Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:41 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

CHECK results for SELEX on nebbiolo2


To the developers/maintainers of the SELEX package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SELEX.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1857/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.31.0  (landing page)
Harmen J. Bussemaker
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/SELEX
git_branch: devel
git_last_commit: 5c5c6eb
git_last_commit_date: 2022-11-01 11:11:08 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: SELEX
Version: 1.31.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SELEX_1.31.0.tar.gz
StartedAt: 2023-04-12 09:18:17 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 09:20:37 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 140.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SELEX_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SELEX.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.31.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
SELEX           27.623  2.356   8.333
selex.seqfilter  9.153  0.274   2.491
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SELEX.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

SELEX.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SELEX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
SELEX27.623 2.356 8.333
selex.affinities1.4780.1100.552
selex.config0.1520.0110.044
selex.countSummary1.2200.0510.417
selex.counts1.7220.0400.685
selex.defineSample0.0930.0030.054
selex.exampledata0.0800.0080.039
selex.fastqPSFM0.8600.0630.466
selex.getAttributes0.1060.0000.087
selex.getRound00.2890.0350.191
selex.getSeqfilter0.0650.0120.049
selex.infogain1.5200.0970.629
selex.infogainSummary0.8220.0440.314
selex.jvmStatus0.2190.0050.049
selex.kmax2.0120.4290.903
selex.kmerPSFM0.6700.0320.263
selex.loadAnnotation0.3970.0120.130
selex.mm0.5630.0240.277
selex.mmProb0.3900.0420.180
selex.mmSummary0.3960.0250.181
selex.revcomp0.7130.0200.444
selex.run1.4630.0970.450
selex.sample0.2250.0040.057
selex.samplePSFM0.7340.0040.211
selex.sampleSummary0.2790.0040.076
selex.saveAnnotation0.1790.0040.046
selex.seqfilter9.1530.2742.491
selex.setwd0.0710.0080.015
selex.split0.4200.0190.132
selex.summary1.1290.0170.427