Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:31:08 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 533/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.27.0 (landing page) Arne Smits
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.27.0 |
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_1.27.0.tar.gz |
StartedAt: 2024-05-31 07:32:15 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 07:49:34 -0400 (Fri, 31 May 2024) |
EllapsedTime: 1038.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DEP.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DEP.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.27.0’ * 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 ‘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 ... WARNING Missing link or links in Rd file 'LFQ.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in Rd file 'TMT.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in Rd file 'impute.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links 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 121.830 0.681 134.309 plot_dist 9.861 0.162 11.145 plot_volcano 7.669 0.106 8.582 plot_heatmap 6.713 0.092 7.565 analyze_dep 4.965 0.169 5.507 * 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 WARNING See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘DEP’ ... ** 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 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) > > test_check("DEP") [ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ] > > proc.time() user system elapsed 125.945 5.977 153.169
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 3.981 | 0.139 | 4.482 | |
TMT | 0.000 | 0.000 | 0.001 | |
add_rejections | 1.819 | 0.052 | 1.995 | |
analyze_dep | 4.965 | 0.169 | 5.507 | |
filter_missval | 1.251 | 0.040 | 1.401 | |
filter_proteins | 0.752 | 0.022 | 0.838 | |
get_df_long | 2.811 | 0.063 | 3.125 | |
get_df_wide | 1.839 | 0.046 | 2.033 | |
get_prefix | 0.006 | 0.001 | 0.007 | |
get_results | 2.383 | 0.070 | 2.653 | |
get_suffix | 0.003 | 0.001 | 0.003 | |
import_IsobarQuant | 0.000 | 0.001 | 0.001 | |
import_MaxQuant | 0.135 | 0.006 | 0.179 | |
impute | 121.830 | 0.681 | 134.309 | |
make_se | 0.099 | 0.001 | 0.107 | |
make_se_parse | 0.155 | 0.011 | 0.180 | |
make_unique | 0.049 | 0.001 | 0.054 | |
manual_impute | 1.616 | 0.039 | 1.847 | |
meanSdPlot | 1.857 | 0.201 | 2.252 | |
normalize_vsn | 0.837 | 0.022 | 0.973 | |
plot_all | 3.947 | 0.103 | 4.398 | |
plot_cond | 2.515 | 0.058 | 2.751 | |
plot_cond_freq | 2.238 | 0.053 | 2.870 | |
plot_cond_overlap | 2.154 | 0.049 | 2.492 | |
plot_cor | 3.083 | 0.070 | 3.505 | |
plot_coverage | 1.205 | 0.035 | 1.388 | |
plot_detect | 1.874 | 0.040 | 2.137 | |
plot_dist | 9.861 | 0.162 | 11.145 | |
plot_frequency | 1.052 | 0.034 | 1.183 | |
plot_gsea | 1.713 | 0.045 | 1.918 | |
plot_heatmap | 6.713 | 0.092 | 7.565 | |
plot_imputation | 2.479 | 0.077 | 2.910 | |
plot_missval | 4.154 | 0.091 | 4.703 | |
plot_normalization | 3.229 | 0.090 | 3.675 | |
plot_numbers | 2.201 | 0.108 | 2.536 | |
plot_p_hist | 3.018 | 0.072 | 3.469 | |
plot_pca | 3.040 | 0.064 | 3.439 | |
plot_single | 3.847 | 0.061 | 4.285 | |
plot_volcano | 7.669 | 0.106 | 8.582 | |
process | 3.381 | 0.079 | 4.073 | |
report | 0.000 | 0.000 | 0.001 | |
run_app | 0.001 | 0.000 | 0.002 | |
se2msn | 0.308 | 0.010 | 0.356 | |
test_diff | 2.144 | 0.065 | 2.476 | |
test_gsea | 1.718 | 0.053 | 1.999 | |
theme_DEP1 | 1.032 | 0.033 | 1.198 | |
theme_DEP2 | 1.186 | 0.034 | 1.341 | |