Package: SELEX

Version: 1.15.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SELEX_1.15.0.tar.gz

StartedAt: 2019-04-09 03:32:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:34:33 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 120.5 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SELEX.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SELEX_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SELEX.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.0’
* 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 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           30.907  2.994  13.571
selex.seqfilter 12.109  0.700   4.577
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SELEX.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SELEX
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SELEX’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SELEX)

name	user	system	elapsed
SELEX	30.907	2.994	13.571
selex.affinities	1.092	0.210	0.854
selex.config	0.213	0.064	0.147
selex.countSummary	1.073	0.240	0.845
selex.counts	1.577	0.253	1.042
selex.defineSample	0.215	0.032	0.108
selex.exampledata	0.30	0.04	0.14
selex.fastqPSFM	1.014	0.087	0.597
selex.getAttributes	0.425	0.039	0.215
selex.getRound0	0.216	0.080	0.270
selex.getSeqfilter	0.263	0.060	0.138
selex.infogain	1.942	0.516	1.588
selex.infogainSummary	1.113	0.234	0.725
selex.jvmStatus	0.252	0.064	0.153
selex.kmax	1.479	0.498	1.280
selex.kmerPSFM	0.565	0.172	0.514
selex.loadAnnotation	0.622	0.072	0.265
selex.mm	0.769	0.209	0.642
selex.mmProb	0.630	0.160	0.633
selex.mmSummary	0.510	0.194	0.629
selex.revcomp	0.804	0.191	0.828
selex.run	2.778	0.467	1.636
selex.sample	0.241	0.067	0.239
selex.samplePSFM	0.418	0.087	0.365
selex.sampleSummary	0.190	0.081	0.230
selex.saveAnnotation	0.136	0.056	0.189
selex.seqfilter	12.109	0.700	4.577
selex.setwd	0.209	0.053	0.129
selex.split	1.316	0.157	0.569
selex.summary	1.324	0.445	1.440