[R] Installation of RCurl Windows binary package from BioC extra repos (was Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7)
Patrick Aboyoun
paboyoun at fhcrc.org
Tue Dec 2 08:10:35 CET 2008
Roger,
Given that you are having problems installing the RCurl package from
source, I recommend you install the binary version of the package
instead. (It sounds like you may need to clean up broken installations
first.) Here is what an installation would look like on a machine
without the libcurl library installed on it:
> source("http://bioconductor.org/biocLite.R")
> biocLite("RCurl")
Running biocinstall version 2.3.9 with R version 2.8.0
Your version of R requires version 2.3 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using
'C:\Users\patrick\Documents/R/win-library/2.8'
trying URL
'http://bioconductor.org/packages/2.3/extra/bin/windows/contrib/2.8/RCurl_0.92-0.zip'
Content type 'application/zip' length 1347812 bytes (1.3 Mb)
opened URL
downloaded 1.3 Mb
package 'RCurl' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Users\patrick\AppData\Local\Temp\RtmpTNKaC7\downloaded_packages
updating HTML package descriptions
> library(RCurl)
> uris <- c("http://www.omegahat.org/RCurl/index.html",
"http://www.omegahat.org/RCurl/philosophy.xml")
> txt <- getURI(uris)
> names(txt)
[1] "http://www.omegahat.org/RCurl/index.html"
"http://www.omegahat.org/RCurl/philosophy.xml"
> nchar(txt)
http://www.omegahat.org/RCurl/index.html
http://www.omegahat.org/RCurl/philosophy.xml
4269 48969
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_0.92-0
loaded via a namespace (and not attached):
[1] tools_2.8.0
Day, Roger S wrote:
> Thanks, Patrick.
> As I mentioned, this results in a hung system,
> I've waited as long as an hour, no progress
> in the GUI past "downloaded 234 Kb".
> The 00LOCK folder is created but is empty.
> An R.INSTALL.nnnn folder is created, with
> the unpacked package file.
> There is a README.windows file,
> but it seems a bit garbled, as if some text were accidentally replaced by line feeds.
> My interpretation:
> Retrieve curl-7.19.2-ssl-sspi-zlib-static-bin-w32 from http://curl.haxx.se/
> (I did not find 7.12.0 there.)
> Set LIBCURL_DIR=where.i.put.it\curl-7.19.2-ssl-sspi-zlib-static-bin-w32
> Go to R.INSTALL.nnnn
> R CMD INSTALL RCurl
> The result:
> ---------- Making package RCurl ------------
> test: and: unknown operand
> Cannot find libcurl.dll in "C:\Documents and Settings\day\Desktop\curl-7.19.2-ssl-sspi-zlib-static-bin-w32"
> make[2]: *** [c:/PROGRA~1/R/R-28~1.0/library/RCurl/zzzz] Error 1
> make[1]: *** [all] Error 2
> make: *** [pkg-RCurl] Error 2
> *** Installation of RCurl failed ***
> Got rid of the "test: and:" error by copying the curl folder to "." and resetting LIBCURL_DIR.
> But libcurl.dll still cannot be found by configure.win (despite its presence).
> Examining configure.win, it turns out that setting CURL_LIB_DIR works. Possibly a bug in configure.win.
> Next problem:
> Cannot find curl/curl.h in curl-7.19.2-ssl-sspi-zlib-static-bin-w32/include
> True, this file is not there. By un-setting LIBCURL_DIR this problem 'vanishes'. (a good thing or not?)
> Next problem:
> cp: cannot stat `curl-7.19.2-ssl-sspi-zlib-static-bin-w32/libcurl.dll':
> (& 3 other dlls)
> By moving everything to "\", to avoid spaces in folder names, two of these messages 'vanish'.
> But still 2 dll's cannot be found, zlib1.dll and ssleay32.dll
> and this is not the fault of the script-- they really are absent this time.
>
> Where to now, trusty guide?
>
> -Roger
>
>
>> -----Original Message-----
>> From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org]
>> Sent: Monday, December 01, 2008 2:10 PM
>> To: Day, Roger S
>> Cc: 'r-help at r-project.org'; Boyce, Richard David
>> Subject: Installation of RCurl Windows binary package from
>> BioC extra repos (was Re: [BioC] Rcurl 0.8-1 update for
>> bioconductor 2.7)
>>
>> Hi Roger,
>> Good to hear from you again. Given that RCurl is hosted in
>> both the CRAN mirrors and in the Bioconductor extra
>> repository, it can be a little confusing how to install it on
>> your system. The recommended path is to follow the steps on
>> the Bioconductor extra home page for RCurl
>>
>> http://bioconductor.org/packages/release/extra/html/RCurl.html
>>
>> To install this package, start R and enter:
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("RCurl")
>>
>>
>>
>> Patrick
>>
>>
>>
>> Day, Roger S wrote:
>>
>>> Hi Patrick,
>>>
>>> Greetings from !(sunny) Pittsburgh.
