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Package 45/264HostnameOS / ArchBUILDCHECKBUILD BIN
BSgenome 1.7.7
H. Pages
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome
Last Changed Rev: 30778 / Revision: 30951
Last Changed Date: 2008-04-01 10:15:10 -0700 (Tue, 01 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: BSgenome
Version: 1.7.7
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check BSgenome_1.7.7.tar.gz
StartedAt: 2008-04-09 05:35:16 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 05:36:30 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 74.3 seconds
RetCode: 0
Status: WARNINGS
CheckDir: BSgenome.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/BSgenome.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.7.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BSgenome' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  available.SNPs injectSNPs SNPlocs_pkgname
Undocumented S4 methods:
  generic 'SNPlocs_pkgname' and siglist 'BSgenome'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating BSgenome-Ex.R ... OK
* checking examples ... OK
* creating BSgenome-manual.tex ... OK
* checking BSgenome-manual.tex using pdflatex ... OK

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.2-bioc/meat/BSgenome.Rcheck/00check.log
for details

BSgenome.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-bioc/meat/BSgenome.Rcheck


---------- Making package BSgenome ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  preparing package BSgenome for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: Biostrings
  installing man source files
  installing indices
  installing help
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \seealso
Note: removing empty section \examples
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \seealso
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \details
 >>> Building/Updating help pages for package 'BSgenome'
     Formats: text html latex example chm 
  BSgenome-class                    text    html    latex   example chm
  available.genomes                 text    html    latex   example chm
  buildDataFiles                    text    html    latex           chm
  getSeq                            text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.2-bioc\meat\BSgenome.Rcheck\00_pkg_src\BSgenome\chm\BSgenome.chm


Compile time: 0 minutes, 0 seconds
5	Topics
45	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.2-bioc\meat\BSgenome.Rcheck\00_pkg_src\BSgenome\chm\BSgenome.chm, 25,689 bytes
Compression decreased file by 7,950 bytes.
  adding MD5 sums

* DONE (BSgenome)