Package: SELEX

Version: 1.10.0

Command: rm -rf SELEX.buildbin-libdir SELEX.Rcheck && mkdir SELEX.buildbin-libdir SELEX.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SELEX.buildbin-libdir SELEX_1.10.0.tar.gz >SELEX.Rcheck\00install.out 2>&1 && cp SELEX.Rcheck\00install.out SELEX-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SELEX.buildbin-libdir --install="check:SELEX-install.out" --force-multiarch --no-vignettes --timings SELEX_1.10.0.tar.gz

StartedAt: 2018-04-12 03:03:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:06:27 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 194.1 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SELEX.buildbin-libdir SELEX.Rcheck && mkdir SELEX.buildbin-libdir SELEX.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SELEX.buildbin-libdir SELEX_1.10.0.tar.gz >SELEX.Rcheck\00install.out 2>&1 && cp SELEX.Rcheck\00install.out SELEX-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SELEX.buildbin-libdir --install="check:SELEX-install.out" --force-multiarch --no-vignettes --timings SELEX_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SELEX.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SELEX/DESCRIPTION' ... OK
* this is package 'SELEX' version '1.10.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SELEX           10.72   4.50   14.95
selex.seqfilter  3.92   2.83    6.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SELEX           34.32   6.20   15.55
selex.seqfilter 13.77   2.34    7.01
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/SELEX.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SELEX' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SELEX'
    finding HTML links ... done
    SELEX                                   html  
    selex.affinities                        html  
    selex.config                            html  
    selex.countSummary                      html  
    selex.counts                            html  
    selex.defineSample                      html  
    selex.exampledata                       html  
    selex.fastqPSFM                         html  
    selex.getAttributes                     html  
    selex.getRound0                         html  
    selex.getSeqfilter                      html  
    selex.infogain                          html  
    selex.infogainSummary                   html  
    selex.jvmStatus                         html  
    selex.kmax                              html  
    selex.kmerPSFM                          html  
    selex.loadAnnotation                    html  
    selex.mm                                html  
    selex.mmProb                            html  
    selex.mmSummary                         html  
    selex.revcomp                           html  
    selex.run                               html  
    selex.sample                            html  
    selex.samplePSFM                        html  
    selex.sampleSummary                     html  
    selex.saveAnnotation                    html  
    selex.seqfilter                         html  
    selex.setwd                             html  
    selex.split                             html  
    selex.summary                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SELEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SELEX' as SELEX_1.10.0.zip
* DONE (SELEX)
In R CMD INSTALL
In R CMD INSTALL