Package: SELEX

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2019-04-09 03:38:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:41:02 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 151.7 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

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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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SELEX.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.15.0’
* 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           38.193  6.026  20.007
selex.seqfilter 12.924  1.339   5.429
* 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-3.9-bioc/meat/SELEX.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SELEX
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

name	user	system	elapsed
SELEX	38.193	6.026	20.007
selex.affinities	1.389	0.403	1.427
selex.config	0.432	0.106	0.299
selex.countSummary	1.685	0.447	1.523
selex.counts	2.224	0.490	1.760
selex.defineSample	0.396	0.098	0.295
selex.exampledata	0.265	0.109	0.306
selex.fastqPSFM	1.015	0.138	0.751
selex.getAttributes	0.588	0.155	0.459
selex.getRound0	0.356	0.129	0.463
selex.getSeqfilter	0.794	0.109	0.305
selex.infogain	2.897	0.908	2.917
selex.infogainSummary	1.595	0.364	1.193
selex.jvmStatus	0.524	0.112	0.316
selex.kmax	1.929	0.840	2.462
selex.kmerPSFM	0.916	0.241	0.800
selex.loadAnnotation	0.788	0.141	0.455
selex.mm	1.492	0.331	1.100
selex.mmProb	0.931	0.346	1.150
selex.mmSummary	0.909	0.353	1.162
selex.revcomp	1.135	0.378	1.377
selex.run	3.490	0.855	2.748
selex.sample	0.462	0.151	0.473
selex.samplePSFM	1.085	0.154	0.817
selex.sampleSummary	0.474	0.140	0.458
selex.saveAnnotation	0.232	0.124	0.358
selex.seqfilter	12.924	1.339	5.429
selex.setwd	0.360	0.092	0.256
selex.split	0.853	0.280	0.935
selex.summary	2.056	0.787	2.650