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CHECK report for ReQON on tokay2

This page was generated on 2018-10-17 08:35:52 -0400 (Wed, 17 Oct 2018).

Package 1223/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReQON 1.26.0
Christopher Cabanski
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ReQON
Branch: RELEASE_3_7
Last Commit: 57a5a21
Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ReQON
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReQON.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ReQON_1.26.0.tar.gz
StartedAt: 2018-10-17 04:21:43 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:24:32 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 169.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ReQON.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReQON.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ReQON_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ReQON.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.26.0'
* 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 24.86   1.28    26.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
ReQON 45.16   1.69   26.36
* 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-3.7-bioc/meat/ReQON.Rcheck/00check.log'
for details.



Installation output

ReQON.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ReQON_1.26.0.tar.gz && rm -rf ReQON.buildbin-libdir && mkdir ReQON.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReQON.buildbin-libdir ReQON_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ReQON_1.26.0.zip && rm ReQON_1.26.0.tar.gz ReQON_1.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1145k  100 1145k    0     0  15.5M      0 --:--:-- --:--:-- --:--:-- 17.2M

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
In R CMD INSTALL

install for x64

* installing *source* package 'ReQON' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReQON' as ReQON_1.26.0.zip
* DONE (ReQON)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ReQON' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

ReQON.Rcheck/examples_i386/ReQON-Ex.timings

nameusersystemelapsed
FWSEplot0.010.000.01
QualFreqPlot0.030.000.03
ReQON24.86 1.2826.80
ReadPosErrorPlot000

ReQON.Rcheck/examples_x64/ReQON-Ex.timings

nameusersystemelapsed
FWSEplot0.020.000.01
QualFreqPlot0.030.000.03
ReQON45.16 1.6926.36
ReadPosErrorPlot000