Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-01 12:04 -0400 (Mon, 01 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 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 554/2320 | 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: 2025-08-31 20:20:47 -0400 (Sun, 31 Aug 2025) |
EndedAt: 2025-08-31 20:28:58 -0400 (Sun, 31 Aug 2025) |
EllapsedTime: 491.0 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 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 50.901 0.276 51.386 * 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-x86_64/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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 14 | SKIP 0 | PASS 333 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ] > > proc.time() user system elapsed 63.154 3.110 67.701
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 1.408 | 0.045 | 1.459 | |
TMT | 0.001 | 0.000 | 0.000 | |
add_rejections | 0.767 | 0.020 | 0.790 | |
analyze_dep | 3.032 | 0.052 | 3.098 | |
filter_missval | 0.445 | 0.006 | 0.453 | |
filter_proteins | 0.280 | 0.010 | 0.292 | |
get_df_long | 0.809 | 0.017 | 0.830 | |
get_df_wide | 0.784 | 0.012 | 0.802 | |
get_prefix | 0.002 | 0.000 | 0.003 | |
get_results | 1.008 | 0.015 | 1.029 | |
get_suffix | 0.002 | 0.001 | 0.002 | |
import_IsobarQuant | 0 | 0 | 0 | |
import_MaxQuant | 0.053 | 0.001 | 0.054 | |
impute | 50.901 | 0.276 | 51.386 | |
make_se | 0.048 | 0.001 | 0.049 | |
make_se_parse | 0.070 | 0.001 | 0.071 | |
make_unique | 0.020 | 0.001 | 0.021 | |
manual_impute | 0.703 | 0.032 | 0.739 | |
meanSdPlot | 0.781 | 0.038 | 0.825 | |
normalize_vsn | 0.341 | 0.006 | 0.348 | |
plot_all | 1.647 | 0.031 | 1.684 | |
plot_cond | 1.106 | 0.036 | 1.153 | |
plot_cond_freq | 0.954 | 0.016 | 0.974 | |
plot_cond_overlap | 0.944 | 0.014 | 0.960 | |
plot_cor | 1.296 | 0.026 | 1.327 | |
plot_coverage | 0.507 | 0.013 | 0.522 | |
plot_detect | 0.739 | 0.007 | 0.750 | |
plot_dist | 4.766 | 0.081 | 4.865 | |
plot_frequency | 0.425 | 0.004 | 0.430 | |
plot_gsea | 0.716 | 0.007 | 0.726 | |
plot_heatmap | 2.849 | 0.036 | 2.903 | |
plot_imputation | 1.078 | 0.015 | 1.101 | |
plot_missval | 1.684 | 0.071 | 1.764 | |
plot_normalization | 1.344 | 0.033 | 1.384 | |
plot_numbers | 0.487 | 0.004 | 0.493 | |
plot_p_hist | 1.231 | 0.014 | 1.250 | |
plot_pca | 1.370 | 0.021 | 1.402 | |
plot_single | 1.712 | 0.018 | 1.746 | |
plot_volcano | 4.082 | 0.038 | 4.137 | |
process | 1.514 | 0.019 | 1.540 | |
report | 0 | 0 | 0 | |
run_app | 0.000 | 0.001 | 0.001 | |
se2msn | 0.130 | 0.001 | 0.132 | |
test_diff | 0.970 | 0.016 | 0.991 | |
test_gsea | 0.772 | 0.016 | 0.794 | |
theme_DEP1 | 0.457 | 0.003 | 0.462 | |
theme_DEP2 | 0.459 | 0.003 | 0.465 | |