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BioC 3.0: CHECK report for bgafun on moscato1

This page was generated on 2015-04-10 09:45:00 -0700 (Fri, 10 Apr 2015).

Package 78/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgafun 1.28.0
Iain Wallace
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/bgafun
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: bgafun
Version: 1.28.0
Command: rm -rf bgafun.buildbin-libdir bgafun.Rcheck && mkdir bgafun.buildbin-libdir bgafun.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bgafun.buildbin-libdir bgafun_1.28.0.tar.gz >bgafun.Rcheck\00install.out 2>&1 && cp bgafun.Rcheck\00install.out bgafun-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=bgafun.buildbin-libdir --install="check:bgafun-install.out" --force-multiarch --no-vignettes --timings bgafun_1.28.0.tar.gz
StartedAt: 2015-04-09 22:53:57 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:55:45 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 108.2 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bgafun.buildbin-libdir bgafun_1.28.0.tar.gz >bgafun.Rcheck\00install.out 2>&1 && cp bgafun.Rcheck\00install.out bgafun-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=bgafun.buildbin-libdir --install="check:bgafun-install.out" --force-multiarch --no-vignettes --timings bgafun_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/bgafun.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.28.0'
* 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 ... 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
** 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'
* 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' ... [28s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 13.31      0    13.3
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 15.32      0   15.32
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.28.0.zip
* DONE (bgafun)

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

nameusersystemelapsed
Calculate_Row_Weights0.170.010.19
add_pseudo_counts13.31 0.0013.30
average_cols_aap0.890.020.91
bgafun4.260.004.29
convert_aln_AAP0.880.000.89
convert_aln_amino0.910.000.90
create_profile_strings2.540.002.54
remove_gaps_groups1.020.001.02
run_between_pca0.760.000.76
top_residues_2_groups2.590.022.61

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

nameusersystemelapsed
Calculate_Row_Weights0.250.000.25
add_pseudo_counts15.32 0.0015.32
average_cols_aap0.930.000.94
bgafun4.390.034.41
convert_aln_AAP0.90.01.9
convert_aln_amino0.920.000.93
create_profile_strings4.280.014.29
remove_gaps_groups1.070.001.07
run_between_pca0.920.020.94
top_residues_2_groups3.590.033.62