Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 640/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.36.0  (landing page)
Sadhika Malladi and Daniel Schmolze
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/EMDomics
git_branch: RELEASE_3_20
git_last_commit: c6619ed
git_last_commit_date: 2024-10-29 10:01:19 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for EMDomics on kjohnson1

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.

raw results


Summary

Package: EMDomics
Version: 2.36.0
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_2.36.0.tar.gz
StartedAt: 2024-12-20 18:32:39 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 18:33:47 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 68.2 seconds
RetCode: 0
Status:   OK  
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EMDomics/DESCRIPTION’ ... OK
* this is package ‘EMDomics’ version ‘2.36.0’
* 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 4.958  0.045    5.05
* 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.


Installation output

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-arm64/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)

Tests output


Example timings

EMDomics.Rcheck/EMDomics-Ex.timings

nameusersystemelapsed
calculate_cvm4.6330.0414.688
calculate_cvm_gene0.0060.0000.006
calculate_emd2.7470.0542.803
calculate_emd_gene0.0030.0000.004
calculate_ks1.1620.0261.188
calculate_ks_gene0.0110.0010.012
plot_cvm_density4.9580.0455.050
plot_cvmnull2.1330.0132.146
plot_cvmperms4.6590.0324.700
plot_emd_density2.6230.0602.714
plot_emdnull1.1530.0251.179
plot_emdperms2.9400.0502.992
plot_ks_density0.8570.0290.894
plot_ksnull0.6720.0120.684
plot_ksperms1.2750.0251.302