Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 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: 1.26.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings DEP_1.26.0.tar.gz |
StartedAt: 2024-10-17 00:46:17 -0400 (Thu, 17 Oct 2024) |
EndedAt: 2024-10-17 00:55:11 -0400 (Thu, 17 Oct 2024) |
EllapsedTime: 533.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DEP.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings DEP_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/DEP.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 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 74.28 0.18 74.58 * 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 'E:/biocbuild/bbs-3.19-bioc/meat/DEP.Rcheck/00check.log' for details.
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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") pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. pdftex: major issue: User/administrator updates are out-of-sync. pdfcrop: major issue: User/administrator updates are out-of-sync. [ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ] > > proc.time() user system elapsed 58.23 2.64 86.20
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 2.49 | 0.06 | 2.56 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.72 | 0.03 | 0.75 | |
analyze_dep | 2.52 | 0.05 | 2.56 | |
filter_missval | 0.56 | 0.02 | 0.57 | |
filter_proteins | 0.30 | 0.02 | 0.32 | |
get_df_long | 0.86 | 0.00 | 0.86 | |
get_df_wide | 1.7 | 0.0 | 1.7 | |
get_prefix | 0.01 | 0.00 | 0.01 | |
get_results | 1.07 | 0.06 | 1.13 | |
get_suffix | 0 | 0 | 0 | |
import_IsobarQuant | 0 | 0 | 0 | |
import_MaxQuant | 0.06 | 0.00 | 0.06 | |
impute | 74.28 | 0.18 | 74.58 | |
make_se | 0.06 | 0.00 | 0.06 | |
make_se_parse | 0.10 | 0.00 | 0.09 | |
make_unique | 0.01 | 0.00 | 0.02 | |
manual_impute | 0.91 | 0.01 | 0.92 | |
meanSdPlot | 1.00 | 0.05 | 1.05 | |
normalize_vsn | 0.45 | 0.03 | 0.48 | |
plot_all | 1.92 | 0.03 | 1.95 | |
plot_cond | 1.14 | 0.02 | 1.16 | |
plot_cond_freq | 1.04 | 0.01 | 1.05 | |
plot_cond_overlap | 1.25 | 0.02 | 1.26 | |
plot_cor | 1.79 | 0.37 | 1.69 | |
plot_coverage | 0.64 | 0.11 | 0.54 | |
plot_detect | 0.87 | 0.00 | 0.88 | |
plot_dist | 4.69 | 0.03 | 4.72 | |
plot_frequency | 0.52 | 0.02 | 0.53 | |
plot_gsea | 0.78 | 0.05 | 0.83 | |
plot_heatmap | 3.17 | 0.04 | 3.22 | |
plot_imputation | 1.33 | 0.02 | 1.35 | |
plot_missval | 2.86 | 0.08 | 2.94 | |
plot_normalization | 1.39 | 0.08 | 1.47 | |
plot_numbers | 0.54 | 0.00 | 0.54 | |
plot_p_hist | 1.55 | 0.03 | 1.58 | |
plot_pca | 1.39 | 0.02 | 1.41 | |
plot_single | 1.66 | 0.03 | 1.69 | |
plot_volcano | 3.67 | 0.09 | 4.18 | |
process | 1.21 | 0.00 | 1.22 | |
report | 0 | 0 | 0 | |
run_app | 0 | 0 | 0 | |
se2msn | 0.11 | 0.00 | 0.11 | |
test_diff | 1.10 | 0.02 | 1.11 | |
test_gsea | 0.67 | 0.03 | 0.70 | |
theme_DEP1 | 0.48 | 0.02 | 0.50 | |
theme_DEP2 | 0.49 | 0.00 | 0.50 | |