Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:28:38 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 87/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
APL 1.9.0 (landing page) Clemens Kohl
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the APL package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/APL.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: APL |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:APL.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings APL_1.9.0.tar.gz |
StartedAt: 2024-05-31 01:25:42 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:33:33 -0400 (Fri, 31 May 2024) |
EllapsedTime: 470.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: APL.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:APL.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings APL_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/APL.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 ‘APL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘APL’ version ‘1.9.0’ * 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 ‘APL’ 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed apl_topGO 5.688 0.268 5.956 plot_enrichment 5.082 0.164 5.246 * 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: OK
APL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL APL ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘APL’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (APL)
APL.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "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(APL) > test_check("APL") Calling cacomp to recompute from matrix. [ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 15.912 1.218 18.099
APL.Rcheck/APL-Ex.timings
name | user | system | elapsed | |
apl | 0.197 | 0.003 | 0.201 | |
apl_coords | 0.006 | 0.000 | 0.006 | |
apl_score | 1.281 | 0.064 | 1.344 | |
apl_topGO | 5.688 | 0.268 | 5.956 | |
as.cacomp | 1.048 | 0.047 | 1.096 | |
as.list-cacomp-method | 0.014 | 0.000 | 0.014 | |
ca_3Dplot | 1.203 | 0.123 | 1.327 | |
ca_biplot | 0.076 | 0.020 | 0.097 | |
ca_coords | 0.006 | 0.000 | 0.006 | |
cacomp-class | 0.011 | 0.000 | 0.011 | |
cacomp | 0.742 | 0.023 | 0.766 | |
cacomp_names | 0.005 | 0.000 | 0.005 | |
cacomp_slot | 0.004 | 0.000 | 0.005 | |
check_cacomp | 0.005 | 0.000 | 0.005 | |
elbow_method | 0.555 | 0.024 | 0.579 | |
pick_dims | 1.132 | 0.027 | 1.159 | |
pipe | 0 | 0 | 0 | |
plot_enrichment | 5.082 | 0.164 | 5.246 | |
runAPL | 1.891 | 0.072 | 1.963 | |
run_APL | 0.397 | 0.004 | 0.400 | |
show.cacomp | 0.005 | 0.000 | 0.005 | |
subset_dims | 0.004 | 0.000 | 0.004 | |
var_rows | 0.009 | 0.000 | 0.010 | |