Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 332/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chimeraviz 1.30.0 (landing page) Stian Lågstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the chimeraviz package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: chimeraviz |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chimeraviz_1.30.0.tar.gz |
StartedAt: 2024-06-09 19:22:08 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 19:33:16 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 667.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chimeraviz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chimeraviz_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/chimeraviz.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chimeraviz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chimeraviz’ version ‘1.30.0’ * 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 code 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 30.328 0.860 32.354 plot_transcripts 18.763 0.486 19.342 plot_fusion_transcript 15.131 0.102 15.277 plot_fusion_transcript_with_protein_domain 9.857 0.044 9.918 plot_fusion_transcripts_graph 9.795 0.100 9.913 get_transcripts_ensembl_db 6.306 0.133 6.454 select_transcript 6.151 0.020 6.218 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/chimeraviz.Rcheck/00check.log’ for details.
chimeraviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chimeraviz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 Attaching package: 'BiocGenerics' 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, aperm, 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, 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:utils': findMatches 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") 2024-06-09 19:30:15.261 R[42062:29570870] XType: com.apple.fonts is not accessible. 2024-06-09 19:30:15.261 R[42062:29570870] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 185.324 4.141 192.423
chimeraviz.Rcheck/chimeraviz-Ex.timings
name | user | system | elapsed | |
add_fusion_reads_alignment | 1.986 | 0.027 | 2.018 | |
create_fusion_report | 1.776 | 0.170 | 2.216 | |
decide_transcript_category | 0.183 | 0.010 | 0.193 | |
down_shift | 0.166 | 0.012 | 0.178 | |
downstream_partner_gene | 0.062 | 0.002 | 0.064 | |
fetch_reads_from_fastq | 0.001 | 0.000 | 0.000 | |
fusion_spanning_reads_count | 0.029 | 0.000 | 0.030 | |
fusion_split_reads_count | 0.041 | 0.001 | 0.043 | |
fusion_to_data_frame | 0.040 | 0.000 | 0.041 | |
get_ensembl_ids | 0.752 | 0.041 | 0.800 | |
get_fusion_by_chromosome | 0.031 | 0.002 | 0.033 | |
get_fusion_by_gene_name | 0.033 | 0.002 | 0.035 | |
get_fusion_by_id | 0.032 | 0.001 | 0.033 | |
get_transcripts_ensembl_db | 6.306 | 0.133 | 6.454 | |
import_aeron | 0.408 | 0.005 | 0.414 | |
import_chimpipe | 0.109 | 0.001 | 0.111 | |
import_defuse | 0.114 | 0.001 | 0.117 | |
import_ericscript | 0.100 | 0.001 | 0.102 | |
import_fusioncatcher | 0.115 | 0.002 | 0.118 | |
import_fusionmap | 0.105 | 0.002 | 0.107 | |
import_infusion | 0.156 | 0.003 | 0.159 | |
import_jaffa | 0.096 | 0.002 | 0.097 | |
import_oncofuse | 0.080 | 0.001 | 0.082 | |
import_prada | 0.108 | 0.002 | 0.110 | |
import_soapfuse | 0.072 | 0.001 | 0.073 | |
import_squid | 0.112 | 0.001 | 0.113 | |
import_starfusion | 0.102 | 0.001 | 0.104 | |
partner_gene_ensembl_id | 0.078 | 0.002 | 0.079 | |
partner_gene_junction_sequence | 0.045 | 0.002 | 0.047 | |
plot_circle | 1.896 | 0.068 | 1.977 | |
plot_fusion | 30.328 | 0.860 | 32.354 | |
plot_fusion_reads | 2.106 | 0.035 | 2.145 | |
plot_fusion_transcript | 15.131 | 0.102 | 15.277 | |
plot_fusion_transcript_with_protein_domain | 9.857 | 0.044 | 9.918 | |
plot_fusion_transcripts_graph | 9.795 | 0.100 | 9.913 | |
plot_transcripts | 18.763 | 0.486 | 19.342 | |
select_transcript | 6.151 | 0.020 | 6.218 | |
split_on_utr_and_add_feature | 0.420 | 0.005 | 0.428 | |
upstream_partner_gene | 0.065 | 0.002 | 0.067 | |
write_fusion_reference | 0.077 | 0.002 | 0.078 | |