Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 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" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 518/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dearseq 1.16.0 (landing page) Boris P. Hejblum
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the dearseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dearseq.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: dearseq |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:dearseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings dearseq_1.16.0.tar.gz |
StartedAt: 2024-06-23 22:22:12 -0400 (Sun, 23 Jun 2024) |
EndedAt: 2024-06-23 22:23:47 -0400 (Sun, 23 Jun 2024) |
EllapsedTime: 95.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: dearseq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:dearseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings dearseq_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/dearseq.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘dearseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dearseq’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 ‘dearseq’ 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 dependencies in R code ... OK * 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 ... NOTE checkRd: (-1) plot.dearseq.Rd:12: Lost braces; missing escapes or markup? 12 | \item{signif_threshold}{a value between \code{0} and {1} specifying the | ^ checkRd: (-1) plot_ord_pvals.Rd:13: Lost braces; missing escapes or markup? 13 | \item{signif_threshold}{a value between \code{0} and {1} specifying the | ^ checkRd: (-1) summary.dearseq.Rd:15: Lost braces; missing escapes or markup? 15 | \item{signif_threshold}{a value between \code{0} and {1} specifying the | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘dearseqUserguide.Rmd’ using rmarkdown trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107991/suppl//GSE107991_edgeR_normalized_Berry_London.xlsx?tool=geoquery' Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 9111773 bytes (8.7 MB) ================================================== downloaded 8.7 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107991/suppl//GSE107991_Raw_counts_Berry_London.xlsx?tool=geoquery' Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 14380825 bytes (13.7 MB) === downloaded 912 KB Quitting from lines 186-212 [London_raw] (dearseqUserguide.Rmd) Error: processing vignette 'dearseqUserguide.Rmd' failed with diagnostics: Failed to download /home/biocbuild/bbs-3.19-bioc/meat/dearseq.Rcheck/vign_test/dearseq/vignettes/GSE107991/GSE107991_Raw_counts_Berry_London.xlsx! --- failed re-building ‘dearseqUserguide.Rmd’ SUMMARY: processing the following file failed: ‘dearseqUserguide.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/dearseq.Rcheck/00check.log’ for details.
dearseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL dearseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘dearseq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (dearseq)
dearseq.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-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(dearseq) > > test_check("dearseq") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] > > proc.time() user system elapsed 3.132 0.220 3.342
dearseq.Rcheck/dearseq-Ex.timings
name | user | system | elapsed | |
PBT_gmt | 0.004 | 0.004 | 0.009 | |
baduel_5gs | 0.001 | 0.000 | 0.001 | |
dear_seq | 0.572 | 0.019 | 0.592 | |
dgsa_seq | 0.144 | 0.008 | 0.153 | |
permPvals | 0.001 | 0.000 | 0.001 | |
plot_hist_pvals | 0.314 | 0.004 | 0.318 | |
plot_ord_pvals | 0.498 | 0.031 | 0.529 | |
plot_weights | 0.023 | 0.000 | 0.023 | |
sp_weights | 0.067 | 0.019 | 0.087 | |
spaghettiPlot1GS | 1.065 | 0.004 | 1.069 | |
vc_score | 0.003 | 0.000 | 0.002 | |
vc_score_h | 0.031 | 0.000 | 0.031 | |
vc_score_h_perm | 0.085 | 0.004 | 0.089 | |
vc_score_perm | 0.235 | 0.000 | 0.235 | |
vc_test_asym | 0.052 | 0.000 | 0.053 | |
vc_test_perm | 0.019 | 0.000 | 0.020 | |
voom_weights | 1.192 | 0.076 | 1.268 | |