Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 843/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeoTcgaData 2.6.0 (landing page) Erqiang Hu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GeoTcgaData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeoTcgaData.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: GeoTcgaData |
Version: 2.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeoTcgaData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeoTcgaData_2.6.0.tar.gz |
StartedAt: 2024-12-20 04:02:20 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:09:36 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 436.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeoTcgaData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeoTcgaData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeoTcgaData_2.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeoTcgaData.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeoTcgaData/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeoTcgaData’ version ‘2.6.0’ * 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 ‘GeoTcgaData’ 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 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed differential_methy 23.744 1.732 26.636 countToFpkm 6.679 0.415 7.122 differential_RNA 5.455 0.281 5.872 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
GeoTcgaData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeoTcgaData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GeoTcgaData’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GeoTcgaData)
GeoTcgaData.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(GeoTcgaData) > > test_check("GeoTcgaData") file1 is over file2 is over file3 is over file4 is over 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns [ FAIL 0 | WARN 0 | SKIP 2 | PASS 11 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test_diff_RNA_ucsc.R:2:5', 'test_differential_RNA.R:2:5' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 11 ] > > proc.time() user system elapsed 25.217 1.367 28.565
GeoTcgaData.Rcheck/GeoTcgaData-Ex.timings
name | user | system | elapsed | |
Merge_methy_tcga | 1.822 | 0.043 | 1.906 | |
SNP_QC | 0.052 | 0.002 | 0.053 | |
array_preprocess | 0.000 | 0.001 | 0.001 | |
cal_mean_module | 0.289 | 0.039 | 0.329 | |
cluster_array | 0 | 0 | 0 | |
combine_pvalue | 0.011 | 0.001 | 0.012 | |
countToFpkm | 6.679 | 0.415 | 7.122 | |
countToTpm | 1.757 | 0.025 | 1.786 | |
differential_RNA | 5.455 | 0.281 | 5.872 | |
differential_SNP | 0.062 | 0.001 | 0.064 | |
differential_SNP_GEO | 0.077 | 0.017 | 0.096 | |
differential_SNP_tcga | 0.055 | 0.001 | 0.057 | |
differential_array | 0.011 | 0.001 | 0.011 | |
differential_cnv | 0.070 | 0.003 | 0.074 | |
differential_limma | 0.012 | 0.001 | 0.013 | |
differential_methy | 23.744 | 1.732 | 26.636 | |
fpkmToTpm | 0.001 | 0.000 | 0.002 | |
gene_ave | 0.003 | 0.001 | 0.004 | |
get_geo_array | 0.000 | 0.001 | 0.001 | |
id_conversion_TCGA | 0.524 | 0.024 | 0.581 | |
prepare_chi | 0.005 | 0.001 | 0.006 | |
repAssign | 0.002 | 0.001 | 0.007 | |
repRemove | 0.002 | 0.000 | 0.004 | |