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:[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 >>>>>>> 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.