Package: ReQON

Version: 1.29.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReQON.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ReQON_1.29.0.tar.gz

StartedAt: 2019-04-09 05:20:17 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:22:56 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 159.5 seconds

RetCode: 0

Status:  OK

CheckDir: ReQON.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReQON.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ReQON_1.29.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ReQON.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ReQON/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReQON' version '1.29.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ReQON' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Rsamtools' 'seqbias'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FWSEplot: no visible global function definition for 'title'
FWSEplot: no visible global function definition for 'rgb'
FWSEplot: no visible global function definition for 'points'
QualFreqPlot: no visible global function definition for 'title'
ReQON: no visible global function definition for 'glm.fit'
ReQON: no visible global function definition for 'binomial'
ReadPosErrorPlot: no visible global function definition for 'title'
Undefined global functions or variables:
  binomial glm.fit points rgb title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "points", "title")
  importFrom("stats", "binomial", "glm.fit")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
ReQON 20.17   1.71   22.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
ReQON 38.77   2.28   20.29
* 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-3.9-bioc/meat/ReQON.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ReQON_1.29.0.tar.gz && rm -rf ReQON.buildbin-libdir && mkdir ReQON.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReQON.buildbin-libdir ReQON_1.29.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ReQON_1.29.0.zip && rm ReQON_1.29.0.tar.gz ReQON_1.29.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 1145k  100 1145k    0     0  5038k      0 --:--:-- --:--:-- --:--:-- 5208k

install for i386

* installing *source* package 'ReQON' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ReQON'
    finding HTML links ... done
    FWSEplot                                html  
    QualFreqPlot                            html  
    ReQON                                   html  
    ReadPosErrorPlot                        html  
** 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

install for x64

* installing *source* package 'ReQON' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReQON' as ReQON_1.29.0.zip
* DONE (ReQON)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ReQON' successfully unpacked and MD5 sums checked