BioC 3.3: CHECK report for SELEX on linux2.bioconductor.org

Package: SELEX

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SELEX_1.3.0.tar.gz

StartedAt: 2015-10-27 07:54:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:56:21 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 93.0 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_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SELEX.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.3.0’
* 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 ... [5s/5s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/29s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           22.114  0.673  11.650
selex.seqfilter  7.607  0.150   3.367
* 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
  ‘/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	22.114	0.673	11.650
selex.affinities	1.199	0.016	0.752
selex.config	0.135	0.000	0.074
selex.countSummary	1.014	0.012	0.610
selex.counts	1.425	0.012	1.084
selex.defineSample	0.158	0.004	0.135
selex.exampledata	0.132	0.004	0.118
selex.fastqPSFM	0.822	0.009	0.554
selex.getAttributes	0.131	0.004	0.105
selex.getRound0	0.218	0.000	0.157
selex.getSeqfilter	0.129	0.000	0.063
selex.infogain	1.363	0.036	1.143
selex.infogainSummary	0.568	0.016	0.564
selex.jvmStatus	0.079	0.000	0.078
selex.kmax	0.872	0.076	0.767
selex.kmerPSFM	0.375	0.012	0.277
selex.loadAnnotation	0.163	0.004	0.151
selex.mm	0.507	0.008	0.382
selex.mmProb	0.307	0.008	0.309
selex.mmSummary	0.347	0.008	0.346
selex.revcomp	0.482	0.016	0.468
selex.run	0.926	0.012	0.905
selex.sample	0.109	0.008	0.117
selex.samplePSFM	0.347	0.012	0.266
selex.sampleSummary	0.158	0.000	0.111
selex.saveAnnotation	0.104	0.013	0.104
selex.seqfilter	7.607	0.150	3.367
selex.setwd	0.101	0.000	0.047
selex.split	0.729	0.004	0.311
selex.summary	1.478	0.032	1.224