RE: [R] r under linux: creating high quality bmp's for win users
I second the use of png() to create portable network graphics format pictures, as MS Word (XP and 2003 at least) can handle these without any problems. I use this format as a matter of course in preparing material for embedding in web pages. Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Prof Brian Ripley Sent: 22 March 2005 11:46 To: Christoph Lehmann Cc: r-help@stat.math.ethz.ch Subject: Re: [R] r under linux: creating high quality bmp's for win users On Tue, 22 Mar 2005, Christoph Lehmann wrote: Hi I produce graphics with R under linux, but my collaborators often use windows and cannot import eps pics e.g. in msword Are they sure? One can import eps images into Word, but you need to print them on a postscript printer. what is the standard way to get e.g. bmp's with the same quality as eps. going the way: creating eps, convert eps2bmp using 'convert' doesn't yield good enough bmp's The bitmap() device might do better, although both are really using gs. I would use png() and convert to bmp with ImageMagick's convert or otherwise. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] subset selection for logistic regression
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wittner, Ben Sent: 02 March 2005 11:33 To: [EMAIL PROTECTED] Subject: [R] subset selection for logistic regression R-packages leaps and subselect implement various methods of selecting best or good subsets of predictor variables for linear regression models, but they do not seem to be applicable to logistic regression models. Does anyone know of software for finding good subsets of predictor variables for linear regression models? Thanks. -Ben p.s., The leaps package references Subset Selection in Regression by Alan Miller. On page 2 of the 2nd edition of that text it states the following: All of the models which will be considered in this monograph will be linear; that is they will be linear in the regression coefficients.Though most of the ideas and problems carry over to the fitting of nonlinear models and generalized linear models (particularly the fitting of logistic relationships), the complexity is greatly increased. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html The LASSO method and the Least Angle Regression method are two such that have both been implemented (efficiently IMHO - only one least squares for all levels of shrinkage IIRC) in the lars package for R of Hastie and Efron. There is a paper by Madigan and Ridgeway that discusses the use of the Least Angle Regresson approach in the context of logistic regression - available for download from Madigan's space at Ruttgers: www.stat.rutgers.edu/~madigan/PAPERS/lars3.pdf HTH Mike __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Bayesian stepwise (was: Forward Stepwise regression based onpartial F test)
oops, Forgot to cc to the list. Regards, Mike -Original Message- From: dr mike [mailto:[EMAIL PROTECTED] Sent: 24 February 2005 19:21 To: 'Spencer Graves' Subject: RE: [R] Bayesian stepwise (was: Forward Stepwise regression based onpartial F test) Spencer, Obviously the problem is one of supersaturation. In view of that, are you aware of the following? A Two-Stage Bayesian Model Selection Strategy for Supersaturated Designs Authors: Beattie S. D; Fong D. K. H; Lin D. K. J Source: Technometrics, 1 February 2002, vol. 44, no. 1, pp. 55-63 And: Analysis Methods for Supersaturated Design: Some Comparisons Authors: Li R; Lin D. K. J Source: Journal of Data Sciences, 1, 2003, pp. 249-260 The latter is available for download in full (pdf) by googling for the title. HTH Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Spencer Graves Sent: 24 February 2005 17:29 To: Frank E Harrell Jr Cc: r-help@stat.math.ethz.ch Subject: [R] Bayesian stepwise (was: Forward Stepwise regression based onpartial F test) Does anyone know of research fully Bayesian stepwise procedures assuming that models not considered by the stepwise would essentially have zero posterior probability? I need to analyze the results of ad hoc experiments run in manufacturing with crazy confounding and possible supersaturation (i.e., more potentially explanatory variables than runs), when each run is very expensive in both time and money. There have to be ways to summarize concisely and intelligently what the data can tell us and what remains uncertain, including the level of partial confounding between alternative explanations. I think I've gotten reasonable results with my own modification of Venables Ripley's stepAIC to compute an approximate posterior over tested models using the AICc criterion described, e.g., by Burnham and Anderson (2002) Model Selection and Multi-Model Inference (Springer). Preliminary simulations showed that when I used the naive prior (that all models are equally likely, including the null model), the null model is usually rejected when true. What a surprise! I think I can fix that using a more intelligent prior. I