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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LowMACA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings LowMACA_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/LowMACA.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 'LowMACA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LowMACA' version '1.24.0'
* 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 'LowMACA' 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 ... 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 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
allPfamAnalysis   190.12   3.01  205.05
lfmSingleSequence 102.19   1.73  109.94
setup              23.12   0.16   63.47
LowMACA-class      15.49   0.48   30.43
LowMACA-package    11.66   0.13   18.44
getMutations        7.61   0.00   10.88
alignSequences      3.33   0.13   21.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
allPfamAnalysis   141.72   3.13  157.01
lfmSingleSequence  77.95   1.59   85.37
setup              16.45   0.14   47.50
LowMACA-class      13.05   0.25   25.46
LowMACA-package     9.22   0.12   16.11
getMutations        4.64   0.00    9.98
alignSequences      3.33   0.14   19.10
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/LowMACA_1.24.0.tar.gz && rm -rf LowMACA.buildbin-libdir && mkdir LowMACA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LowMACA.buildbin-libdir LowMACA_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL LowMACA_1.24.0.zip && rm LowMACA_1.24.0.tar.gz LowMACA_1.24.0.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
  1  110k    1  1139    0     0  13794      0  0:00:08 --:--:--  0:00:08 13722
100  110k  100  110k    0     0   575k      0 --:--:-- --:--:-- --:--:--  574k

install for i386

* installing *source* package 'LowMACA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LowMACA'
    finding HTML links ... done
    BLOSUM62                                html  
    LowMACA-class                           html  
    LowMACA-package                         html  
    LowMACA_AML                             html  
    alignSequences                          html  
    allPfamAnalysis                         html  
    bpAll                                   html  
    entropy                                 html  
    getMutations                            html  
    lfm                                     html  
    lfmSingleSequence                       html  
    lmAlignment                             html  
    lmEntropy                               html  
    lmMutations                             html  
    lmObj                                   html  
    lmParams                                html  
    lmPlot                                  html  
    lmPlotSingleSequence                    html  
    mapMutations                            html  
    newLowMACA                              html  
    nullProfile                             html  
    parallelize                             html  
    protter                                 html  
    setup                                   html  
    showTumorType                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
** testing if installed package can be loaded from final location
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'LowMACA' ...
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* MD5 sums
packaged installation of 'LowMACA' as LowMACA_1.24.0.zip
* DONE (LowMACA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'LowMACA' successfully unpacked and MD5 sums checked