perhaps you need to update your curl-devel infrastructure in linux bash-3.2$ curl-config --version libcurl 7.19.4
On Tue, Apr 6, 2010 at 12:19 AM, Kunbin Qu <[email protected]> wrote: > Now I ran into more problems with the installation from the dependency. > The following is what I have under the library directory for R-2.10.1 > > > > [srp102] ~/R-2.10.1/library 784 >ls > > affy boot foreign IRanges > nnet splines > > affydata BSgenome gcrma KEGG.db > org.Hs.eg.db stats > > affyio BSgenome.Ecoli.NCBI.20080805 genefilter KernSmooth > preprocessCore stats4 > > affyPLM ChIPpeakAnno geneplotter lattice > RColorBrewer survival > > affyQCReport chipseq Genominator limma > R.css tcltk > > annaffy class GO.db marray > RCurl tools > > annotate cluster graphics MASS > rpart utils > > AnnotationDbi codetools grDevices Matrix > RSQLite vsn > > base datasets grid methods > samr XML > > Biobase DBI hgu95av2.db mgcv > ShortRead xtable > > Biostrings DynDoc hwriter multtest > simpleaffy > > bitops edgeR impute nlme > spatial > > [srp102] ~/R-2.10.1/library 785 > > > > > Then I did an update: update.packages(repos=biocinstallRepos(), > ask=FALSE) > > > > After that, it ran into problem with loading RCurl.so > > > > Which is there when I do the ls: > > > > [srp102] ~/R-2.10.1/library 786 >ls -al RCurl/libs/ > > total 132 > > drwxr-xr-x 2 kqu Domain Linux Users 4096 Apr 5 13:39 . > > drwxr-xr-x 12 kqu Domain Linux Users 4096 Apr 5 13:39 .. > > -rwxr-xr-x 1 kqu Domain Linux Users 120958 Apr 5 13:39 RCurl.so > > [srp102] ~/R-2.10.1/library 787 > > > > > > > > install.packages("/home/kqu/rtracklayer_1.6.0.tar.gz", type="source") > > inferring 'repos = NULL' from the file name > > * installing *source* package ?rtracklayer? ... > > ** R > > ** data > > ** demo > > ** inst > > ** preparing package for lazy loading > > Loading required package: bitops > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared library > '/home/kqu/R-2.10.1/library/RCurl/libs/RCurl.so': > > /home/kqu/R-2.10.1/library/RCurl/libs/RCurl.so: undefined symbol: > curl_multi_remove_handle > > Error : package 'RCurl' could not be loaded > > ERROR: lazy loading failed for package ?rtracklayer? > > * removing ?/home/kqu/R-2.10.1/library/rtracklayer? > > Warning message: > > In install.packages("/home/kqu/rtracklayer_1.6.0.tar.gz", type = > "source") : > > installation of package '/home/kqu/rtracklayer_1.6.0.tar.gz' had > non-zero exit status > > > sessionInfo() > > R version 2.10.1 (2009-12-14) > > x86_64-unknown-linux-gnu > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > > loaded via a namespace (and not attached): > > [1] tools_2.10.1 > > > > > > > > > From: Michael Lawrence [mailto:[email protected]] > Sent: Monday, April 05, 2010 4:06 PM > To: Kunbin Qu > Cc: Michael Lawrence; [email protected] > Subject: Re: [Bioc-sig-seq] example(diffPeakSummary) in chipseq > > > > I recommend that you upgrade your R to 2.10 at least, making sure to > install fresh versions of all of the packages. > > On Mon, Apr 5, 2010 at 3:55 PM, Kunbin Qu <[email protected]> wrote: > > Thanks, Michael. > > > > In the ChipSeq vignette, it loads up 3 libraries, one is > GenomicFeatures.Mmusculus.UCSC.mm9 > > > > Here is the output when I ran the example code: > > > > > example(diffPeakSummary) > > > > dffPkS> data(cstest) > > > > dffPkS> library(BSgenome.Mmusculus.UCSC.mm9) > > > > dffPkS> mouse.chromlens <- seqlengths(Mmusculus) > > > > dffPkS> ## extend reads, generate peak summary > > dffPkS> extRanges <- gdapply(cstest, extendReads, seqLen = 200) > > Error in X[[i]] : this S4 class is not subsettable > > Error in gdapply(X[[i]], FUN, ...) : > > error in evaluating the argument 