* using log directory 'd:/Rcompile/CRANpkg/local/2.7/celsius.Rcheck' * using R version 2.7.2 RC (2008-08-18 r46382) * using session charset: ISO8859-1 * checking for file 'celsius/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'celsius' version '1.0.7' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'celsius' 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * creating celsius-Ex.R ... OK * checking examples ... ERROR Running examples in 'celsius-Ex.R' failed. The error most likely occurred in: > ### * celsius > > flush(stderr()); flush(stdout()) > > ### Name: celsius > ### Title: Retrieve Affymetrix microarray measurements and metadata from > ### Celsius > ### Aliases: celsius celsius-package > ### Keywords: data > > ### ** Examples > > > #first make an instance of a celsius Server object. > celsius = new( "celsiusServer", + celsiusUrl = "http://celsius.genomics.ctrl.ucla.edu" ); > > #list all of the platforms supported by the server > platformTable = getPlatformData( celsius ); > > #list all the samples in the server that correspond to the > #HG-U133_Plus_2 platform... > celsius@platform = "HG-U133_Plus_2"; > idList = listSamplesForPlatform( celsius ); > > #map some foreign IDs to the celsius servers internal sample IDs > celsius@platform = 'HG-U133A'; > id = c( "AEX:E-MEXP-402", "GSE6210" ); > mapTable = mapIdToCelsius( celsius, id = id ); Read 28 items > > #get some samples data based on sample IDs > celsius@verbose = TRUE; > data = getSampleData( celsius, id = c( "SN:1005595" ) ); 1 sample ID SN:1005595 was retrieved for 22284 features > > #get some data based on features (affymetrix probesets). > data = getFeatureData( celsius, feature = c( "204412_s_at", "1316_at" ) ); Warning in file(file, "r") : cannot open: HTTP status was '0 (nil)' Tried and Failed 1 times to retrieve data... Warning in file(file, "r") : cannot open: HTTP status was '0 (nil)' Tried and Failed 2 times to retrieve data... Warning in file(file, "r") : cannot open: HTTP status was '0 (nil)' Tried and Failed 3 times to retrieve data... 1 feature ID 204412_s_at was retrieved for samples Warning in file(file, "r") : cannot open: HTTP status was '0 (nil)' Tried and Failed 1 times to retrieve data... Warning in file(file, "r") : cannot open: HTTP status was '0 (nil)' Tried and Failed 2 times to retrieve data... Warning in file(file, "r") : cannot open: HTTP status was '0 (nil)' Tried and Failed 3 times to retrieve data... 2 feature ID 1316_at was retrieved for samples There is no data retrieved from the database! Please check your list of ProbeSets!Error in t.default(mat) : argument is not a matrix Calls: getFeatureData -> t -> t.default Execution halted