Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:36:37 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 634/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.32.0  (landing page)
Sadhika Malladi and Daniel Schmolze
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/EMDomics
git_branch: RELEASE_3_18
git_last_commit: 0f54d25
git_last_commit_date: 2023-10-24 10:43:33 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for EMDomics on palomino4


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: 2.32.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EMDomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings EMDomics_2.32.0.tar.gz
StartedAt: 2024-03-26 00:34:55 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:36:25 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 90.3 seconds
RetCode: 0
Status:   OK  
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EMDomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings EMDomics_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/EMDomics.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'EMDomics/DESCRIPTION' ... OK
* this is package 'EMDomics' version '2.32.0'
* 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 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    7.34   0.10    7.45
plot_cvm_density 7.05   0.11    7.16
plot_cvmperms    6.65   0.09    6.75
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/EMDomics.Rcheck/00check.log'
for details.



Installation output

EMDomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL EMDomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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_cvm7.340.107.45
calculate_cvm_gene0.020.000.02
calculate_emd4.120.024.14
calculate_emd_gene0.020.000.02
calculate_ks2.300.022.31
calculate_ks_gene0.010.000.01
plot_cvm_density7.050.117.16
plot_cvmnull2.690.032.72
plot_cvmperms6.650.096.75
plot_emd_density3.990.034.02
plot_emdnull1.920.021.93
plot_emdperms4.650.084.74
plot_ks_density2.580.012.59
plot_ksnull0.960.000.95
plot_ksperms2.120.012.14