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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:branchpointer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings branchpointer_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/branchpointer.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 'branchpointer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'branchpointer' version '1.20.0'
* 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 'branchpointer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         4.1Mb
    extdata   1.1Mb
* 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 ... OK
* 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 R/sysdata.rda ... 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
makeBranchpointWindowForSNP 10.18   0.44   13.39
plotBranchpointWindow        5.03   0.38    5.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeBranchpointWindowForSNP 9.11   0.13   11.53
plotBranchpointWindow       5.21   0.06    5.28
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/branchpointer.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/branchpointer_1.20.0.tar.gz && rm -rf branchpointer.buildbin-libdir && mkdir branchpointer.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=branchpointer.buildbin-libdir branchpointer_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL branchpointer_1.20.0.zip && rm branchpointer_1.20.0.tar.gz branchpointer_1.20.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 26 4716k   26 1240k    0     0  1193k      0  0:00:03  0:00:01  0:00:02 1193k
 73 4716k   73 3451k    0     0  1689k      0  0:00:02  0:00:02 --:--:-- 1690k
100 4716k  100 4716k    0     0  1887k      0  0:00:02  0:00:02 --:--:-- 1887k

install for i386

* installing *source* package 'branchpointer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'branchpointer'
    finding HTML links ... done
    exonsToIntrons                          html  
    getBranchpointSequence                  html  
    getCanonical3SS                         html  
    getExonDists                            html  
    getPPT                                  html  
    getQueryLoc                             html  
    gtfToExons                              html  
    makeBranchpointWindowForExons           html  
    makeBranchpointWindowForSNP             html  
    plotBranchpointWindow                   html  
    plotStructure                           html  
    predictBranchpoints                     html  
    predictionsToSummary                    html  
    readQueryFile                           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 'branchpointer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'branchpointer' as branchpointer_1.20.0.zip
* DONE (branchpointer)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'branchpointer' successfully unpacked and MD5 sums checked