Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the CancerSubtypes 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: 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: 2024-05-06 20:09:55 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 20:11:04 -0400 (Mon, 06 May 2024) |
EllapsedTime: 68.8 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-mac-arm64/meat/CancerSubtypes.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * 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 sigclustTest 9.903 1.033 10.941 ExecuteCNMF 8.631 0.371 5.928 ExecuteSNF.CC 5.378 0.192 5.570 * 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-mac-arm64/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-arm64/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 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 -- Mon May 6 20:11:00 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 1.196 0.078 1.273
CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings
name | user | system | elapsed | |
DiffExp.limma | 0.108 | 0.011 | 0.118 | |
ExecuteCC | 2.177 | 0.270 | 2.452 | |
ExecuteCNMF | 8.631 | 0.371 | 5.928 | |
ExecuteSNF.CC | 5.378 | 0.192 | 5.570 | |
ExecuteSNF | 0.077 | 0.008 | 0.085 | |
ExecuteWSNF | 0.657 | 0.022 | 0.679 | |
ExecuteiCluster | 1.648 | 0.027 | 1.675 | |
FSbyCox | 1.481 | 0.038 | 1.520 | |
FSbyMAD | 0.055 | 0.002 | 0.058 | |
FSbyPCA | 0.049 | 0.003 | 0.052 | |
FSbyVar | 0.014 | 0.002 | 0.016 | |
GeneExp | 0.006 | 0.001 | 0.006 | |
Ranking | 0.011 | 0.001 | 0.011 | |
affinityMatrix | 0.008 | 0.001 | 0.008 | |
data.checkDistribution | 0.072 | 0.004 | 0.077 | |
data.imputation | 0.002 | 0.000 | 0.002 | |
data.normalization | 0.035 | 0.005 | 0.040 | |
dist2 | 0.005 | 0.001 | 0.006 | |
drawHeatmap | 1.222 | 0.060 | 1.285 | |
miRNAExp | 0.002 | 0.000 | 0.003 | |
saveFigure | 0.303 | 0.018 | 0.322 | |
sigclustTest | 9.903 | 1.033 | 10.941 | |
silhouette_SimilarityMatrix | 0.091 | 0.013 | 0.104 | |
spectralAlg | 0.002 | 0.001 | 0.003 | |
status | 0.001 | 0.001 | 0.001 | |
survAnalysis | 2.701 | 0.075 | 2.777 | |
time | 0.000 | 0.001 | 0.001 | |