Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:00 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
To the developers/maintainers of the DEP package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 505/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.21.0 (landing page) Arne Smits
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: DEP |
Version: 1.21.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DEP_1.21.0.tar.gz |
StartedAt: 2023-02-06 23:39:10 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 23:48:36 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 565.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DEP.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DEP_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DEP.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.21.0’ * 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 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 documentation object 'LFQ.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in documentation object 'TMT.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in documentation object 'impute.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in documentation object '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 73.115 0.168 73.372 plot_dist 5.287 0.000 5.291 plot_volcano 5.260 0.000 5.263 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘DEP.Rmd’ using ‘UTF-8’... OK ‘MissingValues.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/home/biocbuild/bbs-3.17-bioc/meat/DEP.Rcheck/00check.log’ for details.
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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 70.481 1.503 72.562
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 2.686 | 0.044 | 2.736 | |
TMT | 0 | 0 | 0 | |
add_rejections | 1.151 | 0.024 | 1.175 | |
analyze_dep | 3.060 | 0.020 | 3.083 | |
filter_missval | 0.862 | 0.000 | 0.864 | |
filter_proteins | 0.508 | 0.000 | 0.508 | |
get_df_long | 1.967 | 0.000 | 1.971 | |
get_df_wide | 1.123 | 0.004 | 1.129 | |
get_prefix | 0.002 | 0.000 | 0.003 | |
get_results | 1.458 | 0.004 | 1.463 | |
get_suffix | 0.002 | 0.000 | 0.002 | |
import_IsobarQuant | 0.000 | 0.000 | 0.001 | |
import_MaxQuant | 0.073 | 0.000 | 0.073 | |
impute | 73.115 | 0.168 | 73.372 | |
make_se | 0.061 | 0.000 | 0.061 | |
make_se_parse | 0.091 | 0.000 | 0.090 | |
make_unique | 0.028 | 0.000 | 0.027 | |
manual_impute | 1.074 | 0.020 | 1.095 | |
meanSdPlot | 0.930 | 0.004 | 0.941 | |
normalize_vsn | 0.603 | 0.000 | 0.604 | |
plot_all | 2.397 | 0.024 | 2.423 | |
plot_cond | 1.754 | 0.008 | 1.779 | |
plot_cond_freq | 1.395 | 0.000 | 1.396 | |
plot_cond_overlap | 1.403 | 0.000 | 1.404 | |
plot_cor | 1.847 | 0.000 | 1.847 | |
plot_coverage | 0.953 | 0.000 | 0.953 | |
plot_detect | 1.207 | 0.000 | 1.208 | |
plot_dist | 5.287 | 0.000 | 5.291 | |
plot_frequency | 0.695 | 0.000 | 0.695 | |
plot_gsea | 1.117 | 0.012 | 1.130 | |
plot_heatmap | 3.888 | 0.012 | 3.905 | |
plot_imputation | 1.600 | 0.003 | 1.605 | |
plot_missval | 2.387 | 0.012 | 2.400 | |
plot_normalization | 2.091 | 0.052 | 2.145 | |
plot_numbers | 0.854 | 0.000 | 0.855 | |
plot_p_hist | 1.943 | 0.000 | 1.944 | |
plot_pca | 2.151 | 0.000 | 2.273 | |
plot_single | 2.454 | 0.012 | 2.468 | |
plot_volcano | 5.260 | 0.000 | 5.263 | |
process | 2.166 | 0.004 | 2.171 | |
report | 0 | 0 | 0 | |
run_app | 0 | 0 | 0 | |
se2msn | 0.176 | 0.000 | 0.176 | |
test_diff | 1.417 | 0.000 | 1.419 | |
test_gsea | 1.118 | 0.000 | 1.119 | |
theme_DEP1 | 0.676 | 0.004 | 0.681 | |
theme_DEP2 | 1.738 | 0.004 | 1.743 | |