Multiple platform build/check report for BioC 3.6 - CHECK report for bgafun on tokay1

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### Running command:
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###   rm -rf bgafun.buildbin-libdir bgafun.Rcheck && mkdir bgafun.buildbin-libdir bgafun.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bgafun.buildbin-libdir bgafun_1.40.0.tar.gz >bgafun.Rcheck\00install.out 2>&1 && cp bgafun.Rcheck\00install.out bgafun-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bgafun.buildbin-libdir --install="check:bgafun-install.out" --force-multiarch --no-vignettes --timings bgafun_1.40.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/bgafun.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.40.0'
* 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 'bgafun' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'ade4' 'made4' 'seqinr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
run_between_pca: no visible global function definition for 'dudi.pca'
run_between_pca: no visible global function definition for 'bca'
Undefined global functions or variables:
  bca dudi.pca
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
add_pseudo_counts  6.5   0.03    6.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
add_pseudo_counts 6.78      0    6.78
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/bgafun.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'bgafun' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'bgafun'
    finding HTML links ... done
    Calculate_Row_Weights                   html  
    Henikoff_weights                        html  
    LDH                                     html  
    LDH.aap                                 html  
    LDH.aap.ave                             html  
    LDH.amino                               html  
    LDH.amino.gapless                       html  
    LDH.amino.pseudo                        html  
    LDH.groups                              html  
    Weight_Amino                            html  
    add_pseudo_counts                       html  
    amino_counts                            html  
    average_cols_aap                        html  
    bgafun                                  html  
    calculate_pseudo                        html  
    convertAAP.package                      html  
    convert_aln_AAP                         html  
    convert_aln_amino                       html  
    convert_amino.package                   html  
    convert_seq_AAP                         html  
    convert_seq_amino                       html  
    create_colnames_AAP                     html  
    create_colnames_amino                   html  
    create_probab                           html  
    create_profile                          html  
    create_profile_strings                  html  
    pseudo_counts                           html  
    remove_gaps                             html  
    remove_gaps_groups                      html  
    run_between_pca                         html  
    sum_20_aln                              html  
    sum_20_cols                             html  
    sum_aln                                 html  
    top_residues_2_groups                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'bgafun' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bgafun' as bgafun_1.40.0.zip
* DONE (bgafun)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for bgafun on tokay1

Summary

Command output

Installation output

Tests output

Example timings