Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:05 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 558/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Arne Smits
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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: 1.31.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEP_1.31.2.tar.gz |
StartedAt: 2025-09-22 19:06:53 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 19:09:34 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 160.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEP_1.31.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.31.2’ * 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 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'LFQ.Rd': ‘[MSnbase:impute]{impute}’ Non-topic package-anchored link(s) in Rd file 'TMT.Rd': ‘[MSnbase:impute]{impute}’ Non-topic package-anchored link(s) in Rd file 'impute.Rd': ‘[MSnbase:impute]{impute}’ Non-topic package-anchored link(s) in Rd file 'process.Rd': ‘[MSnbase:impute]{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 5.214 0.052 5.439 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/DEP.Rcheck/00check.log’ for details.
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘DEP’ ... ** this is package ‘DEP’ version ‘1.31.2’ ** 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 Warning in fun(libname, pkgname) : Package 'DEP' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'DEP' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package keeps a record of temporary installation path * DONE (DEP)
DEP.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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(DEP) Warning message: In fun(libname, pkgname) : Package 'DEP' is deprecated and will be removed from Bioconductor version 3.23 > > test_check("DEP") [ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ] [ FAIL 0 | WARN 15 | SKIP 0 | PASS 333 ] > > proc.time() user system elapsed 20.458 0.933 21.881
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 0.456 | 0.010 | 0.478 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.618 | 0.004 | 0.670 | |
analyze_dep | 0.695 | 0.020 | 0.745 | |
filter_missval | 0.146 | 0.004 | 0.152 | |
filter_proteins | 0.096 | 0.003 | 0.099 | |
get_df_long | 0.235 | 0.007 | 0.250 | |
get_df_wide | 0.238 | 0.008 | 0.250 | |
get_prefix | 0.001 | 0.000 | 0.001 | |
get_results | 0.690 | 0.011 | 0.705 | |
get_suffix | 0 | 0 | 0 | |
import_IsobarQuant | 0 | 0 | 0 | |
import_MaxQuant | 0.016 | 0.001 | 0.017 | |
impute | 5.214 | 0.052 | 5.439 | |
make_se | 0.014 | 0.000 | 0.013 | |
make_se_parse | 0.019 | 0.001 | 0.020 | |
make_unique | 0.007 | 0.000 | 0.007 | |
manual_impute | 0.612 | 0.011 | 0.635 | |
meanSdPlot | 0.298 | 0.018 | 0.335 | |
normalize_vsn | 0.103 | 0.002 | 0.106 | |
plot_all | 0.533 | 0.012 | 0.551 | |
plot_cond | 0.353 | 0.006 | 0.375 | |
plot_cond_freq | 0.294 | 0.003 | 0.326 | |
plot_cond_overlap | 0.291 | 0.004 | 0.309 | |
plot_cor | 0.410 | 0.007 | 0.428 | |
plot_coverage | 0.173 | 0.001 | 0.177 | |
plot_detect | 0.295 | 0.002 | 0.317 | |
plot_dist | 1.128 | 0.007 | 1.165 | |
plot_frequency | 0.158 | 0.003 | 0.163 | |
plot_gsea | 0.209 | 0.005 | 0.216 | |
plot_heatmap | 0.770 | 0.018 | 0.809 | |
plot_imputation | 0.352 | 0.011 | 0.368 | |
plot_missval | 0.474 | 0.036 | 0.539 | |
plot_normalization | 0.460 | 0.019 | 0.480 | |
plot_numbers | 0.179 | 0.003 | 0.186 | |
plot_p_hist | 0.483 | 0.023 | 0.519 | |
plot_pca | 0.455 | 0.011 | 0.472 | |
plot_single | 0.615 | 0.008 | 0.639 | |
plot_volcano | 1.963 | 0.015 | 2.009 | |
process | 0.521 | 0.009 | 0.532 | |
report | 0 | 0 | 0 | |
run_app | 0 | 0 | 0 | |
se2msn | 0.037 | 0.001 | 0.037 | |
test_diff | 0.266 | 0.008 | 0.290 | |
test_gsea | 0.215 | 0.009 | 0.222 | |
theme_DEP1 | 0.155 | 0.002 | 0.160 | |
theme_DEP2 | 0.191 | 0.003 | 0.203 | |