Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-16 12:03 -0400 (Sat, 16 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 552/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.31.0 (landing page) Arne Smits
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the DEP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEP.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: DEP |
Version: 1.31.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DEP_1.31.0.tar.gz |
StartedAt: 2025-08-15 21:47:20 -0400 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 21:55:34 -0400 (Fri, 15 Aug 2025) |
EllapsedTime: 494.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DEP.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DEP_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.31.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘DEP’ 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 ... 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'LFQ.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link(s) in Rd file 'TMT.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link(s) in Rd file 'impute.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link(s) in Rd file 'process.Rd': ‘[MSnbase:impute-methods]{impute}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... 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 impute 53.39 0.541 53.932 * 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 WARNING See ‘/home/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck/00check.log’ for details.
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘DEP’ ... ** this is package ‘DEP’ version ‘1.31.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (DEP)
DEP.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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(DEP) > > test_check("DEP") [ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ] [ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ] > > proc.time() user system elapsed 51.474 1.844 53.327
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 1.241 | 0.046 | 1.287 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.676 | 0.010 | 0.686 | |
analyze_dep | 2.720 | 0.102 | 2.822 | |
filter_missval | 0.396 | 0.005 | 0.401 | |
filter_proteins | 0.251 | 0.004 | 0.255 | |
get_df_long | 0.685 | 0.010 | 0.695 | |
get_df_wide | 0.669 | 0.050 | 0.719 | |
get_prefix | 0.002 | 0.000 | 0.001 | |
get_results | 0.846 | 0.005 | 0.852 | |
get_suffix | 0.001 | 0.000 | 0.001 | |
import_IsobarQuant | 0.000 | 0.000 | 0.001 | |
import_MaxQuant | 0.052 | 0.000 | 0.052 | |
impute | 53.390 | 0.541 | 53.932 | |
make_se | 0.033 | 0.003 | 0.036 | |
make_se_parse | 0.054 | 0.001 | 0.055 | |
make_unique | 0.016 | 0.000 | 0.016 | |
manual_impute | 0.608 | 0.019 | 0.627 | |
meanSdPlot | 0.521 | 0.030 | 0.552 | |
normalize_vsn | 0.299 | 0.000 | 0.299 | |
plot_all | 1.579 | 0.019 | 1.598 | |
plot_cond | 0.987 | 0.004 | 0.991 | |
plot_cond_freq | 0.839 | 0.011 | 0.850 | |
plot_cond_overlap | 0.787 | 0.002 | 0.789 | |
plot_cor | 1.127 | 0.003 | 1.130 | |
plot_coverage | 0.449 | 0.000 | 0.450 | |
plot_detect | 0.679 | 0.000 | 0.679 | |
plot_dist | 3.444 | 0.001 | 3.445 | |
plot_frequency | 0.388 | 0.000 | 0.388 | |
plot_gsea | 0.65 | 0.00 | 0.65 | |
plot_heatmap | 2.383 | 0.029 | 2.413 | |
plot_imputation | 0.948 | 0.000 | 0.948 | |
plot_missval | 1.423 | 0.019 | 1.441 | |
plot_normalization | 1.215 | 0.004 | 1.219 | |
plot_numbers | 0.536 | 0.000 | 0.536 | |
plot_p_hist | 1.148 | 0.000 | 1.149 | |
plot_pca | 1.155 | 0.001 | 1.156 | |
plot_single | 1.552 | 0.002 | 1.555 | |
plot_volcano | 4.010 | 0.023 | 4.034 | |
process | 1.327 | 0.016 | 1.343 | |
report | 0 | 0 | 0 | |
run_app | 0 | 0 | 0 | |
se2msn | 0.118 | 0.000 | 0.118 | |
test_diff | 0.797 | 0.016 | 0.813 | |
test_gsea | 0.648 | 0.000 | 0.647 | |
theme_DEP1 | 0.372 | 0.001 | 0.373 | |
theme_DEP2 | 0.448 | 0.000 | 0.448 | |