Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 854/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggmsa 1.12.0 (landing page) Lang Zhou
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the ggmsa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggmsa.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: ggmsa |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggmsa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggmsa_1.12.0.tar.gz |
StartedAt: 2024-12-20 00:26:39 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:32:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 338.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggmsa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggmsa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggmsa_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ggmsa.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ggmsa/DESCRIPTION’ ... OK * this is package ‘ggmsa’ version ‘1.12.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * 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 ‘ggmsa’ 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘statebins’ 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 ... OK * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ggSeqBundle 5.604 0.595 6.196 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/ggmsa.Rcheck/00check.log’ for details.
ggmsa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ggmsa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ggmsa’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'seq_len' ** help *** installing help indices *** copying figures ** 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 (ggmsa)
ggmsa.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(ggmsa) ggmsa v1.12.0 Document: http://yulab-smu.top/ggmsa/ If you use ggmsa in published research, please cite: L Zhou, T Feng, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai*, G Yu* ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Briefings in Bioinformatics. DOI:10.1093/bib/bbac222 > > test_check("ggmsa") 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, saveRDS, 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 [ FAIL 0 | WARN 6 | SKIP 0 | PASS 16 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 4.329 0.401 4.718
ggmsa.Rcheck/ggmsa-Ex.timings
name | user | system | elapsed | |
available_colors | 0.001 | 0.000 | 0.001 | |
available_fonts | 0.002 | 0.000 | 0.002 | |
available_msa | 0.001 | 0.000 | 0.000 | |
facet_msa | 0.686 | 0.005 | 0.692 | |
geom_GC | 0.191 | 0.001 | 0.192 | |
geom_helix | 0.566 | 0.009 | 0.575 | |
geom_msa | 0.208 | 0.001 | 0.208 | |
geom_msaBar | 0.715 | 0.001 | 0.716 | |
geom_seed | 2.124 | 0.025 | 2.148 | |
geom_seqlogo | 0.588 | 0.009 | 0.596 | |
ggSeqBundle | 5.604 | 0.595 | 6.196 | |
gghelix | 0.733 | 0.007 | 0.741 | |
ggmsa | 1.105 | 0.023 | 1.129 | |
plot-methods | 0.344 | 0.003 | 0.347 | |
readSSfile | 0.018 | 0.000 | 0.018 | |
seqdiff | 0.011 | 0.001 | 0.012 | |
seqlogo | 0.376 | 0.014 | 0.389 | |
show-methods | 0.011 | 0.000 | 0.011 | |
simplot | 0.271 | 0.028 | 0.300 | |
tidy_msa | 0.025 | 0.004 | 0.029 | |