also think I can evaluate the partial confounding between alternative models by studying the correlation matrix between the predictions of alternative models. Comments? Thanks, Spencer Graves Frank E Harrell Jr wrote: Smit, Robin wrote: I am hoping to get some advise on the following: I am looking for an automatic variable selection procedure to reduce the number of potential predictor variables (~ 50) in a multiple regression model. I would be interested to use the forward stepwise regression using the partial F test. I have looked into possible R-functions but could not find this particular approach. There is a function (stepAIC) that uses the Akaike criterion or Mallow's Cp criterion. In addition, the drop1 and add1 functions came closest to what I want but with them I cannot perform the required procedure. Do you have any ideas? Kind regards, Robin Smit Business Unit TNO Automotive Environmental Studies Testing PO Box 6033, 2600 JA Delft THE NETHERLANDS Robin, If you are looking for a method that does not offer the best predictive accuracy and that violates every aspect of statistical inference, you are on the right track. See http://www.stata.com/support/faqs/stat/stepwise.html for details. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Drawing maps of UK
The package blighty allows you to draw the UK coastline. Regards Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: 08 February 2005 13:25 To: r-help@stat.math.ethz.ch Subject: [R] Drawing maps of UK Hi I have downloaded the maps package from CRAN, along with a few other map* packages that I could find - but there didn't seem to be data on the UK. What I actually want to do (finally) is draw some maps of data that I have which is organised by postcode (sort of equivalent of US Zip code for those who don't know). I think this may be quite ambitious, but I wanted to see just how far I could get with R. I have seen examples on the list (e.g. http://www.r-project.org/nocvs/mail/r-help/2000/4480.html) giving examples of drawing maps of the UK at county level (map(uk,fill=T,color=pop.colour)) but this didn't work on my system - as I don't seem to have the correct data for the UK. Thanks in advance for your help Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] genetic algorithm
To my knowledge, two packages have an implementation of an evolutionary, or genentic, algorithm. Gafit is a curve fitting package and rgenoud for function minimisation (combined with, iirc, a derivative-based Quasi-Newton approach for unconstrained problems). One thing, in the S-Plus robust library, the robust regression package lmRob has an option to use a genetic algorithm in the resampling scheme to obtain initial S-estimates. Regards Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of WeiWei Shi Sent: 04 February 2005 17:01 To: R-help@stat.math.ethz.ch Subject: [R] genetic algorithm Hi, I am doing some research on feature selection for classfication problem using genetic algorithm in a wrapper approach. I am wondering if there is some package which is already built for this purpose. I was advised before about dprep package but I don't think it used GA there (if I am wrong, please correct me!) Thanks, Ed __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] using RODBC
Have you consulted the R Data Import/Export Manual, available from the Rgui via the Help tab? Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jessica Higgs Sent: 28 January 2005 19:24 To: R-help@stat.math.ethz.ch Subject: [R] using RODBC I am trying to bring data into R from an excel spreadsheet in order to perform several statistical tests on it. I was trying to use odbcConnectExcel in the RODBC package. Once I am connected to the excel file, how do I select rows and columns from the file in order to analysis them in R. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Cauchy's theorem
I don't know about the 'in R' bit, but ISTR that Monte-Carlo (or pseudo Monte-Carlo) Integration is a way of doing this 'numerically'. I know that Mathematica implements the (pseudo Monte-Carlo) Halton-Hammersley-Wozniakowski algorithm as Nintegrate. Perhaps something equivalent has been coded by someone for WINBUGS (OPENBUGS) (accessible from R via the BRUGS package). HTH Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robin Hankin Sent: 20 January 2005 14:14 To: R-help@stat.math.ethz.ch Subject: [R] Cauchy's theorem In complex analysis, Cauchy's integral theorem states (loosely speaking) that the path integral of any entire differentiable function, around any closed curve, is zero. I would like to see this numerically, using R (and indeed I would like to use the residue theorem as well). Has anyone coded up path integration? -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] XML
