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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RcisTarget.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RcisTarget_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RcisTarget.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RcisTarget/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RcisTarget' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'RcisTarget' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
* 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
Namespace in Imports field not imported from: 'feather'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertToTargetRegions: no visible global function definition for
  'isClass'
convertToTargetRegions: no visible global function definition for
  'findOverlaps'
convertToTargetRegions: no visible global function definition for
  'pintersect'
convertToTargetRegions: no visible global function definition for
  'subjectHits'
convertToTargetRegions: no visible global function definition for
  'width'
convertToTargetRegions: no visible global function definition for
  'elementMetadata'
Undefined global functions or variables:
  elementMetadata findOverlaps isClass pintersect subjectHits width
Consider adding
  importFrom("methods", "isClass")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in documentation object 'getDbRegionsLoc'
  'indexCol'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
addSignificantGenes     23.68   6.17   29.94
addMotifAnnotation      18.97   6.19   26.53
getMotifAnnotation      13.51   5.83   19.39
aucScores-class         13.28   4.95   18.23
reRank                  11.81   5.09   16.91
rankingRcisTarget-class 12.04   3.48   15.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
addSignificantGenes     17.64   0.77   18.41
addMotifAnnotation      15.53   0.56   16.06
aucScores-class         10.28   0.31   10.59
getMotifAnnotation      10.16   0.10   10.27
reRank                   9.52   0.06    9.58
rankingRcisTarget-class  8.84   0.15    9.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/RcisTarget.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/RcisTarget_1.12.0.tar.gz && rm -rf RcisTarget.buildbin-libdir && mkdir RcisTarget.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RcisTarget.buildbin-libdir RcisTarget_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RcisTarget_1.12.0.zip && rm RcisTarget_1.12.0.tar.gz RcisTarget_1.12.0.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
 13 8477k   13 1156k    0     0  2228k      0  0:00:03 --:--:--  0:00:03 2227k
 61 8477k   61 5221k    0     0  3438k      0  0:00:02  0:00:01  0:00:01 3437k
100 8477k  100 8477k    0     0  3881k      0  0:00:02  0:00:02 --:--:-- 3883k

install for i386

* installing *source* package 'RcisTarget' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RcisTarget'
    finding HTML links ... done
    RcisTarget                              html  
    finding level-2 HTML links ... done

    addLogo                                 html  
    addMotifAnnotation                      html  
    addSignificantGenes                     html  
    aucScores-class                         html  
    calcAUC                                 html  
    convertToTargetRegions                  html  
    dbRegionsLoc                            html  
    getDbRegionsLoc                         html  
    getMotifAnnotation                      html  
    importAnnotations                       html  
    importRankings                          html  
    motifAnnotations                        html  
    rankingRcisTarget-class                 html  
    reRank                                  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 'RcisTarget' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RcisTarget' as RcisTarget_1.12.0.zip
* DONE (RcisTarget)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'RcisTarget' successfully unpacked and MD5 sums checked