Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:55 -0400 (Fri, 31 May 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" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.26.0 |
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: 2024-05-31 03:04:09 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 03:11:56 -0400 (Fri, 31 May 2024) |
EllapsedTime: 467.0 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 54.412 0.431 54.846 * 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 46.994 1.887 48.881
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 1.895 | 0.028 | 1.923 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.655 | 0.001 | 0.655 | |
analyze_dep | 1.817 | 0.036 | 1.853 | |
filter_missval | 0.406 | 0.000 | 0.406 | |
filter_proteins | 0.259 | 0.000 | 0.259 | |
get_df_long | 0.702 | 0.000 | 0.703 | |
get_df_wide | 1.568 | 0.008 | 1.576 | |
get_prefix | 0.002 | 0.000 | 0.002 | |
get_results | 0.854 | 0.016 | 0.871 | |
get_suffix | 0.001 | 0.000 | 0.001 | |
import_IsobarQuant | 0.001 | 0.000 | 0.000 | |
import_MaxQuant | 0.041 | 0.000 | 0.041 | |
impute | 54.412 | 0.431 | 54.846 | |
make_se | 0.035 | 0.000 | 0.035 | |
make_se_parse | 0.059 | 0.009 | 0.067 | |
make_unique | 0.012 | 0.003 | 0.016 | |
manual_impute | 0.582 | 0.004 | 0.586 | |
meanSdPlot | 0.527 | 0.055 | 0.582 | |
normalize_vsn | 0.307 | 0.028 | 0.335 | |
plot_all | 1.494 | 0.020 | 1.513 | |
plot_cond | 0.938 | 0.000 | 0.938 | |
plot_cond_freq | 0.784 | 0.000 | 0.784 | |
plot_cond_overlap | 0.776 | 0.003 | 0.780 | |
plot_cor | 1.096 | 0.020 | 1.117 | |
plot_coverage | 0.424 | 0.000 | 0.425 | |
plot_detect | 0.637 | 0.004 | 0.641 | |
plot_dist | 3.383 | 0.036 | 3.419 | |
plot_frequency | 0.345 | 0.000 | 0.345 | |
plot_gsea | 0.634 | 0.004 | 0.639 | |
plot_heatmap | 2.285 | 0.016 | 2.301 | |
plot_imputation | 0.889 | 0.008 | 0.897 | |
plot_missval | 1.402 | 0.020 | 1.423 | |
plot_normalization | 1.152 | 0.008 | 1.160 | |
plot_numbers | 0.503 | 0.000 | 0.504 | |
plot_p_hist | 1.143 | 0.044 | 1.186 | |
plot_pca | 1.138 | 0.004 | 1.143 | |
plot_single | 1.449 | 0.000 | 1.449 | |
plot_volcano | 3.967 | 0.000 | 3.968 | |
process | 1.283 | 0.000 | 1.283 | |
report | 0 | 0 | 0 | |
run_app | 0.001 | 0.000 | 0.000 | |
se2msn | 0.107 | 0.000 | 0.106 | |
test_diff | 0.86 | 0.00 | 0.86 | |
test_gsea | 0.622 | 0.000 | 0.622 | |
theme_DEP1 | 0.382 | 0.016 | 0.398 | |
theme_DEP2 | 0.419 | 0.012 | 0.431 | |