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\DownloadsR 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 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
[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 ___ Bioconductor mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ___ Bioconductor mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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 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
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:::menuInstallLocal), and get
