Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 549/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.26.0 (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 | ![]() | ||||||||
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: 1.26.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DEP_1.26.0.tar.gz |
StartedAt: 2024-06-12 22:26:24 -0400 (Wed, 12 Jun 2024) |
EndedAt: 2024-06-12 22:34:26 -0400 (Wed, 12 Jun 2024) |
EllapsedTime: 481.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DEP.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DEP_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DEP.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.26.0’ * 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 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 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 53.354 0.491 53.846 * 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-3.19-bioc/meat/DEP.Rcheck/00check.log’ for details.
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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 50.221 1.893 52.120
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 2.002 | 0.100 | 2.102 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.653 | 0.008 | 0.662 | |
analyze_dep | 1.958 | 0.064 | 2.022 | |
filter_missval | 0.421 | 0.011 | 0.434 | |
filter_proteins | 0.264 | 0.000 | 0.264 | |
get_df_long | 1.445 | 0.099 | 1.546 | |
get_df_wide | 0.640 | 0.028 | 0.669 | |
get_prefix | 0.002 | 0.000 | 0.002 | |
get_results | 0.837 | 0.016 | 0.853 | |
get_suffix | 0.001 | 0.000 | 0.001 | |
import_IsobarQuant | 0.000 | 0.000 | 0.001 | |
import_MaxQuant | 0.058 | 0.001 | 0.058 | |
impute | 53.354 | 0.491 | 53.846 | |
make_se | 0.032 | 0.004 | 0.036 | |
make_se_parse | 0.059 | 0.007 | 0.067 | |
make_unique | 0.012 | 0.004 | 0.016 | |
manual_impute | 0.561 | 0.007 | 0.569 | |
meanSdPlot | 0.520 | 0.056 | 0.576 | |
normalize_vsn | 0.312 | 0.012 | 0.324 | |
plot_all | 1.521 | 0.017 | 1.537 | |
plot_cond | 0.929 | 0.011 | 0.941 | |
plot_cond_freq | 0.783 | 0.004 | 0.787 | |
plot_cond_overlap | 0.797 | 0.000 | 0.797 | |
plot_cor | 1.113 | 0.004 | 1.117 | |
plot_coverage | 0.399 | 0.000 | 0.399 | |
plot_detect | 0.689 | 0.000 | 0.689 | |
plot_dist | 3.343 | 0.011 | 3.355 | |
plot_frequency | 0.347 | 0.000 | 0.347 | |
plot_gsea | 0.675 | 0.005 | 0.679 | |
plot_heatmap | 2.267 | 0.039 | 2.307 | |
plot_imputation | 0.891 | 0.003 | 0.895 | |
plot_missval | 1.406 | 0.016 | 1.422 | |
plot_normalization | 2.142 | 0.120 | 2.262 | |
plot_numbers | 0.414 | 0.016 | 0.430 | |
plot_p_hist | 1.096 | 0.023 | 1.119 | |
plot_pca | 1.056 | 0.000 | 1.055 | |
plot_single | 1.379 | 0.000 | 1.379 | |
plot_volcano | 3.838 | 0.044 | 3.882 | |
process | 1.210 | 0.016 | 1.226 | |
report | 0.001 | 0.000 | 0.000 | |
run_app | 0 | 0 | 0 | |
se2msn | 0.103 | 0.004 | 0.108 | |
test_diff | 0.808 | 0.008 | 0.816 | |
test_gsea | 0.603 | 0.008 | 0.610 | |
theme_DEP1 | 0.375 | 0.004 | 0.380 | |
theme_DEP2 | 0.395 | 0.000 | 0.396 | |