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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RIPAT_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RIPAT.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RIPAT/DESCRIPTION' ... OK
* this is package 'RIPAT' version '1.0.0'
* package encoding: UTF-8
* 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 'RIPAT' 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
annoByCpG: no visible global function definition for 'hist'
annoByCpG: no visible binding for global variable 'Range'
annoByCpG: no visible binding for global variable 'Freq'
annoByCpG: no visible binding for global variable 'Group'
annoByGene: no visible global function definition for 'hist'
annoByGene: no visible binding for global variable 'Range'
annoByGene: no visible binding for global variable 'Freq'
annoByGene: no visible binding for global variable 'Group'
annoByRepeat: no visible global function definition for 'hist'
annoByRepeat: no visible binding for global variable 'all_dist_dup_m'
annoByRepeat: no visible binding for global variable 'Range'
annoByRepeat: no visible binding for global variable 'Freq'
annoByRepeat: no visible binding for global variable 'Group'
annoByVar: no visible global function definition for 'hist'
annoByVar: no visible binding for global variable 'Range'
annoByVar: no visible binding for global variable 'Freq'
annoByVar: no visible binding for global variable 'Group'
makeDocument : <anonymous>: no visible global function definition for
  'hist'
makeDocument: no visible binding for global variable 'group'
makeDocument: no visible binding for global variable 'type'
makeDocument: no visible binding for global variable 'convert_p'
makeDocument: no visible global function definition for 'par'
Undefined global functions or variables:
  Freq Group Range all_dist_dup_m convert_p group hist par type
Consider adding
  importFrom("graphics", "hist", "par")
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 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
drawingKaryo 9.27   1.03   11.86
makeData     9.66   0.19   11.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
drawingKaryo 14.07   0.42   16.03
makeData     12.16   0.19   14.06
annoByCpG     6.92   0.25    7.17
* 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-3.12-bioc/meat/RIPAT.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RIPAT_1.0.0.tar.gz && rm -rf RIPAT.buildbin-libdir && mkdir RIPAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPAT.buildbin-libdir RIPAT_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RIPAT_1.0.0.zip && rm RIPAT_1.0.0.tar.gz RIPAT_1.0.0.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 2808k    0 11435    0     0  24820      0  0:01:55 --:--:--  0:01:55 24804
100 2808k  100 2808k    0     0  4262k      0 --:--:-- --:--:-- --:--:-- 4261k

install for i386

* installing *source* package 'RIPAT' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RIPAT'
    finding HTML links ... done
    annoByCpG                               html  
    annoByGene                              html  
    annoByRepeat                            html  
    annoByVar                               html  
    blast_gene                              html  
    blast_obj                               html  
    cpg_exam_db                             html  
    drawingKaryo                            html  
    gene_exam_db                            html  
    makeData                                html  
    makeDocument                            html  
    makeInputObj                            html  
    makeInputObj2                           html  
    micro_exam_db                           html  
    repeat_exam_db                          html  
    tss_exam_db                             html  
    var_exam_db                             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 'RIPAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPAT' as RIPAT_1.0.0.zip
* DONE (RIPAT)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RIPAT' successfully unpacked and MD5 sums checked