BioC 3.1: CHECK report for SELEX on morelia

Package: SELEX

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.0.0.tar.gz

StartedAt: 2015-10-09 06:09:06 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:10:56 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 110.2 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/SELEX.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [7s/7s] 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 ... [52s/34s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           20.870  2.770  13.340
selex.seqfilter  6.449  0.642   4.002
* 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-3.1-bioc/meat/SELEX.Rcheck/00check.log’
for details.

* installing *source* package ‘SELEX’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (SELEX)

name	user	system	elapsed
SELEX	20.87	2.77	13.34
selex.affinities	1.469	0.079	0.731
selex.config	0.171	0.004	0.115
selex.countSummary	1.009	0.087	0.691
selex.counts	1.036	0.119	0.955
selex.defineSample	0.308	0.045	0.198
selex.exampledata	0.108	0.008	0.109
selex.fastqPSFM	0.892	0.070	0.558
selex.getAttributes	0.136	0.006	0.136
selex.getRound0	0.243	0.010	0.211
selex.getSeqfilter	0.199	0.003	0.111
selex.infogain	1.704	0.138	1.275
selex.infogainSummary	0.575	0.088	0.591
selex.jvmStatus	0.146	0.008	0.154
selex.kmax	1.197	0.336	1.234
selex.kmerPSFM	0.429	0.067	0.392
selex.loadAnnotation	0.236	0.009	0.231
selex.mm	0.717	0.046	0.547
selex.mmProb	0.461	0.049	0.484
selex.mmSummary	0.548	0.042	0.518
selex.revcomp	0.907	0.034	0.750
selex.run	1.074	0.086	1.080
selex.sample	0.181	0.008	0.159
selex.samplePSFM	0.514	0.012	0.358
selex.sampleSummary	0.254	0.012	0.185
selex.saveAnnotation	0.193	0.030	0.154
selex.seqfilter	6.449	0.642	4.002
selex.setwd	0.153	0.003	0.070
selex.split	0.624	0.098	0.448
selex.summary	1.209	0.144	1.267