Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:38:57 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 271/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Taosheng Xu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the CancerSubtypes package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CancerSubtypes.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: CancerSubtypes |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CancerSubtypes_1.30.0.tar.gz |
StartedAt: 2024-05-03 20:39:09 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 20:42:42 -0400 (Fri, 03 May 2024) |
EllapsedTime: 213.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CancerSubtypes.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CancerSubtypes_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CancerSubtypes.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CancerSubtypes/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CancerSubtypes’ version ‘1.30.0’ * 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 ‘CancerSubtypes’ 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 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 ... NOTE displayClusters: no visible global function definition for ‘grey’ plotiCluster: no visible global function definition for ‘gray’ Undefined global functions or variables: gray grey Consider adding importFrom("grDevices", "gray", "grey") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'ExecuteiCluster.Rd': ‘iCluster2’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ExecuteCNMF 34.979 1.775 24.240 sigclustTest 22.648 2.535 25.487 ExecuteSNF.CC 17.464 1.062 18.725 survAnalysis 10.682 0.231 11.015 ExecuteCC 6.820 1.724 8.672 FSbyCox 6.699 0.144 6.924 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/CancerSubtypes.Rcheck/00check.log’ for details.
CancerSubtypes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CancerSubtypes ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘CancerSubtypes’ ... ** 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 Warning in fun(libname, pkgname) : Package 'CancerSubtypes' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'CancerSubtypes' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (CancerSubtypes)
CancerSubtypes.Rcheck/tests/runTests.Rout
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 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. > BiocGenerics:::testPackage("CancerSubtypes") NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 2/2 To enable shared memory capabilities, try: install.extras(' NMF ') RUNIT TEST PROTOCOL -- Fri May 3 20:42:31 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : CancerSubtypes RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 Warning message: In fun(libname, pkgname) : Package 'CancerSubtypes' is deprecated and will be removed from Bioconductor version 3.20 > > proc.time() user system elapsed 3.562 0.312 3.911
CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings
name | user | system | elapsed | |
DiffExp.limma | 0.288 | 0.035 | 0.325 | |
ExecuteCC | 6.820 | 1.724 | 8.672 | |
ExecuteCNMF | 34.979 | 1.775 | 24.240 | |
ExecuteSNF.CC | 17.464 | 1.062 | 18.725 | |
ExecuteSNF | 0.226 | 0.020 | 0.248 | |
ExecuteWSNF | 1.869 | 0.090 | 1.977 | |
ExecuteiCluster | 3.533 | 0.092 | 3.660 | |
FSbyCox | 6.699 | 0.144 | 6.924 | |
FSbyMAD | 0.193 | 0.012 | 0.208 | |
FSbyPCA | 0.107 | 0.006 | 0.113 | |
FSbyVar | 0.041 | 0.003 | 0.045 | |
GeneExp | 0.011 | 0.002 | 0.013 | |
Ranking | 0.031 | 0.002 | 0.034 | |
affinityMatrix | 0.036 | 0.016 | 0.053 | |
data.checkDistribution | 0.215 | 0.011 | 0.227 | |
data.imputation | 0.007 | 0.001 | 0.009 | |
data.normalization | 0.094 | 0.014 | 0.108 | |
dist2 | 0.011 | 0.002 | 0.012 | |
drawHeatmap | 3.803 | 0.214 | 4.059 | |
miRNAExp | 0.004 | 0.002 | 0.005 | |
saveFigure | 0.804 | 0.064 | 0.877 | |
sigclustTest | 22.648 | 2.535 | 25.487 | |
silhouette_SimilarityMatrix | 0.246 | 0.015 | 0.266 | |
spectralAlg | 0.004 | 0.002 | 0.006 | |
status | 0.001 | 0.002 | 0.003 | |
survAnalysis | 10.682 | 0.231 | 11.015 | |
time | 0.001 | 0.001 | 0.002 | |