Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:06 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 541/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.25.0 (landing page) Arne Smits
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.25.0 |
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_1.25.0.tar.gz |
StartedAt: 2024-03-02 02:53:55 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 03:11:36 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1060.4 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_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DEP.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.25.0’ * 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 R 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 121.335 1.257 148.724 plot_dist 8.942 0.127 11.623 plot_volcano 7.308 0.119 8.584 plot_heatmap 6.319 0.105 7.868 analyze_dep 4.608 0.172 5.697 * 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-3.19-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 116.713 5.973 142.460
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 3.902 | 0.134 | 4.916 | |
TMT | 0.001 | 0.001 | 0.001 | |
add_rejections | 1.722 | 0.055 | 2.138 | |
analyze_dep | 4.608 | 0.172 | 5.697 | |
filter_missval | 1.168 | 0.042 | 1.424 | |
filter_proteins | 0.704 | 0.026 | 0.874 | |
get_df_long | 2.662 | 0.064 | 3.236 | |
get_df_wide | 1.730 | 0.060 | 2.165 | |
get_prefix | 0.005 | 0.001 | 0.006 | |
get_results | 2.246 | 0.067 | 2.744 | |
get_suffix | 0.002 | 0.000 | 0.002 | |
import_IsobarQuant | 0.001 | 0.000 | 0.001 | |
import_MaxQuant | 0.113 | 0.002 | 0.145 | |
impute | 121.335 | 1.257 | 148.724 | |
make_se | 0.093 | 0.001 | 0.109 | |
make_se_parse | 0.150 | 0.015 | 0.190 | |
make_unique | 0.047 | 0.002 | 0.057 | |
manual_impute | 1.554 | 0.039 | 1.879 | |
meanSdPlot | 1.747 | 0.215 | 2.332 | |
normalize_vsn | 0.801 | 0.023 | 0.969 | |
plot_all | 3.755 | 0.115 | 4.589 | |
plot_cond | 2.478 | 0.070 | 3.041 | |
plot_cond_freq | 2.080 | 0.053 | 2.526 | |
plot_cond_overlap | 2.092 | 0.056 | 2.568 | |
plot_cor | 2.969 | 0.098 | 3.888 | |
plot_coverage | 1.130 | 0.038 | 1.418 | |
plot_detect | 1.710 | 0.044 | 2.101 | |
plot_dist | 8.942 | 0.127 | 11.623 | |
plot_frequency | 0.972 | 0.036 | 1.234 | |
plot_gsea | 1.634 | 0.048 | 2.167 | |
plot_heatmap | 6.319 | 0.105 | 7.868 | |
plot_imputation | 2.231 | 0.079 | 2.632 | |
plot_missval | 3.845 | 0.104 | 4.312 | |
plot_normalization | 3.001 | 0.089 | 3.715 | |
plot_numbers | 1.147 | 0.040 | 1.397 | |
plot_p_hist | 2.950 | 0.064 | 3.437 | |
plot_pca | 2.860 | 0.058 | 3.395 | |
plot_single | 3.710 | 0.153 | 4.506 | |
plot_volcano | 7.308 | 0.119 | 8.584 | |
process | 3.242 | 0.083 | 3.838 | |
report | 0.000 | 0.001 | 0.001 | |
run_app | 0.001 | 0.000 | 0.001 | |
se2msn | 0.275 | 0.003 | 0.312 | |
test_diff | 2.074 | 0.072 | 2.491 | |
test_gsea | 1.626 | 0.046 | 1.937 | |
theme_DEP1 | 1.026 | 0.034 | 1.219 | |
theme_DEP2 | 1.133 | 0.039 | 1.315 | |