Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2024-12-04 09:55 -0500 (Wed, 04 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" | 861 |
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Package 210/216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
vsn 3.75.0 (landing page) Wolfgang Huber
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
To the developers/maintainers of the vsn 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: vsn |
Version: 3.75.0 |
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:vsn.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings vsn_3.75.0.tar.gz |
StartedAt: 2024-12-04 09:32:42 -0500 (Wed, 04 Dec 2024) |
EndedAt: 2024-12-04 09:33:44 -0500 (Wed, 04 Dec 2024) |
EllapsedTime: 62.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: vsn.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:vsn.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings vsn_3.75.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/vsn.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘vsn/DESCRIPTION’ ... OK * this is package ‘vsn’ version ‘3.75.0’ * 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 ‘vsn’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 NOTE See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/vsn.Rcheck/00check.log’ for details.
vsn.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL vsn ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘vsn’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vsn.c -o vsn.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vsn2.c -o vsn2.o gcc -shared -L/usr/local/lib -o vsn.so init.o vsn.o vsn2.o installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-vsn/00new/vsn/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (vsn)
vsn.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" 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("vsn") Loading required package: Biobase Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > > test_check("vsn") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_calib.R:1:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ] > > proc.time() user system elapsed 1.259 0.154 1.399
vsn.Rcheck/vsn-Ex.timings
name | user | system | elapsed | |
class.vsn | 0.122 | 0.018 | 0.140 | |
justvsn | 0.635 | 0.001 | 0.637 | |
kidney | 0.015 | 0.001 | 0.017 | |
lymphoma | 0.020 | 0.003 | 0.023 | |
meanSdPlot | 0.370 | 0.029 | 0.401 | |
normalize.AffyBatch.vsn | 0 | 0 | 0 | |
sagmbSimulateData | 0.553 | 0.000 | 0.553 | |
scalingFactorTransformation | 0 | 0 | 0 | |
vsn2 | 0.135 | 0.005 | 0.140 | |
vsn2trsf | 0.027 | 0.001 | 0.028 | |
vsnLikelihood | 1.129 | 0.020 | 1.150 | |