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BioC 3.3: CHECK report for bgafun on moscato2

This page was generated on 2016-10-13 12:48:23 -0700 (Thu, 13 Oct 2016).

Package 90/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgafun 1.34.0
Iain Wallace
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/bgafun
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bgafun
Version: 1.34.0
Command: rm -rf bgafun.buildbin-libdir bgafun.Rcheck && mkdir bgafun.buildbin-libdir bgafun.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bgafun.buildbin-libdir bgafun_1.34.0.tar.gz >bgafun.Rcheck\00install.out 2>&1 && cp bgafun.Rcheck\00install.out bgafun-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=bgafun.buildbin-libdir --install="check:bgafun-install.out" --force-multiarch --no-vignettes --timings bgafun_1.34.0.tar.gz
StartedAt: 2016-10-13 01:18:41 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:20:41 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 120.1 seconds
RetCode: 0
Status:  OK  
CheckDir: bgafun.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bgafun.buildbin-libdir bgafun.Rcheck && mkdir bgafun.buildbin-libdir bgafun.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bgafun.buildbin-libdir bgafun_1.34.0.tar.gz >bgafun.Rcheck\00install.out 2>&1 && cp bgafun.Rcheck\00install.out bgafun-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=bgafun.buildbin-libdir --install="check:bgafun-install.out" --force-multiarch --no-vignettes --timings bgafun_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/bgafun.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.34.0'
* 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 13.68      0   13.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 16.61   0.01   16.63
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/bgafun.Rcheck/00check.log'
for details.


bgafun.Rcheck/00install.out:


install for i386

* installing *source* package 'bgafun' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'bgafun' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bgafun' as bgafun_1.34.0.zip
* DONE (bgafun)

bgafun.Rcheck/examples_i386/bgafun-Ex.timings:

nameusersystemelapsed
Calculate_Row_Weights0.150.030.19
add_pseudo_counts13.68 0.0013.68
average_cols_aap1.110.001.11
bgafun3.820.013.84
convert_aln_AAP0.880.000.87
convert_aln_amino0.430.020.45
create_profile_strings2.750.012.76
remove_gaps_groups0.750.020.76
run_between_pca0.830.030.86
top_residues_2_groups3.010.023.03

bgafun.Rcheck/examples_x64/bgafun-Ex.timings:

nameusersystemelapsed
Calculate_Row_Weights0.320.000.31
add_pseudo_counts16.61 0.0116.63
average_cols_aap1.10.01.1
bgafun4.290.004.29
convert_aln_AAP1.020.001.02
convert_aln_amino0.950.000.95
create_profile_strings3.770.003.77
remove_gaps_groups1.020.021.03
run_between_pca0.810.010.83
top_residues_2_groups2.930.022.95