Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-22 11:36:29 -0400 (Wed, 22 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" | 4665 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
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 2040/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SurfR 1.1.0 (landing page) Aurora Maurizio
| 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 | see weekly results here | ||||||||||||
To the developers/maintainers of the SurfR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SurfR.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: SurfR |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SurfR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SurfR_1.1.0.tar.gz |
StartedAt: 2024-05-21 03:25:15 -0400 (Tue, 21 May 2024) |
EndedAt: 2024-05-21 03:34:57 -0400 (Tue, 21 May 2024) |
EllapsedTime: 582.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SurfR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SurfR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SurfR_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SurfR.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 ‘SurfR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SurfR’ version ‘1.1.0’ * 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 ‘SurfR’ 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 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Annotate_SPID 51.377 5.708 62.718 Gene2SProtein 11.404 1.449 12.857 Splot 6.826 1.440 8.266 TCGA_download 2.909 0.194 11.682 DownloadArchS4 0.902 0.140 15.329 enrichr_download 0.075 0.003 11.461 * 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
SurfR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SurfR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘SurfR’ ... ** using staged installation ** R ** data ** 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 (SurfR)
SurfR.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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SurfR) > > test_check("SurfR") 1 out of 1 genes have a matching surface protein 2 out of 4 genes have a matching surface protein [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ] > > proc.time() user system elapsed 32.947 1.576 34.516
SurfR.Rcheck/SurfR-Ex.timings
name | user | system | elapsed | |
Annotate_SPID | 51.377 | 5.708 | 62.718 | |
DGE | 3.281 | 0.224 | 3.506 | |
DownloadArchS4 | 0.902 | 0.140 | 15.329 | |
Enrichment | 0.325 | 0.048 | 1.778 | |
Enrichment_barplot | 0.376 | 0.103 | 1.139 | |
GEOmetadata | 0.355 | 0.036 | 0.391 | |
Gene2SProtein | 11.404 | 1.449 | 12.857 | |
SVenn | 0.016 | 0.003 | 0.021 | |
Splot | 6.826 | 1.440 | 8.266 | |
TCGA_download | 2.909 | 0.194 | 11.682 | |
combine_fisher_invnorm | 0.011 | 0.000 | 0.010 | |
dot-format_str | 0 | 0 | 0 | |
enrichr_download | 0.075 | 0.003 | 11.461 | |
metaRNAseq | 0.004 | 0.000 | 0.003 | |
plotPCA | 0.488 | 0.080 | 0.567 | |