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BioC 2.13: CHECK report for dagLogo on moscato1

This page was generated on 2014-04-05 09:51:31 -0700 (Sat, 05 Apr 2014).

Package 184/750HostnameOS / ArchBUILDCHECKBUILD BIN
dagLogo 1.0.0
Jianhong Ou
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/dagLogo
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 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: dagLogo
Version: 1.0.0
Command: D:\biocbld\bbs-2.13-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings dagLogo_1.0.0.tar.gz
StartedAt: 2014-04-05 03:21:36 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:35:25 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 829.1 seconds
RetCode: 0
Status:  OK  
CheckDir: dagLogo.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/dagLogo.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 'dagLogo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dagLogo' version '1.0.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'dagLogo' can be installed ... [69s] 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
Namespace in Imports field not imported from: 'XML'
  All declared Imports should be used.
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' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'dagLogo.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ... [105s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
testDAU              13.10   0.01   13.12
buildBackgroundModel 13.09   0.01   13.40
dagLogo-package       6.91   0.11   14.20
dagLogo               6.53   0.11   13.60
dagHeatmap            6.39   0.00    6.39
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [53s]
 [54s] OK
* 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/dagLogo.Rcheck/00check.log'
for details.

dagLogo.Rcheck/00install.out:

* installing *source* package 'dagLogo' ...
** 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 (dagLogo)

dagLogo.Rcheck/dagLogo-Ex.timings:

nameusersystemelapsed
buildBackgroundModel13.09 0.0113.40
colorsets0.040.000.05
dagHeatmap6.390.006.39
dagLogo-package 6.91 0.1114.20
dagLogo 6.53 0.1113.60
ecoli.proteome0.270.000.26
fetchSequence1.170.053.51
formatSequence0.030.000.03
nameHash0.040.000.03
prepareProteome0.030.000.03
proteome.example0.120.000.12
seq.example0.060.000.06
testDAU13.10 0.0113.12