Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-02-22 12:48:35 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 634/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.33.0  (landing page)
Sadhika Malladi and Daniel Schmolze
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/EMDomics
git_branch: devel
git_last_commit: 1ea72b3
git_last_commit_date: 2023-10-24 10:43:33 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for EMDomics on palomino3


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: 2.33.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EMDomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings EMDomics_2.33.0.tar.gz
StartedAt: 2024-02-22 02:46:42 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 02:47:58 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 75.6 seconds
RetCode: 0
Status:   OK  
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EMDomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings EMDomics_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/EMDomics.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* 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 '2.33.0'
* 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 ... 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_cvmperms    6.60   0.11    6.72
plot_cvm_density 6.15   0.14    6.30
calculate_cvm    5.70   0.17    5.87
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/EMDomics.Rcheck/00check.log'
for details.



Installation output

EMDomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL EMDomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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_cvm5.700.175.87
calculate_cvm_gene0.010.000.01
calculate_emd3.270.103.36
calculate_emd_gene0.030.000.03
calculate_ks1.390.081.47
calculate_ks_gene000
plot_cvm_density6.150.146.30
plot_cvmnull2.400.082.46
plot_cvmperms6.600.116.72
plot_emd_density3.410.093.50
plot_emdnull1.550.051.61
plot_emdperms3.750.093.85
plot_ks_density1.740.041.77
plot_ksnull0.830.000.83
plot_ksperms1.500.041.54