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This page was generated on 2023-10-20 09:38:12 -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 1876/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.32.0  (landing page)
Harmen J. Bussemaker
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SELEX
git_branch: RELEASE_3_17
git_last_commit: 8cf8897
git_last_commit_date: 2023-04-25 10:37:47 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for SELEX on kjohnson2


To the developers/maintainers of the SELEX 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: SELEX
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SELEX_1.32.0.tar.gz
StartedAt: 2023-10-18 23:56:15 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-19 00:00:01 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 225.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SELEX_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SELEX.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 ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SELEX’ 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 startup messages can be suppressed ... 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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
SELEX           16.331  1.615  15.087
selex.seqfilter  5.729  0.384   5.255
* 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: OK


Installation output

SELEX.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SELEX’ ...
** 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 (SELEX)

Tests output


Example timings

SELEX.Rcheck/SELEX-Ex.timings

nameusersystemelapsed
SELEX16.331 1.61515.087
selex.affinities0.7320.0420.783
selex.config0.1260.0060.107
selex.countSummary1.0280.0440.804
selex.counts1.4980.0511.307
selex.defineSample0.1260.0100.100
selex.exampledata0.1320.0110.101
selex.fastqPSFM0.5610.0220.614
selex.getAttributes0.1120.0100.132
selex.getRound00.2330.0130.258
selex.getSeqfilter0.0570.0030.068
selex.infogain1.2750.0681.094
selex.infogainSummary0.6990.0330.585
selex.jvmStatus0.0950.0040.081
selex.kmax1.0440.2391.621
selex.kmerPSFM0.4030.0510.433
selex.loadAnnotation0.2790.0150.222
selex.mm0.5590.0300.513
selex.mmProb0.5270.0280.418
selex.mmSummary0.5280.0290.491
selex.revcomp0.9880.0550.879
selex.run1.4250.0611.130
selex.sample0.2150.0100.172
selex.samplePSFM0.4200.0200.343
selex.sampleSummary0.1510.0120.161
selex.saveAnnotation0.0450.0090.089
selex.seqfilter5.7290.3845.255
selex.setwd0.1060.0040.066
selex.split0.4940.0220.399
selex.summary0.7840.0601.060