Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 532/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEP 1.22.0 (landing page) Arne Smits
| kjohnson2 | macOS 12.6.1 Monterey / 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: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2023-10-17 15:08:45 -0400 (Tue, 17 Oct 2023) |
EndedAt: 2023-10-17 15:19:18 -0400 (Tue, 17 Oct 2023) |
EllapsedTime: 633.6 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DEP.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEP/DESCRIPTION’ ... OK * this is package ‘DEP’ version ‘1.22.0’ * 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 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 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 28.203 0.256 42.672 plot_dist 4.485 0.060 6.862 plot_volcano 4.046 0.062 6.264 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/Users/biocbuild/bbs-3.17-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/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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 14 | SKIP 0 | PASS 333 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ] > > proc.time() user system elapsed 64.609 3.407 107.846
DEP.Rcheck/DEP-Ex.timings
name | user | system | elapsed | |
LFQ | 2.204 | 0.057 | 3.424 | |
TMT | 0 | 0 | 0 | |
add_rejections | 0.880 | 0.032 | 1.400 | |
analyze_dep | 2.565 | 0.084 | 3.555 | |
filter_missval | 0.535 | 0.015 | 0.784 | |
filter_proteins | 0.34 | 0.01 | 0.46 | |
get_df_long | 1.571 | 0.027 | 2.296 | |
get_df_wide | 0.912 | 0.022 | 1.263 | |
get_prefix | 0.002 | 0.000 | 0.005 | |
get_results | 1.164 | 0.028 | 1.675 | |
get_suffix | 0.001 | 0.000 | 0.001 | |
import_IsobarQuant | 0 | 0 | 0 | |
import_MaxQuant | 0.055 | 0.001 | 0.086 | |
impute | 28.203 | 0.256 | 42.672 | |
make_se | 0.045 | 0.001 | 0.070 | |
make_se_parse | 0.068 | 0.001 | 0.106 | |
make_unique | 0.020 | 0.000 | 0.032 | |
manual_impute | 0.814 | 0.035 | 1.315 | |
meanSdPlot | 0.728 | 0.043 | 1.142 | |
normalize_vsn | 0.382 | 0.012 | 0.609 | |
plot_all | 1.943 | 0.053 | 2.966 | |
plot_cond | 1.345 | 0.033 | 2.095 | |
plot_cond_freq | 1.085 | 0.025 | 1.703 | |
plot_cond_overlap | 1.069 | 0.024 | 1.663 | |
plot_cor | 1.510 | 0.059 | 2.449 | |
plot_coverage | 0.696 | 0.018 | 1.092 | |
plot_detect | 1.586 | 0.029 | 2.489 | |
plot_dist | 4.485 | 0.060 | 6.862 | |
plot_frequency | 0.478 | 0.013 | 0.764 | |
plot_gsea | 0.833 | 0.019 | 1.312 | |
plot_heatmap | 2.979 | 0.052 | 4.587 | |
plot_imputation | 1.225 | 0.034 | 1.919 | |
plot_missval | 1.810 | 0.072 | 2.896 | |
plot_normalization | 1.614 | 0.047 | 2.547 | |
plot_numbers | 0.639 | 0.019 | 1.002 | |
plot_p_hist | 1.491 | 0.030 | 2.375 | |
plot_pca | 1.680 | 0.029 | 2.520 | |
plot_single | 1.954 | 0.033 | 3.042 | |
plot_volcano | 4.046 | 0.062 | 6.264 | |
process | 1.716 | 0.037 | 2.690 | |
report | 0.000 | 0.001 | 0.001 | |
run_app | 0.001 | 0.001 | 0.001 | |
se2msn | 0.139 | 0.002 | 0.221 | |
test_diff | 1.106 | 0.027 | 1.745 | |
test_gsea | 0.818 | 0.019 | 1.284 | |
theme_DEP1 | 0.519 | 0.016 | 0.803 | |
theme_DEP2 | 0.610 | 0.014 | 0.951 | |