BioC 3.3: CHECK report for SELEX on oaxaca

Package: SELEX

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.4.0.tar.gz

StartedAt: 2016-10-13 06:11:03 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:13:21 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 137.3 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SELEX.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.0’
* 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           25.102  2.223  16.082
selex.seqfilter  7.635  0.379   4.812
* 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-3.3-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	25.102	2.223	16.082
selex.affinities	1.499	0.037	0.963
selex.config	0.252	0.006	0.166
selex.countSummary	1.387	0.032	0.940
selex.counts	1.286	0.034	1.164
selex.defineSample	0.292	0.012	0.173
selex.exampledata	0.299	0.009	0.158
selex.fastqPSFM	0.668	0.020	0.525
selex.getAttributes	0.404	0.014	0.232
selex.getRound0	0.365	0.012	0.303
selex.getSeqfilter	0.248	0.005	0.147
selex.infogain	1.804	0.053	1.626
selex.infogainSummary	1.195	0.041	0.758
selex.jvmStatus	0.130	0.004	0.133
selex.kmax	1.528	0.338	1.603
selex.kmerPSFM	0.462	0.061	0.462
selex.loadAnnotation	0.279	0.012	0.280
selex.mm	0.872	0.025	0.717
selex.mmProb	0.607	0.022	0.612
selex.mmSummary	0.770	0.023	0.657
selex.revcomp	1.017	0.029	0.852
selex.run	1.594	0.050	1.570
selex.sample	0.251	0.012	0.250
selex.samplePSFM	0.680	0.017	0.475
selex.sampleSummary	0.295	0.010	0.226
selex.saveAnnotation	0.191	0.011	0.189
selex.seqfilter	7.635	0.379	4.812
selex.setwd	0.241	0.009	0.118
selex.split	0.762	0.024	0.528
selex.summary	1.551	0.045	1.527