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This page was generated on 2023-10-20 09:38:07 -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 1366/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nearBynding 1.10.0  (landing page)
Veronica Busa
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/nearBynding
git_branch: RELEASE_3_17
git_last_commit: 6367769
git_last_commit_date: 2023-04-25 11:22:45 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for nearBynding on kjohnson2


To the developers/maintainers of the nearBynding 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: nearBynding
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nearBynding_1.10.0.tar.gz
StartedAt: 2023-10-18 11:06:34 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 11:14:32 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 477.9 seconds
RetCode: 0
Status:   OK  
CheckDir: nearBynding.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nearBynding.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nearBynding_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nearBynding.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 ‘nearBynding/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nearBynding’ version ‘1.10.0’
* package encoding: UTF-8
* 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 ‘nearBynding’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
processCapRout           20.745  0.473  31.700
visualizeCapRStereogene   6.933  0.126  10.391
visualizeStereogene       6.266  0.070   9.053
GenomeMappingToChainFile  5.694  0.103   8.241
liftOverToExomicBG        5.604  0.057   8.390
getChainChrSize           4.918  0.051   7.494
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nearBynding.Rcheck/00check.log’
for details.



Installation output

nearBynding.Rcheck/00install.out

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


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

Tests output


Example timings

nearBynding.Rcheck/nearBynding-Ex.timings

nameusersystemelapsed
CleanBAMtoBG0.0460.0150.094
CleanBEDtoBG0.0150.0270.096
ExtractTranscriptomeSequence000
GenomeMappingToChainFile5.6940.1038.241
assessGrouping1.3490.0422.141
bindingContextDistance0.2000.0230.328
bindingContextDistanceCapR0.3850.0250.628
getChainChrSize4.9180.0517.494
get_outfiles0.0060.0130.031
liftOverToExomicBG5.6040.0578.390
nearBynding-package0.0000.0000.001
processCapRout20.745 0.47331.700
runCapR0.0030.0070.035
runStereogene0.0030.0060.026
runStereogeneOnCapR0.0160.0330.162
symmetryCapR0.4210.0240.689
symmetryContext0.0610.0150.118
visualizeCapRStereogene 6.933 0.12610.391
visualizeStereogene6.2660.0709.053
write_config0.0000.0010.001
write_fasta0.0000.0010.002