[R] Installation of RCurl Windows binary package from BioC extra repos (was Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7)
rdb20+ at pitt.edu
rdb20+ at pitt.edu
Tue Dec 2 15:17:43 CET 2008
Roger,
I had success installing RCurl per Patrick's instructions.
I also got DAVIDQuery to install and run correctly but I had to run R CMD
INSTALL DAVIDQuery from a cygwin terminal after 1) I replaced cygwin's
make program v3.81 with the same version patched for windows from the
mingw project. Make has stopped supporting windows path-names as of v
3.81. (see http://www.cygwin.com/ml/cygwin-announce/2006-07/msg00008.html)
2) I had to replace the perl used by cygwin to the port provided by
ActiveState in c:\Perl\bin (see
http://tolstoy.newcastle.edu.au/R/help/02a/3915.html).
NOTE: I tried using the R GUI to install DAVIDQuery but it reported:
> utils:::menuInstallLocal()
updating HTML package descriptions
> library("DAVIDQuery")
Error in library("DAVIDQuery") :
'DAVIDQuery' is not a valid package -- installed < 2.0.0?
NOTE: I tried to use the windows terminal but it reported:
'make' is not recognized as an internal or external c
operable program or batch file.
c:\Users\boycerd\Downloads>R CMD INSTALL DAVIDQuery
installing to 'c:/PROGRA~1/R/R-28~1.0/library'
'mv' is not recognized as an internal or external com
operable program or batch file.
'make' is not recognized as an internal or external c
operable program or batch file.
*** Installation of DAVIDQuery failed ***
Removing 'c:/PROGRA~1/R/R-28~1.0/library/DAVIDQuery'
hope it helps,
-rdb
> 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
>>>>> 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
>>>>>
>>>>>
>
>
More information about the R-help
mailing list