Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4813 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 552/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.31.0 (landing page) Arne Smits
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
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: 2025-08-05 21:49:09 -0400 (Tue, 05 Aug 2025) |
EndedAt: 2025-08-05 21:57:26 -0400 (Tue, 05 Aug 2025) |
EllapsedTime: 497.4 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 24.04.2 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 52.762 0.532 53.296 * 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 50.623 1.984 52.616
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 1.214 | 0.047 | 1.260 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.665 | 0.010 | 0.675 | |
analyze_dep | 2.581 | 0.122 | 2.703 | |
filter_missval | 0.383 | 0.005 | 0.389 | |
filter_proteins | 0.245 | 0.009 | 0.255 | |
get_df_long | 0.674 | 0.010 | 0.684 | |
get_df_wide | 0.656 | 0.027 | 0.683 | |
get_prefix | 0.001 | 0.000 | 0.002 | |
get_results | 0.838 | 0.013 | 0.852 | |
get_suffix | 0.001 | 0.000 | 0.001 | |
import_IsobarQuant | 0.000 | 0.001 | 0.001 | |
import_MaxQuant | 0.051 | 0.000 | 0.052 | |
impute | 52.762 | 0.532 | 53.296 | |
make_se | 0.035 | 0.001 | 0.036 | |
make_se_parse | 0.053 | 0.002 | 0.055 | |
make_unique | 0.015 | 0.000 | 0.015 | |
manual_impute | 0.604 | 0.018 | 0.623 | |
meanSdPlot | 0.502 | 0.028 | 0.530 | |
normalize_vsn | 0.299 | 0.001 | 0.300 | |
plot_all | 1.569 | 0.023 | 1.592 | |
plot_cond | 0.978 | 0.004 | 0.983 | |
plot_cond_freq | 0.819 | 0.019 | 0.838 | |
plot_cond_overlap | 0.795 | 0.002 | 0.796 | |
plot_cor | 1.116 | 0.000 | 1.115 | |
plot_coverage | 0.444 | 0.002 | 0.446 | |
plot_detect | 0.657 | 0.001 | 0.659 | |
plot_dist | 3.361 | 0.000 | 3.362 | |
plot_frequency | 0.362 | 0.000 | 0.362 | |
plot_gsea | 0.63 | 0.00 | 0.63 | |
plot_heatmap | 2.328 | 0.036 | 2.364 | |
plot_imputation | 0.928 | 0.001 | 0.930 | |
plot_missval | 1.406 | 0.020 | 1.426 | |
plot_normalization | 1.223 | 0.005 | 1.228 | |
plot_numbers | 0.532 | 0.001 | 0.533 | |
plot_p_hist | 1.131 | 0.015 | 1.147 | |
plot_pca | 1.166 | 0.009 | 1.176 | |
plot_single | 1.575 | 0.013 | 1.589 | |
plot_volcano | 3.994 | 0.040 | 4.035 | |
process | 1.353 | 0.022 | 1.375 | |
report | 0 | 0 | 0 | |
run_app | 0.001 | 0.000 | 0.000 | |
se2msn | 0.112 | 0.000 | 0.112 | |
test_diff | 0.799 | 0.013 | 0.812 | |
test_gsea | 0.658 | 0.039 | 0.698 | |
theme_DEP1 | 0.376 | 0.008 | 0.384 | |
theme_DEP2 | 0.440 | 0.002 | 0.442 | |