[R] 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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Patrick Aboyoun
Sent: Thursday, May 29, 2008 8:49 PM
To: Steve Lianoglou
Cc: Yan Zhou; [EMAIL PROTECTED]
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
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Re: [R] Installation of RCurl Windows binary package from BioC extra repos (was Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7)
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. 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.
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/] 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:[EMAIL PROTECTED]
> Sent: Monday, December 01, 2008 2:10 PM
> To: Day, Roger S
> Cc: 'r-help@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: [EMAIL PROTECTED]
> >> [mailto:[EMAIL PROTECTED] On Behalf
> Of Patrick
> >> Aboyoun
> >> Sent: Thursday, May 29, 2008 8:49 PM
> >> To: Steve Lianoglou
> >> Cc: Yan Zhou; [EMAIL PROTECTED]
> >> 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
> >>>
Re: [R] Installation of RCurl Windows binary package from BioC extra repos (was Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7)
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
426948969
> 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. 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.
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/] 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:[EMAIL PROTECTED]
Sent: Monday, December 01, 2008 2:10 PM
To: Day, Roger S
Cc: 'r-help@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:
Re: [R] Installation of RCurl Windows binary package from BioC extra repos (was Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7)
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/msg8.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
>
> 426948969
> > 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. 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.
>> 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/] 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 t
