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
>
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or copying of this message or any attachment is strictly prohibited. If you
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