BioC 3.2: CHECK report for SELEX on perceval

Package: SELEX

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.2.0.tar.gz

StartedAt: 2015-11-10 09:20:47 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:23:17 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 149.6 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 --no-vignettes --timings SELEX_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SELEX.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.2.0’
* 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 ... [10s/10s] 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 ... OK
* 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 ... [83s/47s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           33.034  3.643  17.639
selex.seqfilter 10.902  0.639   5.340
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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	33.034	3.643	17.639
selex.affinities	2.358	0.088	0.982
selex.config	0.302	0.008	0.155
selex.countSummary	1.516	0.074	0.986
selex.counts	1.932	0.070	1.260
selex.defineSample	0.331	0.014	0.166
selex.exampledata	0.194	0.012	0.143
selex.fastqPSFM	1.256	0.045	0.760
selex.getAttributes	0.264	0.013	0.228
selex.getRound0	0.393	0.017	0.316
selex.getSeqfilter	0.265	0.008	0.141
selex.infogain	2.600	0.098	1.680
selex.infogainSummary	1.493	0.077	0.974
selex.jvmStatus	0.138	0.006	0.143
selex.kmax	1.962	0.540	1.900
selex.kmerPSFM	0.563	0.101	0.555
selex.loadAnnotation	0.289	0.018	0.284
selex.mm	1.259	0.042	0.706
selex.mmProb	0.643	0.033	0.640
selex.mmSummary	1.258	0.045	0.719
selex.revcomp	1.964	0.054	0.960
selex.run	2.048	0.077	1.573
selex.sample	0.273	0.019	0.260
selex.samplePSFM	0.564	0.025	0.447
selex.sampleSummary	0.376	0.018	0.261
selex.saveAnnotation	0.188	0.013	0.187
selex.seqfilter	10.902	0.639	5.340
selex.setwd	0.225	0.023	0.110
selex.split	1.433	0.058	0.577
selex.summary	2.079	0.076	1.641