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Package 35/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
biomaRt 1.12.0 Steffen Durinck Last Changed Date: 2007-10-02 17:41:09 -0700 Last Changed Rev: 27709 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | OK | OK | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | [ WARNINGS ] | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | OK | OK |
Package: biomaRt |
Version: 1.12.0 |
Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check biomaRt_1.12.0.tar.gz |
RetCode: 0 |
Time: 220.2 seconds |
Status: WARNINGS |
CheckDir: biomaRt.Rcheck |
Warnings: 3 |
* checking for working latex ... OK * using log directory 'E:/biocbld/bbs-2.1-bioc/meat/biomaRt.Rcheck' * using R version 2.6.0 (2007-10-03) * checking for file 'biomaRt/DESCRIPTION' ... OK * this is package 'biomaRt' version '1.12.0' * 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 ... 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' ... OK * creating biomaRt-manual.tex ... OK * checking biomaRt-manual.tex ... OK WARNING: There were 3 warnings, see E:/biocbld/bbs-2.1-bioc/meat/biomaRt.Rcheck/00check.log for details
biomaRt.Rcheck/00install.out:
installing R.css in E:/biocbld/bbs-2.1-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 >>> 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 getFeature 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-2.1-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm Compile time: 0 minutes, 0 seconds 25 Topics 49 Local links 9 Internet links 1 Graphic Created e:\biocbld\bbs-2.1-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm, 35,964 bytes Compression decreased file by 31,207 bytes. adding MD5 sums * DONE (biomaRt)