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BioC 3.0: CHECK report for dagLogo on moscato1

This page was generated on 2015-04-10 09:49:38 -0700 (Fri, 10 Apr 2015).

Package 218/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dagLogo 1.4.1
Jianhong Ou
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/dagLogo
Last Changed Rev: 97144 / Revision: 102249
Last Changed Date: 2014-11-26 06:47:23 -0800 (Wed, 26 Nov 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: dagLogo
Version: 1.4.1
Command: D:\biocbld\bbs-3.0-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings dagLogo_1.4.1.tar.gz
StartedAt: 2015-04-10 00:16:14 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:21:32 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 317.9 seconds
RetCode: 0
Status:  OK  
CheckDir: dagLogo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbld\bbs-3.0-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings dagLogo_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/dagLogo.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 'dagLogo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dagLogo' version '1.4.1'
* 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 ... 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 ... [30s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... [40s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
dagLogo-package 2.23   0.03     9.9
dagLogo         1.76   0.14     9.9
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [18s]
 [18s] 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
* DONE

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/dagLogo.Rcheck/00check.log'
for details.

dagLogo.Rcheck/00install.out:

* installing *source* package 'dagLogo' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'graphics::plot' when loading 'seqLogo'
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::plot' when loading 'seqLogo'
No methods found in "IRanges" for requests: sapply
* DONE (dagLogo)

dagLogo.Rcheck/dagLogo-Ex.timings:

nameusersystemelapsed
buildBackgroundModel0.760.010.78
colorsets000
dagHeatmap0.870.001.00
dagLogo-package2.230.039.90
dagLogo1.760.149.90
ecoli.proteome0.210.020.22
fetchSequence0.960.083.39
formatSequence000
nameHash000
prepareProteome000
proteome.example0.100.000.73
seq.example0.040.000.05
testDAU1.060.011.07