This cropped up in a previous posting here (Monday this week, in fact), responded to by Prof. Ripley. It also cropped up on the Bioconductor mailing list before Christmas, in relation to the AnnBuilder package. For those who have reposTools installed, the solution provided by John Zhang was, from the command line enter: library(reposTools) install.pacakges2(XML) Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc Schwartz Sent: 14 January 2005 22:13 To: Shawn Way Cc: R-Help Subject: Re: [R] XML On Fri, 2005-01-14 at 15:52 -0600, Shawn Way wrote: I thought I would take a look at the StatDataML package for some work I'm doing, but I receive the following error when starting: version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R library(StatDataML) Loading required package: XML Error: package 'XML' could not be loaded In addition: Warning message: There is no package called 'XML' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) Realizing that I don't have the Package XML, I've tried to download it, and I cannot find the file. Can anyone point me in the right direction, or at lease upload it to CRAN? Thanks... The Windows ZIP file for package XML is available here: http://www.stats.ox.ac.uk/pub/RWin/2.0.0/ thanks to Prof. Ripley. The current build report for the Windows packages indicates that this is one of the packages that will not build out of the box. The Windows build report is here: http://cran.us.r-project.org/bin/windows/contrib/checkSummaryWin.html and the README file that covers this issue is here: http://cran.us.r-project.org/bin/windows/contrib/2.0/ReadMe HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R, postgresql, windows bsd
You can do this in Perl (see e.g. Interchange, using Perl-DBI and TCP-IP instead of sockets). If you're familiar with Perl, that is .. Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: 13 January 2005 14:07 To: r-help Subject: [R] R, postgresql, windows bsd I usually work with R on a windows querying data through RODBC from a postgresql db on a freebsd machine on my offcie lan. Now I have the chance to use R also on a linux gentoo client box and to connect to the same db. I know that I can install the unixodbc stuff and stick to RODBC, BUT my question is: Is there any more 'linuxish' way of querying a postgresql server from a client? Ciao Vittorio __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Installation of XML library can't find libxml2.dll
My reading of this is that you may have installed the 'Windows binary' package from the Omegahat site - if so, it would appear that this is for versions of R 2.0 . Further to the pointer to the reply by Prof Ripley, hisa link provides the correct Windows binary for R = 2.0. Regards Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: 10 January 2005 14:41 To: R list Subject: [R] Installation of XML library can't find libxml2.dll Sorry to ask a (probably) dumb question, but I am trying to install XML package on Windows XP, R 2.0.1, and I get the error: This application has failed to start because libxml2.dll was not found. Re-installing the application may fix this problem library(XML) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library C:/PROGRA~1/R/rw2001/library/XML/libs/XML.dll: LoadLibrary failure: The specified module could not be found. Error in library(XML) : package/namespace load failed for 'XML' Now, having read the website at http://www.omegahat.org/RSXML/, I find that the package: uses libxml2, by default and only libxml(version 1) if libxml2 is not present And here's my dumb question - what is libxml2 in a windows context and where do I get it from? Thanks Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Searching for a string in RSQLite
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Duncan Murdoch Sent: 25 November 2004 15:38 To: [EMAIL PROTECTED] Subject: [R] Searching for a string in RSQLite I'd like to search for a particular string in an SQLite database using RSQLite, but I'm running into problems constructing the query properly, because of embedded quotes and parens in the string. Is there a function that escapes these for me, or some other fixup that would let me do the queries below? In the real situation I don't have control over what strings get searched for. Example based on ?SQLite: library(RSQLite) m - dbDriver(SQLite) con - dbConnect(m, dbname = base.dbms) data(USArrests) dbWriteTable(con, USArrests, USArrests, overwrite = T) [1] TRUE state - Wyoming # this works fine: dbGetQuery(con, paste(SELECT * from USArrests where row_names=',state,',sep=)) row_names Murder Assault UrbanPop Rape 1 Wyoming6.8 161 60 15.6 # Buf if the search string contains characters that SQL interprets, I # get an error state - messy: ' ( dbGetQuery(con, paste(SELECT * from USArrests where row_names=',state,',sep=)) Error in sqliteExecStatement(con, statement) : RS-DBI driver: (error in statement: near (: syntax error) Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html The normal character for escaping the next character to prevent it being interpreted in SQL (including SQLite) is the backslash (i.e. \). Unless, of course, I'm not understanding the precise nature of your request. Regards Mike __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc Schwartz Sent: 09 August 2004 15:13 To: Dr Mike Waters Cc: R-Help Subject: RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3) On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote: snip Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. OK, that helps. I still have a lingering concern that, given the facts above, there may be other integrity issues in the RPM database, if not elsewhere. From reading the WB web site FAQ's (http://www.whiteboxlinux.org/faq.html) , it appears that they are using up2date/yum for system updates. Depending upon the version in use, there have been issues especially with up2date (hangs, incomplete updates, etc.) which could result in other problems. I use yum via the console here (under FC2), though I note that a GUI version of yum has been created, including replacing the RHN/up2date system tray alert icon. A thought relative to this specifically: If there is or may be an integrity problem related to the rpm database, you should review the information here: http://www.rpm.org/hintskinks/repairdb/ which provides instructions on repairing the database. Note the important caveats regarding backups, etc. The two key steps there are to remove any residual lock files using (as root): rm -f /var/lib/rpm/__* and then rebuilding the rpm database using (also as root): rpm -vv --rebuilddb I think that there needs to be some level of comfort that this basic foundation for the system is intact and correct. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? I would not use the FC2 RPM, since FC2 has many underlying changes not the least of which includes the use of the 2.6 kernel series and the change from XFree86 to x.org. Both changes resulted in significant havoc during the FC2 testing phases and there was at least one issue here with R due to the change in X. According to the WB FAQs: If you cannot find a package built specifically for RHEL3 or WBEL3 you can try a package for RH9 since many of the packages in RHEL3 are the exact same packages as appeared in RH9. Thus, it would seem reasonable to use the RH9 RPM that Martyn has created. An alternative would certainly be to compile R from the source tarball. In either case, I would remove the current installation of R and after achieving a level of comfort that your RPM database is OK, reinstall R using one of the above methods. Pay close attention to any output during the installation process, noting any error or warning messages that may occur. If you go the RPM route, be sure that the MD5SUM of the RPM file matches the value that Martyn has listed on CRAN to ensure that the file has been downloaded in an intact fashion. These are my thoughts at this point. You need to get to a point where the underlying system is stable and intact, then get R to the same state before attempting to install new packages. HTH, Marc From unpacking the tarball and running ./configure in the R source directory, I obtain the fact that crti.o is needed by ld.so and was not found. This file is not present on the system. This file, along with crtn.o is usually installed by the gnu libc packages, I believe. However, I know that not all *nix
RE: [R] R packages install problems linux - X not found(WhiteBoxEL 3)
Marc, Yes - the glibc-devel package was shown to be installed using rpm -qa. It is also one of the packages upgraded by up2date from the original version supplied with the WhiteBox distribution. I concluded that there were probably more such improperly/incompletely upgraded packages and cut my losses. Everything seems to be fine second time around. I must have been unlucky. Regards Mike -Original Message- From: Marc Schwartz [mailto:[EMAIL PROTECTED] Sent: 10 August 2004 15:30 To: Dr Mike Waters Cc: R-Help Subject: RE: [R] R packages install problems linux - X not found(WhiteBoxEL 3) On Tue, 2004-08-10 at 08:15, Dr Mike Waters wrote: snip From unpacking the tarball and running ./configure in the R source directory, I obtain the fact that crti.o is needed by ld.so and was not found. This file is not present on the system. This file, along with crtn.o is usually installed by the gnu libc packages, I believe. However, I know that not all *nix distributions include these files among their packages. From a web search, I have not been able to ascertain whether this lack of a crti.o is due to there not being one in the distribution, or to another incomplete package install. So, I did a completely fresh installation of WhiteBox, followed by R built from source, checked that it ran and then installed the R packages. Only then did I run up2date. At least crti.o and crtn.o are still there this time, along with the XFree86 includes. A bit of a cautionary tale, all in all. Thanks for all the help and support. Regards M Mike, From my FC2 system: $ rpm -qf /usr/lib/crti.o glibc-devel-2.3.3-27 $ rpm -qf /usr/lib/crtn.o glibc-devel-2.3.3-27 So, you are correct relative to the source of these two files. A follow up question might be, did you include the devel packages during your initial install? If not, that would explain the lack of these files. if you did, then it would add another data point to support the notion that your system was, to some level, compromised and a clean install was probably needed, rather than just trying to re-create the RPM database. Glad that you are up and running at this point. Given Martyn's follow up messages, it looks like there may be an issue with the RH9 RPM, so for the time being using the source tarball would be appropriate. Best regards, Marc __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
