BioC 3.4: CHECK report for SELEX on morelia

Package: SELEX

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.6.0.tar.gz

StartedAt: 2017-04-15 07:54:29 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:56:30 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 121.1 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 --no-vignettes --timings SELEX_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SELEX.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.6.0’
* 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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           27.140  3.595  12.594
selex.seqfilter  9.146  0.898   4.316
* 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-3.4-bioc/meat/SELEX.Rcheck/00check.log’
for details.

* installing *source* package ‘SELEX’ ...
** R
** inst
** preparing 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	27.140	3.595	12.594
selex.affinities	1.092	0.238	0.909
selex.config	0.165	0.058	0.145
selex.countSummary	1.315	0.276	0.972
selex.counts	1.601	0.269	1.220
selex.defineSample	0.266	0.072	0.301
selex.exampledata	0.137	0.071	0.162
selex.fastqPSFM	0.794	0.109	0.592
selex.getAttributes	0.261	0.096	0.249
selex.getRound0	0.274	0.097	0.317
selex.getSeqfilter	0.171	0.070	0.179
selex.infogain	3.348	0.682	1.928
selex.infogainSummary	0.645	0.242	0.779
selex.jvmStatus	0.097	0.064	0.160
selex.kmax	1.168	0.615	1.470
selex.kmerPSFM	0.573	0.178	0.565
selex.loadAnnotation	0.220	0.093	0.298
selex.mm	1.384	0.253	0.809
selex.mmProb	0.877	0.243	0.726
selex.mmSummary	0.764	0.240	0.766
selex.revcomp	0.884	0.252	0.955
selex.run	3.475	0.616	1.886
selex.sample	0.274	0.098	0.285
selex.samplePSFM	1.012	0.104	0.685
selex.sampleSummary	0.504	0.096	0.325
selex.saveAnnotation	0.141	0.100	0.240
selex.seqfilter	9.146	0.898	4.316
selex.setwd	0.094	0.069	0.139
selex.split	0.610	0.197	0.560
selex.summary	1.147	0.426	1.465