Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 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" | 4685 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4400 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4349 |
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 627/2242 | 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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EMDomics_2.35.0.tar.gz |
StartedAt: 2024-06-14 22:41:51 -0400 (Fri, 14 Jun 2024) |
EndedAt: 2024-06-14 22:42:56 -0400 (Fri, 14 Jun 2024) |
EllapsedTime: 65.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EMDomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EMDomics_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * 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 ‘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 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 ... 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 calculate_cvm 5.549 0.041 5.589 plot_cvmperms 5.513 0.039 5.552 plot_cvm_density 5.441 0.039 5.481 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck/00check.log’ for details.
EMDomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL EMDomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 | 5.549 | 0.041 | 5.589 | |
calculate_cvm_gene | 0.006 | 0.000 | 0.006 | |
calculate_emd | 3.096 | 0.035 | 3.131 | |
calculate_emd_gene | 0.004 | 0.001 | 0.003 | |
calculate_ks | 1.219 | 0.004 | 1.223 | |
calculate_ks_gene | 0.01 | 0.00 | 0.01 | |
plot_cvm_density | 5.441 | 0.039 | 5.481 | |
plot_cvmnull | 2.157 | 0.008 | 2.165 | |
plot_cvmperms | 5.513 | 0.039 | 5.552 | |
plot_emd_density | 3.395 | 0.025 | 3.418 | |
plot_emdnull | 1.414 | 0.004 | 1.418 | |
plot_emdperms | 3.281 | 0.040 | 3.322 | |
plot_ks_density | 1.339 | 0.000 | 1.339 | |
plot_ksnull | 0.742 | 0.000 | 0.742 | |
plot_ksperms | 1.331 | 0.000 | 1.332 | |