Package: SELEX

Version: 1.18.0

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_1.18.0.tar.gz

StartedAt: 2020-04-15 05:34:37 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:37:02 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 145.6 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SELEX.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.18.0’
* 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           35.197  5.654  18.465
selex.seqfilter 12.224  1.264   5.293
* 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-3.10-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’ ...
** 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)

name	user	system	elapsed
SELEX	35.197	5.654	18.465
selex.affinities	1.312	0.363	1.330
selex.config	0.401	0.113	0.362
selex.countSummary	1.619	0.412	1.483
selex.counts	1.882	0.421	1.618
selex.defineSample	0.250	0.105	0.303
selex.exampledata	0.246	0.106	0.293
selex.fastqPSFM	0.766	0.156	0.717
selex.getAttributes	0.499	0.136	0.415
selex.getRound0	0.353	0.131	0.453
selex.getSeqfilter	0.848	0.110	0.304
selex.infogain	2.829	0.942	2.995
selex.infogainSummary	1.633	0.393	1.258
selex.jvmStatus	0.478	0.092	0.282
selex.kmax	1.994	0.842	2.494
selex.kmerPSFM	0.917	0.270	0.853
selex.loadAnnotation	0.822	0.143	0.475
selex.mm	1.164	0.372	1.209
selex.mmProb	0.965	0.357	1.161
selex.mmSummary	0.954	0.304	0.993
selex.revcomp	1.237	0.373	1.389
selex.run	3.999	0.877	2.755
selex.sample	0.391	0.113	0.377
selex.samplePSFM	0.624	0.138	0.554
selex.sampleSummary	0.611	0.138	0.435
selex.saveAnnotation	0.237	0.121	0.361
selex.seqfilter	12.224	1.264	5.293
selex.setwd	0.165	0.069	0.211
selex.split	0.934	0.317	0.986
selex.summary	2.280	0.821	2.685