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Package 45/294HostnameOS / ArchBUILDCHECKBUILD BIN
biomaRt 1.16.0
Steffen Durinck
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/biomaRt
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: biomaRt
Version: 1.16.0
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes biomaRt_1.16.0.tar.gz
StartedAt: 2009-04-18 18:20:30 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:21:08 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 38.5 seconds
RetCode: 0
Status: OK
CheckDir: biomaRt.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/biomaRt.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '1.16.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'biomaRt' 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 ... NOTE
getBM: no visible global function definition for 'dbGetQuery'
getHomolog: no visible global function definition for 'dbGetQuery'
getSequence: no visible global function definition for 'dbConnect'
getSequence: no visible global function definition for 'dbGetQuery'
getSNP: no visible global function definition for 'dbGetQuery'
listDatasets: no visible global function definition for 'dbGetQuery'
listMarts: no visible global function definition for 'dbDriver'
listMarts: no visible global function definition for 'dbConnect'
listMarts: no visible global function definition for 'dbGetQuery'
listMarts: no visible global function definition for 'dbDisconnect'
martDisconnect: no visible global function definition for
  'dbDisconnect'
useDataset: no visible global function definition for 'dbGetQuery'
useMart: no visible global function definition for 'dbDriver'
useMart: no visible global function definition for 'dbConnect'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating biomaRt-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating biomaRt-manual.tex ... OK
* checking biomaRt-manual.tex using pdflatex ... OK

biomaRt.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/biomaRt.Rcheck


---------- Making package biomaRt ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  preparing package biomaRt for lazy loading
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'biomaRt'
     Formats: text html latex example chm 
  Mart-class                        text    html    latex           chm
  attributeSummary                  text    html    latex   example chm
  exportFASTA                       text    html    latex   example chm
  filterOptions                     text    html    latex   example chm
  filterSummary                     text    html    latex   example chm
  filterType                        text    html    latex   example chm
  getAffyArrays                     text    html    latex   example chm
  getBM                             text    html    latex   example chm
  getGO                             text    html    latex   example chm
  getGene                           text    html    latex   example chm
  getHomolog                        text    html    latex   example chm
  getLDS                            text    html    latex   example chm
  getSNP                            text    html    latex   example chm
  getSequence                       text    html    latex   example chm
  listAttributes                    text    html    latex   example chm
  listDatasets                      text    html    latex   example chm
  listFilters                       text    html    latex   example chm
Note: removing empty section \seealso in file 'listMarts.Rd'
Note: removing empty section \seealso in file 'listMarts.Rd'
  listMarts                         text    html    latex   example chm
  martDisconnect                    text    html    latex   example chm
  parseAttributes                   text    html    latex           chm
  parseFilters                      text    html    latex           chm
  useDataset                        text    html    latex   example chm
  useMart                           text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm


Compile time: 0 minutes, 0 seconds
24	Topics
47	Local links
9	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm, 34,656 bytes
Compression decreased file by 29,387 bytes.
  adding MD5 sums

* DONE (biomaRt)