>>>
>>> What's the scoop on RCurl on windows (XP)?
>>> I've tried to install RCurl_0.92-0.zip and RCurl_0.9-3.zip,
>>>
>> with both
>>
>>> R 2.7.2 and R 2.8.0 from the RGUI
>>>
>> (utils:::menuInstallLocal), and get
>>
>>> the error
>>> "Windows binary packages in zipfiles are not supported".
>>> which (according to google's one and only hit) comes from a
>>>
>> perl script.
>>
>>> Your suggestion (below) to use biocLite hangs the R
>>>
>> session, at this point:
>>
>>> Running biocinstall version 2.3.9 with R version 2.8.0
>>> Your version of R requires version 2.3 of Bioconductor.
>>> trying URL
>>>
>> 'http://bioconductor.org/packages/2.3/extra/src/contrib/RCurl_
>> 0.92-0.tar.gz'
>>
>>> Content type 'application/x-gzip' length 239873 bytes (234 Kb)
>>> opened URL
>>> downloaded 234 Kb
>>> (In this case, R 2.7.2.)
>>> We also tried to build RCurl from the tarballs, in DOS
>>>
>> window and in
>>
>>> Cygwin window, with a variety of problems.
>>>
>>> Is there a current solution to installing RCurl on windows?
>>>
>>> (I'm moving this topic to r-help from bioconductor on
>>>
>> suggestions seen
>>
>>> on that list.)
>>>
>>> Thanks for your help.
>>> -Roger
>>>
>>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: bioconductor-bounces at stat.math.ethz.ch
>>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf
>>>>
>> Of Patrick
>>
>>>> Aboyoun
>>>> Sent: Thursday, May 29, 2008 8:49 PM
>>>> To: Steve Lianoglou
>>>> Cc: Yan Zhou; bioconductor at stat.math.ethz.ch
>>>> Subject: Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7
>>>>
>>>> Steve and Yan,
>>>> We just uploaded source, Windows binary, and MacOS X Tiger binary
>>>> packages for RCurl 0.9-3 to the Bioconductor CRAN-like repository
>>>> http://bioconductor.org/packages/2.2/extra. This
>>>>
>> repository is make
>>
>>>> available when you use R 2.7.0 and type
>>>>
>>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite("RCurl")
>>>>
>>>> Let me know if this meets your needs.
>>>>
>>>>
>>>> Cheers,
>>>> Patrick
>>>>
>>>>
>>>>
>>>> Steve Lianoglou wrote:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>>
>>>>>
>>>>>> I'm seeking help here regarding updating the Rcurl for
>>>>>>
>> macOSX to a
>>
>>>>>> newer version so it'll accomodate to bioconductor 2.7.
>>>>>>
>> The current
>>
>>>>>> version of Rcurl 0.8-1 (in bioconductor 2.7 for macOSX) is
>>>>>>
>>>>>>
>>>> built for
>>>>
>>>>
>>>>>> bioconductor 2.6; Is there anyone who could help to put the
>>>>>> bioconductor 2.7 compatible version of Rcurl into the
>>>>>>
>>>>>>
>>>> database? So we
>>>>
>>>>
>>>>>> could use packages depending on Rcurl? Any kind help is greatly
>>>>>> appreciated!
>>>>>>
>>>>>>
>>>>> When this was brought up earlier, I think the consensus was
>>>>>
>>>>>
>>>> that since
>>>>
>>>>
>>>>> this isn't a bioconductor hosted package, you'd better
>>>>>
>>>>>
>>>> inquire over at
>>>>
>>>>
>>>>> R-help.
>>>>>
>>>>> That said, someone also suggested earlier to install it
>>>>>
>>>>>
>>>> straight from
>>>>
>>>>
>>>>> the source via this incantation:
>>>>>
>>>>>
>>>>>
>>>>>> install.packages("RCurl", repos = "http://www.omegahat.org/R")
>>>>>>
>>>>>>
>>>>> I don't think that worked for me, and I ended up d/ling
>>>>>
>> the source
>>
>>>>> package and installing it manually, by first d/ling it and
>>>>> uncompressing it. You'll get an RCurl folder. At the
>>>>>
>>>>>
>>>> command line, you
>>>>
>>>>
>>>>> can then:
>>>>>
>>>>> $ R CMD BUILD RCurl
>>>>> $ R CMD CHECK RCurl_0.9-3.tar.gz
>>>>> $ R CMD INSTALL RCurl_0.9-3.tar.gz
>>>>>
>>>>> I'm not sure if this is the best way, but I seem to have a fully
>>>>> functioning RCurl again since the biomaRt package relies on
>>>>>
>>>>>
>>>> that, and
>>>>
>>>>
>>>>> that works now.
>>>>>
>>>>> Btw - you can get RCurl here: http://www.omegahat.org/RCurl/
>>>>>
>>>>> HTH,
>>>>> -steve
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>>
>>>>
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