Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 626/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EMDomics 2.35.0 (landing page) Sadhika Malladi
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the EMDomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EMDomics.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: EMDomics |
Version: 2.35.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EMDomics_2.35.0.tar.gz |
StartedAt: 2024-06-10 03:07:21 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 03:10:29 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 188.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EMDomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EMDomics_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EMDomics/DESCRIPTION’ ... OK * this is package ‘EMDomics’ version ‘2.35.0’ * 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 ‘EMDomics’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre] Daniel Schmolze <emd@schmolze.com> [aut, cre] * 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 ... NOTE .cvm_pairwise_q: no visible global function definition for ‘combn’ .cvm_pairwise_q : <anonymous>: no visible global function definition for ‘median’ .emd_gene_pairwise: no visible global function definition for ‘hist’ .emd_pairwise_q: no visible global function definition for ‘combn’ .emd_pairwise_q : <anonymous>: no visible global function definition for ‘median’ .ks_pairwise_table: no visible global function definition for ‘ks.test’ calculate_cvm: no visible global function definition for ‘combn’ calculate_cvm : <anonymous>: no visible global function definition for ‘median’ calculate_cvm_gene: no visible global function definition for ‘combn’ calculate_emd: no visible global function definition for ‘combn’ calculate_emd : <anonymous>: no visible global function definition for ‘median’ calculate_emd_gene: no visible global function definition for ‘combn’ calculate_ks: no visible global function definition for ‘combn’ calculate_ks : <anonymous>: no visible global function definition for ‘p.adjust’ calculate_ks : <anonymous>: no visible global function definition for ‘median’ calculate_ks_gene: no visible global function definition for ‘combn’ calculate_ks_gene: no visible global function definition for ‘ks.test’ Undefined global functions or variables: combn hist ks.test median p.adjust Consider adding importFrom("graphics", "hist") importFrom("stats", "ks.test", "median", "p.adjust") importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'emdomics-package.Rd': ‘emdomics-package’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_cvm_density 16.135 0.106 18.261 plot_cvmperms 16.070 0.102 17.522 calculate_cvm 15.993 0.101 17.761 plot_emd_density 9.010 0.089 9.939 plot_emdperms 8.738 0.068 9.714 calculate_emd 8.268 0.097 9.427 plot_cvmnull 6.271 0.045 6.868 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck/00check.log’ for details.
EMDomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EMDomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘EMDomics’ ... ** using staged installation ** R ** 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 (EMDomics)
EMDomics.Rcheck/EMDomics-Ex.timings
name | user | system | elapsed | |
calculate_cvm | 15.993 | 0.101 | 17.761 | |
calculate_cvm_gene | 0.016 | 0.001 | 0.022 | |
calculate_emd | 8.268 | 0.097 | 9.427 | |
calculate_emd_gene | 0.008 | 0.001 | 0.010 | |
calculate_ks | 3.438 | 0.035 | 3.801 | |
calculate_ks_gene | 0.017 | 0.002 | 0.021 | |
plot_cvm_density | 16.135 | 0.106 | 18.261 | |
plot_cvmnull | 6.271 | 0.045 | 6.868 | |
plot_cvmperms | 16.070 | 0.102 | 17.522 | |
plot_emd_density | 9.010 | 0.089 | 9.939 | |
plot_emdnull | 3.781 | 0.036 | 4.515 | |
plot_emdperms | 8.738 | 0.068 | 9.714 | |
plot_ks_density | 3.888 | 0.034 | 4.323 | |
plot_ksnull | 2.041 | 0.022 | 2.221 | |
plot_ksperms | 3.781 | 0.037 | 4.301 | |