BioC 3.3: CHECK report for SELEX on zin2

Package: SELEX

Version: 1.4.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SELEX_1.4.0.tar.gz

StartedAt: 2016-10-13 06:38:14 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:39:55 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 100.4 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SELEX_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SELEX.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.4.0’
* 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           21.709  1.160  13.364
selex.seqfilter  7.747  0.126   5.274
* 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
  ‘/home/biocbuild/bbs-3.3-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	21.709	1.160	13.364
selex.affinities	1.119	0.020	0.711
selex.config	0.189	0.000	0.120
selex.countSummary	0.980	0.008	0.668
selex.counts	1.398	0.012	1.094
selex.defineSample	0.319	0.003	0.155
selex.exampledata	0.161	0.000	0.100
selex.fastqPSFM	0.878	0.005	0.749
selex.getAttributes	0.215	0.000	0.210
selex.getRound0	0.241	0.000	0.228
selex.getSeqfilter	0.166	0.003	0.121
selex.infogain	1.310	0.021	1.103
selex.infogainSummary	0.546	0.003	0.466
selex.jvmStatus	0.096	0.000	0.095
selex.kmax	0.892	0.100	0.861
selex.kmerPSFM	0.439	0.021	0.357
selex.loadAnnotation	0.231	0.004	0.210
selex.mm	0.894	0.012	0.480
selex.mmProb	0.531	0.008	0.445
selex.mmSummary	0.434	0.020	0.435
selex.revcomp	0.542	0.016	0.547
selex.run	0.946	0.028	0.958
selex.sample	0.151	0.008	0.158
selex.samplePSFM	0.483	0.008	0.322
selex.sampleSummary	0.228	0.000	0.158
selex.saveAnnotation	0.124	0.000	0.113
selex.seqfilter	7.747	0.126	5.274
selex.setwd	0.139	0.000	0.071
selex.split	0.593	0.004	0.373
selex.summary	1.326	0.031	1.093