BioC 2.13: CHECK report for bgafun on moscato1

Package: bgafun

Version: 1.24.1

Command: rm -rf bgafun.buildbin-libdir && mkdir bgafun.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bgafun.buildbin-libdir bgafun_1.24.1.tar.gz >bgafun-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=bgafun.buildbin-libdir --install="check:bgafun-install.out" --force-multiarch --no-vignettes --timings bgafun_1.24.1.tar.gz && mv bgafun.buildbin-libdir/* bgafun.Rcheck/ && rmdir bgafun.buildbin-libdir

StartedAt: 2014-04-05 02:26:02 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:27:59 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 116.2 seconds

RetCode: 0

Status:  OK

CheckDir: bgafun.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/bgafun.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.24.1'
* 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
* 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'mystyle.bst'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'bgafun.rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [35s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 15.02   0.00   15.04
bgafun             5.19   0.02    5.30
** running examples for arch 'x64' ... [37s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 16.13      0   16.13
bgafun             5.98      0    6.82
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-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
** 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_1.24.1.zip
* DONE (bgafun)

name	user	system	elapsed
Calculate_Row_Weights	0.18	0.00	0.19
add_pseudo_counts	15.02	0.00	15.04
average_cols_aap	1.28	0.00	1.28
bgafun	5.19	0.02	5.30
convert_aln_AAP	1.17	0.00	1.17
convert_aln_amino	1.17	0.00	1.17
create_profile_strings	3.34	0.01	3.35
remove_gaps_groups	1.17	0.02	1.19
run_between_pca	0.94	0.00	0.94
top_residues_2_groups	3.95	0.00	4.00

name	user	system	elapsed
Calculate_Row_Weights	0.2	0.0	0.2
add_pseudo_counts	16.13	0.00	16.13
average_cols_aap	1.11	0.00	1.11
bgafun	5.98	0.00	6.82
convert_aln_AAP	1.12	0.02	1.14
convert_aln_amino	1.06	0.00	1.06
create_profile_strings	3.70	0.05	3.74
remove_gaps_groups	1.17	0.00	1.17
run_between_pca	0.82	0.00	1.67
top_residues_2_groups	3.70	0.01	3.71