Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the chimeraviz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chimeraviz.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 289/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chimeraviz 1.18.0 (landing page) Stian Lågstad
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: chimeraviz |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chimeraviz_1.18.0.tar.gz |
StartedAt: 2021-10-14 09:13:21 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:23:25 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 603.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chimeraviz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chimeraviz_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/chimeraviz.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.18.0’ * 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 ... 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 30.387 0.872 32.485 plot_transcripts 21.018 0.471 21.494 plot_fusion_transcript 18.046 0.036 18.083 plot_fusion_transcripts_graph 11.579 0.014 11.594 plot_fusion_transcript_with_protein_domain 10.315 0.016 10.332 get_transcripts_ensembl_db 8.176 0.195 8.372 select_transcript 6.468 0.000 6.468 * 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-3.13-bioc/meat/chimeraviz.Rcheck/00check.log’ for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things" 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 objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicRanges Loading required package: Gviz Loading required package: grid Attaching package: 'grid' The following object is masked from 'package:Biostrings': pattern 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 182.010 5.378 188.253
chimeraviz.Rcheck/chimeraviz-Ex.timings
name | user | system | elapsed | |
add_fusion_reads_alignment | 2.054 | 0.040 | 2.094 | |
create_fusion_report | 1.761 | 0.117 | 1.890 | |
decide_transcript_category | 0.194 | 0.004 | 0.199 | |
down_shift | 0.059 | 0.000 | 0.058 | |
downstream_partner_gene | 0.074 | 0.000 | 0.075 | |
fetch_reads_from_fastq | 0 | 0 | 0 | |
fusion_spanning_reads_count | 0.034 | 0.008 | 0.041 | |
fusion_split_reads_count | 0.037 | 0.003 | 0.042 | |
fusion_to_data_frame | 0.043 | 0.001 | 0.044 | |
get_ensembl_ids | 0.420 | 0.023 | 0.443 | |
get_fusion_by_chromosome | 0.042 | 0.000 | 0.043 | |
get_fusion_by_gene_name | 0.040 | 0.000 | 0.041 | |
get_fusion_by_id | 0.041 | 0.000 | 0.041 | |
get_transcripts_ensembl_db | 8.176 | 0.195 | 8.372 | |
import_aeron | 0.547 | 0.001 | 0.550 | |
import_chimpipe | 0.118 | 0.002 | 0.121 | |
import_defuse | 0.115 | 0.000 | 0.115 | |
import_ericscript | 0.119 | 0.000 | 0.119 | |
import_fusioncatcher | 0.112 | 0.000 | 0.112 | |
import_fusionmap | 0.144 | 0.004 | 0.148 | |
import_infusion | 0.108 | 0.000 | 0.107 | |
import_jaffa | 0.11 | 0.00 | 0.11 | |
import_oncofuse | 0.115 | 0.000 | 0.115 | |
import_prada | 0.108 | 0.004 | 0.112 | |
import_soapfuse | 0.153 | 0.000 | 0.154 | |
import_squid | 0.108 | 0.000 | 0.108 | |
import_starfusion | 0.117 | 0.000 | 0.117 | |
partner_gene_ensembl_id | 0.117 | 0.000 | 0.117 | |
partner_gene_junction_sequence | 0.046 | 0.000 | 0.045 | |
plot_circle | 0.584 | 0.032 | 0.616 | |
plot_fusion | 30.387 | 0.872 | 32.485 | |
plot_fusion_reads | 2.477 | 0.020 | 2.497 | |
plot_fusion_transcript | 18.046 | 0.036 | 18.083 | |
plot_fusion_transcript_with_protein_domain | 10.315 | 0.016 | 10.332 | |
plot_fusion_transcripts_graph | 11.579 | 0.014 | 11.594 | |
plot_transcripts | 21.018 | 0.471 | 21.494 | |
select_transcript | 6.468 | 0.000 | 6.468 | |
split_on_utr_and_add_feature | 0.444 | 0.004 | 0.448 | |
upstream_partner_gene | 0.08 | 0.00 | 0.08 | |
write_fusion_reference | 0.045 | 0.000 | 0.045 | |