Package: OrderedList

Version: 1.56.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OrderedList.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OrderedList_1.56.0.tar.gz

StartedAt: 2019-10-16 05:45:36 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:46:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 62.8 seconds

RetCode: 0

Status:  OK

CheckDir: OrderedList.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:OrderedList.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OrderedList_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/OrderedList.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OrderedList/DESCRIPTION' ... OK
* this is package 'OrderedList' version '1.56.0'
* 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 'OrderedList' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'methods' 'twilight'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.OrderedList plot.listComparison plot.listComparisonOverlap
  plot.shuffledRandomScores print.OrderedList print.listComparison
  print.listComparisonOverlap print.shuffledRandomScores
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'OrderedList/R/a.R':
  .First.lib has wrong argument list 'libname, pkgname, where'

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
See section 'Good practice' in '?.onAttach'.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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/OrderedList.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/OrderedList_1.56.0.tar.gz && rm -rf OrderedList.buildbin-libdir && mkdir OrderedList.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OrderedList.buildbin-libdir OrderedList_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL OrderedList_1.56.0.zip && rm OrderedList_1.56.0.tar.gz OrderedList_1.56.0.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  490k  100  490k    0     0  4867k      0 --:--:-- --:--:-- --:--:-- 5219k

install for i386

* installing *source* package 'OrderedList' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OrderedList'
    finding HTML links ... done
    OL.data                                 html  
    OL.result                               html  
    OrderedList                             html  
    check.test.args                         html  
    compareLists                            html  
    getOverlap                              html  
    overlap                                 html  
    plot.OrderedList                        html  
    prepareData                             html  
    preparePermutations                     html  
    print.OrderedList                       html  
    scoreOrderComparison                    html  
    scoreRankings                           html  
    shuffledRandomScores                    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 'OrderedList' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OrderedList' as OrderedList_1.56.0.zip
* DONE (OrderedList)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'OrderedList' successfully unpacked and MD5 sums checked