Back to Multiple platform build/check report for BioC 3.13
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).

CHECK results for EMDomics on machv2

To the developers/maintainers of the EMDomics package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 566/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.22.0  (landing page)
Sadhika Malladi and Daniel Schmolze
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/EMDomics
git_branch: RELEASE_3_13
git_last_commit: 86b3e22
git_last_commit_date: 2021-05-19 12:13:42 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EMDomics
Version: 2.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EMDomics_2.22.0.tar.gz
StartedAt: 2021-10-14 18:42:19 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:45:03 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 164.5 seconds
RetCode: 0
Status:   OK  
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EMDomics_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/EMDomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EMDomics/DESCRIPTION’ ... OK
* this is package ‘EMDomics’ version ‘2.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
calculate_cvm    15.119  0.140  15.299
plot_cvm_density 14.431  0.126  14.573
plot_cvmperms    14.331  0.130  14.483
plot_emdperms    10.182  0.090  10.286
plot_emd_density  9.973  0.099  10.085
calculate_emd     9.263  0.086   9.367
plot_cvmnull      8.562  0.059   8.634
plot_ksperms      7.744  0.032   7.786
plot_emdnull      6.785  0.048   6.841
calculate_ks      6.780  0.040   6.831
plot_ks_density   6.557  0.028   6.589
plot_ksnull       6.092  0.031   6.134
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/EMDomics.Rcheck/00check.log’
for details.



Installation output

EMDomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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_cvm15.119 0.14015.299
calculate_cvm_gene0.0110.0010.012
calculate_emd9.2630.0869.367
calculate_emd_gene0.0040.0000.005
calculate_ks6.7800.0406.831
calculate_ks_gene0.0170.0020.019
plot_cvm_density14.431 0.12614.573
plot_cvmnull8.5620.0598.634
plot_cvmperms14.331 0.13014.483
plot_emd_density 9.973 0.09910.085
plot_emdnull6.7850.0486.841
plot_emdperms10.182 0.09010.286
plot_ks_density6.5570.0286.589
plot_ksnull6.0920.0316.134
plot_ksperms7.7440.0327.786