Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:32 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the DEP package: - 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: /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_1.26.0.tar.gz |
StartedAt: 2024-05-06 21:02:38 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 21:04:59 -0400 (Mon, 06 May 2024) |
EllapsedTime: 141.5 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/DEP.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * 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 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 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 'impute.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in Rd file 'LFQ.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in Rd file 'process.Rd': ‘[MSnbase:impute-methods]{impute}’ Missing link or links in Rd file 'TMT.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 5.529 0.03 5.562 * 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-mac-arm64/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-arm64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 18.730 0.789 19.653
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 0.432 | 0.015 | 0.454 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.266 | 0.005 | 0.272 | |
analyze_dep | 0.97 | 0.03 | 1.00 | |
filter_missval | 0.146 | 0.007 | 0.152 | |
filter_proteins | 0.082 | 0.004 | 0.087 | |
get_df_long | 0.225 | 0.014 | 0.240 | |
get_df_wide | 0.207 | 0.009 | 0.217 | |
get_prefix | 0.001 | 0.000 | 0.001 | |
get_results | 0.271 | 0.014 | 0.284 | |
get_suffix | 0.000 | 0.000 | 0.001 | |
import_IsobarQuant | 0 | 0 | 0 | |
import_MaxQuant | 0.014 | 0.000 | 0.015 | |
impute | 5.529 | 0.030 | 5.562 | |
make_se | 0.013 | 0.001 | 0.014 | |
make_se_parse | 0.018 | 0.001 | 0.019 | |
make_unique | 0.006 | 0.000 | 0.006 | |
manual_impute | 0.193 | 0.013 | 0.205 | |
meanSdPlot | 0.232 | 0.006 | 0.245 | |
normalize_vsn | 0.106 | 0.003 | 0.110 | |
plot_all | 0.485 | 0.021 | 0.507 | |
plot_cond | 0.326 | 0.010 | 0.337 | |
plot_cond_freq | 0.277 | 0.006 | 0.284 | |
plot_cond_overlap | 0.285 | 0.014 | 0.300 | |
plot_cor | 0.403 | 0.016 | 0.421 | |
plot_coverage | 0.140 | 0.005 | 0.145 | |
plot_detect | 0.235 | 0.006 | 0.242 | |
plot_dist | 1.474 | 0.032 | 1.505 | |
plot_frequency | 0.129 | 0.005 | 0.134 | |
plot_gsea | 0.207 | 0.009 | 0.216 | |
plot_heatmap | 0.747 | 0.013 | 0.761 | |
plot_imputation | 0.296 | 0.016 | 0.312 | |
plot_missval | 0.464 | 0.015 | 0.479 | |
plot_normalization | 0.370 | 0.017 | 0.388 | |
plot_numbers | 0.142 | 0.007 | 0.149 | |
plot_p_hist | 0.359 | 0.009 | 0.368 | |
plot_pca | 0.351 | 0.009 | 0.361 | |
plot_single | 0.442 | 0.015 | 0.457 | |
plot_volcano | 1.427 | 0.018 | 1.447 | |
process | 0.417 | 0.021 | 0.437 | |
report | 0 | 0 | 0 | |
run_app | 0 | 0 | 0 | |
se2msn | 0.036 | 0.001 | 0.036 | |
test_diff | 0.303 | 0.016 | 0.319 | |
test_gsea | 0.209 | 0.009 | 0.219 | |
theme_DEP1 | 0.131 | 0.005 | 0.137 | |
theme_DEP2 | 0.151 | 0.014 | 0.165 | |