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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings REDseq_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/REDseq.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'REDseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REDseq' version '1.40.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'BSgenome.Celegans.UCSC.ce2', 'multtest',
  'Biostrings', 'BSgenome', 'ChIPpeakAnno'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'REDseq' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildREmap: no visible global function definition for 'start<-'
Undefined global functions or variables:
  start<-
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
buildREmap 7.83   0.11   10.85
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
buildREmap 5.79   0.08    5.87
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/REDseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/REDseq_1.40.0.tar.gz && rm -rf REDseq.buildbin-libdir && mkdir REDseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=REDseq.buildbin-libdir REDseq_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL REDseq_1.40.0.zip && rm REDseq_1.40.0.tar.gz REDseq_1.40.0.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 30794  100 30794    0     0   256k      0 --:--:-- --:--:-- --:--:--  259k

install for i386

* installing *source* package 'REDseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** help
*** installing help indices
  converting help for package 'REDseq'
    finding HTML links ... done
    REDseq-package                          html  
    assignSeq2REsite                        html  
    binom.test.REDseq                       html  
    buildREmap                              html  
    compareREDseq                           html  
    distanceHistSeq2RE                      html  
    example.REDseq                          html  
    example.assignedREDseq                  html  
    example.map                             html  
    plotCutDistribution                     html  
    searchPattern                           html  
    summarizeByRE                           html  
    summarizeBySeq                          html  
    writeHits                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'REDseq' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
* MD5 sums
packaged installation of 'REDseq' as REDseq_1.40.0.zip
* DONE (REDseq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'REDseq' successfully unpacked and MD5 sums checked