Package: SELEX

Version: 1.10.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SELEX_1.10.0.tar.gz

StartedAt: 2018-04-12 02:49:00 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:50:38 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 97.7 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SELEX_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SELEX.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 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           28.740  2.876  11.121
selex.seqfilter  9.296  0.580   3.195
* 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-3.6-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	28.740	2.876	11.121
selex.affinities	0.896	0.196	0.763
selex.config	0.156	0.032	0.108
selex.countSummary	1.088	0.160	0.654
selex.counts	1.828	0.212	0.923
selex.defineSample	0.116	0.044	0.102
selex.exampledata	0.096	0.052	0.096
selex.fastqPSFM	0.712	0.060	0.427
selex.getAttributes	0.164	0.068	0.160
selex.getRound0	0.188	0.040	0.192
selex.getSeqfilter	0.332	0.052	0.112
selex.infogain	2.692	0.520	1.596
selex.infogainSummary	0.596	0.152	0.581
selex.jvmStatus	0.116	0.040	0.155
selex.kmax	1.244	0.456	1.262
selex.kmerPSFM	0.568	0.156	0.462
selex.loadAnnotation	0.532	0.064	0.278
selex.mm	0.604	0.168	0.644
selex.mmProb	0.356	0.156	0.430
selex.mmSummary	0.352	0.140	0.436
selex.revcomp	1.088	0.168	0.871
selex.run	2.272	0.444	1.248
selex.sample	0.220	0.060	0.208
selex.samplePSFM	0.412	0.048	0.316
selex.sampleSummary	0.168	0.072	0.159
selex.saveAnnotation	0.056	0.072	0.127
selex.seqfilter	9.296	0.580	3.195
selex.setwd	0.228	0.044	0.088
selex.split	0.784	0.128	0.358
selex.summary	1.032	0.352	1.069