Back to Build/check report for BioC 3.18 experimental data |
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This page was generated on 2024-03-28 14:52:06 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
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 399/429 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
TCGAWorkflowData 1.26.0 (landing page) Tiago Chedraoui Silva
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
To the developers/maintainers of the TCGAWorkflowData 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: TCGAWorkflowData |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings TCGAWorkflowData_1.26.0.tar.gz |
StartedAt: 2024-03-28 12:16:58 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 12:24:47 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 469.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCGAWorkflowData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:TCGAWorkflowData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings TCGAWorkflowData_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/TCGAWorkflowData.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘TCGAWorkflowData/DESCRIPTION’ ... OK * this is package ‘TCGAWorkflowData’ version ‘1.26.0’ * 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 ‘TCGAWorkflowData’ can be installed ... OK * checking installed package size ... NOTE installed size is 68.8Mb sub-directories of 1Mb or more: data 68.6Mb * 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 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 TCGAWorkflowData 30.969 0.971 31.942 tmp.biogrid 13.834 0.024 13.859 gistic_allbygene 11.792 0.144 11.936 gistic_thresholedbygene 10.578 0.100 10.678 maf 5.630 0.064 5.694 * 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 ... ‘TCGAWorkflowData.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.18-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’ for details.
TCGAWorkflowData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL TCGAWorkflowData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘TCGAWorkflowData’ ... ** 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 (TCGAWorkflowData)
TCGAWorkflowData.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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(TCGAWorkflowData) > > test_check("TCGAWorkflowData") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 36.678 1.346 38.014
TCGAWorkflowData.Rcheck/TCGAWorkflowData-Ex.timings
name | user | system | elapsed | |
TCGAWorkflowData | 30.969 | 0.971 | 31.942 | |
exp | 0.551 | 0.019 | 0.571 | |
exp_gbm | 1.076 | 0.055 | 1.132 | |
exp_lgg | 1.077 | 0.053 | 1.129 | |
gbm.samples | 0.568 | 0.016 | 0.584 | |
genes | 0.209 | 0.000 | 0.209 | |
genes_GR | 0.339 | 0.011 | 0.351 | |
gistic_allbygene | 11.792 | 0.144 | 11.936 | |
gistic_thresholedbygene | 10.578 | 0.100 | 10.678 | |
histone.marks | 1.393 | 0.048 | 1.442 | |
lgg.samples | 0.548 | 0.008 | 0.556 | |
maf | 5.630 | 0.064 | 5.694 | |
met | 0.562 | 0.000 | 0.562 | |
tmp.biogrid | 13.834 | 0.024 | 13.859 | |