I am concerned by your indications of previously having had RH9 on the same box and that you had to force an update of the XFree Devel RPM. Forcing the installation of an RPM is almost always a bad thing. When you installed WB on the system, did you do a clean installation or some type of upgrade? If the latter, it is reasonable to consider that there may be some level of mixing and matching of RPMS from the two distributions going on. This could result in a level of marginally or wholly incompatible versions of RPMS being installed. Could you clarify that point? Also, be sure that you have the same versions of the XFree series RPMS installed. Use: rpm -qa | grep XFree in a console and be sure that the RPMS return the same version schema. If not, it is possible that one of your problems is the mixing of versions. Take note of the output of the above and be sure that the XFree86-Mesa-libGL and XFree86-Mesa-libGLU RPMS are installed as well. Some of the messages above would also suggest a problem finding R related headers. How did you install R? This may be a red herring of sorts, given the other problems, but may be helpful. Marc __ Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? Regards M __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R packages install problems linux - X not found (WhiteBox EL 3)
Good evening everyone, I am used to using R under Windows, but have done an install of 1.9.1 under WhiteBox linux 3 (based on RHEL 3). This all went without a hitch, along with most of the additional package installs. However, while trying to install car and rgl I hit a problem regarding the X environment not being found. As I was doing the install from a console *within* the X environment, this is obviously down to a missing environment variable or link. The X11 directories all seem to be in the usual places. I've checked as much as I can through the archives and googled around, but to no avail. Any help appreciated. Thanks for taking the time to read this. Regards M [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
FW: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
-Original Message- From: Dr Mike Waters [mailto:[EMAIL PROTECTED] Sent: 08 August 2004 20:11 To: '[EMAIL PROTECTED]' Subject: RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3) -Original Message- Correction on the above URL. I pasted the wrong one here. It should be: https://www.stat.math.ethz.ch/pipermail/r-help/2004-August/053994.html Marc Thanks for the responses guys. I used to have RH9 installed on this machine and I found out about the separate developer packages then. I thought that I had got the relevant XFree devel package installed, but although it showed up in the rpm database as being present, the required files were not present. I did a forced rpm upgrade from the WhiteBox updates directory and that problem is now fixed, at least for car. Marc, thanks for the pointer on the rgl problem. However, I have a slightly different problem with the install of this package. It gets through to the point where it tries to make the rgl.so from the various .o files and fails then, as follows: g++ -I/usr/lib/R/include -I/usr/X11R6/include -DHAVE_PNG_H -I/usr/include -I/usr/local/include -Wall -pedantic -fno-exceptions -fno-rtti -fPIC -O2 -g -march=i386 -mcpu=i686 -c glgui.cpp -o glgui.o g++ -L/usr/local/lib -o rgl.so x11lib.o x11gui.o types.o math.o fps.o pixmap.o gui.o api.o device.o devicemanager.o rglview.o scene.o glgui.o -L/usr/X11R6/lib -L/usr/lib -lstdc++ -lX11 -lXext -lGL -lGLU -lpng /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/../../../crt1.o(.text+0x18): In function `_start': : undefined reference to `main' x11lib.o(.text+0x84): In function `set_R_handler': /tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to `R_InputHandlers' x11lib.o(.text+0x92):/tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to `addInputHandler' x11lib.o(.text+0xfb): In function `unset_R_handler': /tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to `R_InputHandlers' x11lib.o(.text+0x103):/tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to `removeInputHandler' collect2: ld returned 1 exit status make: *** [rgl.so] Error 1 ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' - No doubt another failed dependency... DOH! Regards M __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
