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)
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://www.stat.math.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)
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
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 __ [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
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Sun, 2004-08-08 at 22:22, Prof Brian Ripley wrote: On Sun, 8 Aug 2004, Marc Schwartz wrote: On Sun, 2004-08-08 at 14:10, Dr Mike Waters wrote: snip 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 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. I think it is the exact point. Those entry points are in R.bin, so should be missing. The g++ line is missing `-shared', which is picked up from R_HOME/etc/Makeconf, specifically from SHLIB_CXXLDFLAGS = -shared So the R installation doesn't have the right flags. This could be my fault. It transpires that this is not set correctly in the RPMs for RH9 and 8.x. I will look into it (this is most probably due to a missing BuildRequires). This isn't the first time someone has had this problem. I apologize for not fixing it, but at the time I was convinced the RPMS were OK. Martyn __ [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
Re: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
Maybe you can try with the other RHEL clone like CentOS-3: http://install.linux.duke.edu/pub/linux/add-on/distrib/centos-3.1/i386/rpms/R-1.9.0-0.duke.1.el3.i386.rpm http://install.linux.duke.edu/pub/linux/add-on/distrib/centos-3.1/i386/srpms/R-1.9.0-0.duke.1.el3.src.rpm Best wishes, Muhammad Subianto On this day 09/08/2004 04:12 PM, Marc Schwartz wrote: 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 __ [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 __ [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
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Mon, 2004-08-09 at 15:13, Dr Mike Waters wrote: [SNIP] 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? The Red Hat 9 RPM is appropriate for you, but it is currently buggy, so you are best compiling from source. I need to add gcc-g++ to the list of BuildRequires (packages that must be installed at build time). This isn't strictly necessary to build R, but if R is configured without a C++ compiler, of course it does not know how to build packages with C++ code in them. Martyn __ [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
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Sun, 2004-08-08 at 14:10, Dr Mike Waters wrote: snip 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 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 __ [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
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Sun, 8 Aug 2004, Marc Schwartz wrote: On Sun, 2004-08-08 at 14:10, Dr Mike Waters wrote: snip 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 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. I think it is the exact point. Those entry points are in R.bin, so should be missing. The g++ line is missing `-shared', which is picked up from R_HOME/etc/Makeconf, specifically from SHLIB_CXXLDFLAGS = -shared So the R installation doesn't have the right flags. -- 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 __ [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
