biomaRt 1.13.10
Steffen Durinck
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biomaRt | | Last Changed Rev: 30604 / Revision: 30951 | | Last Changed Date: 2008-03-20 19:35:56 -0700 (Thu, 20 Mar 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/biomaRt.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '1.13.10'
* 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 ... WARNING
Loading required package: methods
Loading required package: RCurl
Error in paste(normalizePath(file.path(libname, pkgname, "libs")), file.path(Sys.getenv("R_HOME"), :
could not find function "normalizePath"
Error : .onLoad failed in 'loadNamespace' for 'XML'
Error: package/namespace load failed for 'biomaRt'
Execution halted
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking whether the name space can be loaded with stated dependencies ... WARNING
Error in paste(normalizePath(file.path(libname, pkgname, "libs")), file.path(Sys.getenv("R_HOME"), :
could not find function "normalizePath"
Error: .onLoad failed in 'loadNamespace' for 'XML'
Execution halted
A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking for unstated dependencies in R code ... WARNING
Error: package/namespace load failed for 'biomaRt'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
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 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' ... WARNING
*** Weave Errors ***
File E:/biocbld/bbs-2.2-bioc/meat/biomaRt.Rcheck/inst/doc/biomaRt.Rnw :
Error : chunk 8
Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2", :
Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report.
*** Source Errors ***
File E:/biocbld/bbs-2.2-bioc/meat/biomaRt.Rcheck/inst/doc/biomaRt.R :
Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2", :
Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report.
* creating biomaRt-manual.tex ... OK
* checking biomaRt-manual.tex using pdflatex ... OK
WARNING: There were 4 warnings, see
E:/biocbld/bbs-2.2-bioc/meat/biomaRt.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.2-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
Loading required package: RCurl
installing man source files
installing indices
installing help
Note: removing empty section \seealso
Note: removing empty section \seealso
>>> 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
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-2.2-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-2.2-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm, 34,650 bytes
Compression decreased file by 29,410 bytes.
adding MD5 sums
* DONE (biomaRt)