimeraviz-Ex.timings
name | user | system | elapsed | |
add_fusion_reads_alignment | 1.816 | 0.024 | 1.856 | |
create_fusion_report | 4.112 | 0.480 | 4.769 | |
decide_transcript_category | 0.248 | 0.012 | 0.293 | |
down_shift | 0.084 | 0.016 | 0.104 | |
downstream_partner_gene | 0.104 | 0.004 | 0.110 | |
fetch_reads_from_fastq | 0 | 0 | 0 | |
fusion_spanning_reads_count | 0.052 | 0.008 | 0.060 | |
fusion_split_reads_count | 0.056 | 0.000 | 0.057 | |
fusion_to_data_frame | 0.056 | 0.004 | 0.061 | |
get_ensembl_ids | 0.444 | 0.020 | 0.462 | |
get_fusion_by_chromosome | 0.036 | 0.000 | 0.037 | |
get_fusion_by_gene_name | 0.032 | 0.008 | 0.039 | |
get_fusion_by_id | 0.040 | 0.000 | 0.041 | |
get_transcripts_ensembl_db | 8.868 | 0.152 | 9.038 | |
import_aeron | 0.680 | 0.004 | 0.696 | |
import_chimpipe | 0.108 | 0.000 | 0.108 | |
import_defuse | 0.108 | 0.000 | 0.106 | |
import_ericscript | 0.128 | 0.000 | 0.130 | |
import_fusioncatcher | 0.100 | 0.000 | 0.102 | |
import_fusionmap | 0.148 | 0.000 | 0.165 | |
import_infusion | 0.164 | 0.000 | 0.172 | |
import_jaffa | 0.156 | 0.000 | 0.173 | |
import_oncofuse | 0.100 | 0.000 | 0.102 | |
import_prada | 0.104 | 0.000 | 0.106 | |
import_soapfuse | 0.112 | 0.000 | 0.112 | |
import_squid | 0.156 | 0.004 | 0.160 | |
import_starfusion | 0.168 | 0.000 | 0.168 | |
partner_gene_ensembl_id | 0.116 | 0.000 | 0.117 | |
partner_gene_junction_sequence | 0.072 | 0.000 | 0.070 | |
plot_circle | 0.740 | 0.020 | 0.761 | |
plot_fusion | 36.552 | 0.704 | 38.861 | |
plot_fusion_reads | 2.564 | 0.020 | 2.596 | |
plot_fusion_transcript | 19.092 | 0.008 | 19.128 | |
plot_fusion_transcript_with_protein_domain | 12.096 | 0.004 | 12.121 | |
plot_fusion_transcripts_graph | 11.500 | 0.028 | 11.543 | |
plot_transcripts | 24.156 | 0.312 | 24.509 | |
select_transcript | 7.456 | 0.000 | 7.466 | |
split_on_utr_and_add_feature | 0.424 | 0.004 | 0.425 | |
upstream_partner_gene | 0.108 | 0.000 | 0.107 | |
write_fusion_reference | 0.040 | 0.000 | 0.041 | |