Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.13: CHECK report for bgafun on perceval

This page was generated on 2014-04-05 09:52:01 -0700 (Sat, 05 Apr 2014).

Package 69/750HostnameOS / ArchBUILDCHECKBUILD BIN
bgafun 1.24.1
Iain Wallace
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/bgafun
Last Changed Rev: 83852 / Revision: 88450
Last Changed Date: 2013-12-03 10:06:58 -0800 (Tue, 03 Dec 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: bgafun
Version: 1.24.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bgafun_1.24.1.tar.gz
StartedAt: 2014-04-04 23:41:00 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:42:16 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 76.1 seconds
RetCode: 0
Status:  OK 
CheckDir: bgafun.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/bgafun.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bgafun’ can be installed ... [2s/2s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [42s/44s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
add_pseudo_counts 18.804   0.10  20.113
bgafun             6.238   0.17   6.508
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/bgafun.Rcheck/00check.log’
for details.

bgafun.Rcheck/00install.out:

* 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
* DONE (bgafun)

bgafun.Rcheck/bgafun-Ex.timings:

nameusersystemelapsed
Calculate_Row_Weights0.3660.0130.385
add_pseudo_counts18.804 0.10020.113
average_cols_aap1.2280.0241.256
bgafun6.2380.1706.508
convert_aln_AAP1.1860.0191.298
convert_aln_amino1.0460.0621.202
create_profile_strings4.3830.1694.926
remove_gaps_groups1.1430.0551.306
run_between_pca1.0560.0481.146
top_residues_2_groups4.4200.1694.661