BioC 3.2: CHECK report for SELEX on perceval

Package: SELEX

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.1.0.tar.gz

StartedAt: 2015-08-24 05:01:23 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:04:12 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 169.7 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_1.1.0.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 (2015-08-14 r69078)
* 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 ‘1.1.0’
* 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 ... [12s/12s] 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 ... [76s/52s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           29.721  3.870  20.165
selex.seqfilter 10.675  0.739   6.635
* 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	29.721	3.870	20.165
selex.affinities	1.576	0.069	1.124
selex.config	0.202	0.005	0.160
selex.countSummary	1.579	0.064	1.107
selex.counts	1.768	0.074	1.373
selex.defineSample	0.282	0.020	0.166
selex.exampledata	0.223	0.016	0.167
selex.fastqPSFM	1.214	0.057	0.803
selex.getAttributes	0.244	0.014	0.235
selex.getRound0	0.362	0.021	0.331
selex.getSeqfilter	0.218	0.006	0.148
selex.infogain	2.372	0.109	1.761
selex.infogainSummary	1.231	0.072	1.073
selex.jvmStatus	0.139	0.015	0.153
selex.kmax	1.831	0.578	2.090
selex.kmerPSFM	0.590	0.109	0.612
selex.loadAnnotation	0.276	0.021	0.280
selex.mm	0.977	0.044	0.742
selex.mmProb	0.685	0.042	0.660
selex.mmSummary	0.903	0.049	0.748
selex.revcomp	1.181	0.056	0.991
selex.run	1.773	0.088	1.669
selex.sample	0.265	0.020	0.266
selex.samplePSFM	0.433	0.025	0.378
selex.sampleSummary	0.296	0.023	0.261
selex.saveAnnotation	0.177	0.017	0.196
selex.seqfilter	10.675	0.739	6.635
selex.setwd	0.210	0.017	0.113
selex.split	0.971	0.062	0.611
selex.summary	1.925	0.083	1.705