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CHECK report for bgafun on tokay2

This page was generated on 2019-10-16 12:21:29 -0400 (Wed, 16 Oct 2019).

Package 127/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgafun 1.46.0
Iain Wallace
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/bgafun
Branch: RELEASE_3_9
Last Commit: 0e02f64
Last Changed Date: 2019-05-02 11:53:08 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bgafun
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bgafun.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings bgafun_1.46.0.tar.gz
StartedAt: 2019-10-16 02:08:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:10:10 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 72.8 seconds
RetCode: 0
Status:  OK  
CheckDir: bgafun.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bgafun.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings bgafun_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/bgafun.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.46.0'
* 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
* 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 ... 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 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 6.73      0    6.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 11.11   0.02   11.12
* 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-3.9-bioc/meat/bgafun.Rcheck/00check.log'
for details.



Installation output

bgafun.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bgafun_1.46.0.tar.gz && rm -rf bgafun.buildbin-libdir && mkdir bgafun.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bgafun.buildbin-libdir bgafun_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bgafun_1.46.0.zip && rm bgafun_1.46.0.tar.gz bgafun_1.46.0.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  157k  100  157k    0     0  1073k      0 --:--:-- --:--:-- --:--:-- 1126k

install for i386

* installing *source* package 'bgafun' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 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 'bgafun' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bgafun' as bgafun_1.46.0.zip
* DONE (bgafun)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'bgafun' successfully unpacked and MD5 sums checked

Tests output


Example timings

bgafun.Rcheck/examples_i386/bgafun-Ex.timings

nameusersystemelapsed
Calculate_Row_Weights0.090.020.11
add_pseudo_counts6.730.006.73
average_cols_aap0.330.000.33
bgafun2.930.053.00
convert_aln_AAP0.610.020.63
convert_aln_amino0.390.010.40
create_profile_strings2.300.072.36
remove_gaps_groups0.440.010.45
run_between_pca0.560.030.60
top_residues_2_groups1.440.021.45

bgafun.Rcheck/examples_x64/bgafun-Ex.timings

nameusersystemelapsed
Calculate_Row_Weights0.110.050.15
add_pseudo_counts11.11 0.0211.12
average_cols_aap0.680.030.70
bgafun2.700.012.72
convert_aln_AAP0.370.020.39
convert_aln_amino0.270.000.26
create_profile_strings1.700.031.74
remove_gaps_groups0.260.000.26
run_between_pca0.410.020.43
top_residues_2_groups2.250.012.26