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This page was generated on 2023-10-20 09:38:06 -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 1262/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff2 1.28.0  (landing page)
Gabriele Schweikert
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MMDiff2
git_branch: RELEASE_3_17
git_last_commit: c860c9b
git_last_commit_date: 2023-04-25 10:46:55 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MMDiff2 on kjohnson2


To the developers/maintainers of the MMDiff2 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: MMDiff2
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMDiff2_1.28.0.tar.gz
StartedAt: 2023-10-18 08:28:23 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 08:36:25 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 481.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MMDiff2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMDiff2_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MMDiff2.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 ‘MMDiff2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff2’ version ‘1.28.0’
* 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 ‘MMDiff2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DBAmmd: no visible global function definition for ‘new’
getReads: no visible global function definition for ‘IRangesList’
Undefined global functions or variables:
  IRangesList new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
compDists        22.300  3.208  34.457
plotPeak          8.015  0.343  12.788
DBAmmd-Accessors  3.437  0.608   5.412
* 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/MMDiff2.Rcheck/00check.log’
for details.



Installation output

MMDiff2.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MMDiff2
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘MMDiff2’ ...
** using staged installation
** R
** data
** 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 (MMDiff2)

Tests output


Example timings

MMDiff2.Rcheck/MMDiff2-Ex.timings

nameusersystemelapsed
Cfp1-Peaks0.0000.0000.002
DBAmmd-Accessors3.4370.6085.412
DBAmmd-class0.0370.0030.049
MMD000
compDists22.300 3.20834.457
compHists3.1160.2534.668
compPvals2.1510.1113.198
estimateFragmentCenters1.6350.0932.504
getPeakReads0.3000.0280.489
mm9-Genes000
plotDISTS4Peak1.3120.0892.070
plotDists1.2940.0792.070
plotPeak 8.015 0.34312.788
reportResults1.3330.0792.222
runShinyMMDiff20.0000.0000.001
server.MMDiff2000
ui.MMDiff20.0000.0000.001