'X' in selecting a method for > function 'gdapply' > > > cstest > > An object of class ?GenomeDataList? > > Slot "annotation": > > Error in slot(object, what) : > > no slot of name "annotation" for this object of class "GenomeDataList" > > > > > > > "cstest" output is quite different from the vignette, so I assume > GenomicFeatures.Mmusculus.UCSC.mm9 is required. > > > > -Kunbin > > > > > > From: Michael Lawrence [mailto:[email protected]] > Sent: Monday, April 05, 2010 3:49 PM > To: Kunbin Qu > Cc: [email protected] > Subject: Re: [Bioc-sig-seq] example(diffPeakSummary) in chipseq > > > > The example code (in svn at least) looks like it needs > BSgenome.Mmusculus.UCSC.mm9, not GenomicFeatures. Maybe you're talking > about the contextDistribution example, which could be considered > deprecated/obsolete, until I figure out how chipseq should interact with > the new generation of GenomicFeatures. > > Michael > > On Mon, Apr 5, 2010 at 3:38 PM, Kunbin Qu <[email protected]> wrote: > > Hi, > > I was trying to run the diffPeakSummary example code in chipseq. It > needs to install GenomicFeatures.Mmusculus.UCSC.mm9. When I tried to > install it, it gave the following error messages. Please help, thanks. > > -Kunbin > > > > > install.packages("/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar > .gz", type="source") > inferring 'repos = NULL' from the file name > * Installing *source* package ?GenomicFeatures.Mmusculus.UCSC.mm9? ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: rtracklayer > Loading required package: RCurl > Loading required package: bitops > Warning: Multiple methods tables found for 'duplicated' > Warning: Multiple methods tables found for 'unique' > Warning: Multiple methods tables found for 'sort' > Warning: Multiple methods tables found for 'rank' > Warning in namespaceImportFrom(self, asNamespace(ns)) : > replacing previous import: .__C__Dups > Warning in namespaceImportFrom(self, asNamespace(ns)) : > replacing previous import: match > Warning in namespaceImportFrom(self, asNamespace(ns)) : > replacing previous import: summary > Warning in namespaceImportFrom(self, asNamespace(ns)) : > replacing previous import: .__C__Dups > Warning in namespaceImportFrom(self, asNamespace(ns)) : > replacing previous import: match > ** help > *** installing help indices > >>> Building/Updating help pages for package > 'GenomicFeatures.Mmusculus.UCSC.mm9' > Formats: text html latex example > > > ******* Syntax error: \enumerate in > /----- > A data frame with 16026 observations on the following 4 variables. > \enumeratenormal-bracket12bracket-normal\----- > ERROR: building help failed for package > ?GenomicFeatures.Mmusculus.UCSC.mm9? > * Removing > ?/mnt/opt/R/R-2.9.2/x86_64-unknown-linux-gnu/lib64/R/library/GenomicFeat > ures.Mmusculus.UCSC.mm9? > Warning message: > In > install.packages("/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar > .gz", : > installation of package > '/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar.gz' had non-zero > exit status > > sessionInfo() > R version 2.9.2 (2009-08-24) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U > TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME= > C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI > ON=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] BSgenome.Mmusculus.UCSC.mm9_1.3.13 chipseq_0.2.1 > > [3] ShortRead_1.2.1 lattice_0.17-26 > > [5] BSgenome_1.12.5 Biostrings_2.12.10 > > [7] IRanges_1.4.16 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.1 grid_2.9.2 hwriter_1.2 tools_2.9.2 > > > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. 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