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CHECK report for SELEX on merida1

This page was generated on 2019-04-16 11:58:21 -0400 (Tue, 16 Apr 2019).

Package 1410/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.14.0
Harmen Bussemaker
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/SELEX
Branch: RELEASE_3_8
Last Commit: 00b9541
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SELEX
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SELEX_1.14.0.tar.gz
StartedAt: 2019-04-16 02:40:38 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:43:11 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 153.1 seconds
RetCode: 0
Status:  OK 
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SELEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SELEX_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SELEX.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.14.0’
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
selex.config: no visible global function definition for ‘read.table’
selex.config: no visible global function definition for ‘write.table’
selex.counts: no visible global function definition for ‘flush.console’
selex.infogain: no visible global function definition for
  ‘flush.console’
selex.kmax: no visible global function definition for ‘flush.console’
selex.loadCountTable: no visible global function definition for
  ‘flush.console’
selex.mm: no visible global function definition for ‘flush.console’
selex.revcomp: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  complete.cases flush.console read.table write.table
Consider adding
  importFrom("stats", "complete.cases")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
* 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 or elapsed time > 5s
                  user system elapsed
SELEX           37.602  6.101  19.916
selex.seqfilter 12.830  1.411   5.691
selex.run        4.918  0.930   2.918
* 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-3.8-bioc/meat/SELEX.Rcheck/00check.log’
for details.



Installation output

SELEX.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SELEX
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SELEX’ ...
** 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
* DONE (SELEX)

Tests output


Example timings

SELEX.Rcheck/SELEX-Ex.timings

nameusersystemelapsed
SELEX37.602 6.10119.916
selex.affinities1.3470.3961.374
selex.config0.3930.0970.285
selex.countSummary1.6470.4051.439
selex.counts1.9980.4861.729
selex.defineSample0.2450.0980.290
selex.exampledata0.2310.1150.318
selex.fastqPSFM0.8870.1510.707
selex.getAttributes0.5750.1410.435
selex.getRound00.3770.1530.513
selex.getSeqfilter0.9140.1210.318
selex.infogain2.8700.9533.030
selex.infogainSummary1.7200.3991.299
selex.jvmStatus0.5060.1090.314
selex.kmax2.0090.8692.571
selex.kmerPSFM0.9270.2590.866
selex.loadAnnotation0.8220.1480.487
selex.mm1.4830.3561.166
selex.mmProb0.9600.3401.145
selex.mmSummary0.9200.3471.143
selex.revcomp1.4170.3861.433
selex.run4.9180.9302.918
selex.sample0.4330.1340.432
selex.samplePSFM0.6050.1440.578
selex.sampleSummary0.4390.1410.445
selex.saveAnnotation0.2530.1400.394
selex.seqfilter12.830 1.411 5.691
selex.setwd0.5620.1120.297
selex.split1.3980.3240.997
selex.summary2.3190.8482.810