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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 624/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.30.0  (landing page)
Sadhika Malladi and Daniel Schmolze
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/EMDomics
git_branch: RELEASE_3_17
git_last_commit: 02891ab
git_last_commit_date: 2023-04-25 10:39:44 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for EMDomics on kjohnson2


To the developers/maintainers of the EMDomics 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.

raw results


Summary

Package: EMDomics
Version: 2.30.0
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_2.30.0.tar.gz
StartedAt: 2023-10-17 17:31:09 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:33:38 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 149.1 seconds
RetCode: 0
Status:   OK  
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_2.30.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/EMDomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EMDomics/DESCRIPTION’ ... OK
* this is package ‘EMDomics’ version ‘2.30.0’
* 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 ‘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 R 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 ... OK
* 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 7.631  0.085  11.931
calculate_cvm    7.566  0.078  11.676
plot_cvmperms    7.509  0.082  11.665
plot_emd_density 4.185  0.062   6.297
plot_emdperms    4.101  0.062   5.388
calculate_emd    4.011  0.059   6.253
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/EMDomics.Rcheck/00check.log’
for details.



Installation output

EMDomics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EMDomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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_cvm 7.566 0.07811.676
calculate_cvm_gene0.0070.0000.013
calculate_emd4.0110.0596.253
calculate_emd_gene0.0230.0040.039
calculate_ks2.1350.0333.345
calculate_ks_gene0.0130.0010.023
plot_cvm_density 7.631 0.08511.931
plot_cvmnull3.0270.0324.715
plot_cvmperms 7.509 0.08211.665
plot_emd_density4.1850.0626.297
plot_emdnull1.8820.0282.446
plot_emdperms4.1010.0625.388
plot_ks_density2.3670.0403.566
plot_ksnull1.1210.0191.544
plot_ksperms2.1860.0323.396