Hi Everyone: Gavin's been so generous and patient that I figured I'd give him a break and send this snag to the list. When I do get this working, I will send an "How to build R from the tarball " instructions message to this list for posterity's sake ( and myself and anyone else who doesn't know how to build R from the tarball ). So, here's my latest snag: Gavin got me through the configure and the make. So, then I did make check and I get below. But, since that error didn't seem that serious, I figured I'd see whether R would run anyway. The output of the R command is below what's below. It's expecting a file in /usr/lib/R I think ? But maybe the fact that the tests don't complete successfully causes that. I looked to see if I have an ENVIRONMENT variable for R in my .bashrc but it doesn't have one. Thanks for all the help. From past experiences, I knew it was going to be a long road and it has been but I'm getting close. Mark END OF make check OUTPUT #========================================================================================================make[2]: Entering directory `/home/markleeds/R/2.14/build/tests' running regression tests ... make[3]: Entering directory `/home/markleeds/R/2.14/build/tests' running code in '../../tests/reg-tests-1a.R' ... OK running code in '../../tests/reg-tests-1b.R' ... OK running code in '../../tests/reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to '../../tests/reg-tests-2.Rout.save' ... OK running code in '../../tests/reg-examples1.R' ... OK running code in '../../tests/reg-examples2.R' ... OK running code in '../../tests/reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error 1 make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests' make[2]: *** [test-Reg] Error 2 make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests' make: *** [check] Error 2 # THEN TRY TO RUN R #================================================================================================= :~/R/2.14/build> R /usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory :~/R/2.14/build> ^C :~/R/2.14/build> [[alternative HTML version deleted]]
i just realized that I had earlier instructions from marc schwartz, that after I do the make check, to then log in as root and do make install. So, I did that, logged out as root and typed R but still get the same message. Below is some of the output from make install. There were no errors. Thanks. make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/unix' make[2]: Entering directory `/home/markleeds/R/2.14/build/src/main' mkdir -p -- /usr/local/lib/R/bin/exec make[3]: Entering directory `/home/markleeds/R/2.14/build/src/main' make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/main' make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/main' make[2]: Entering directory `/home/markleeds/R/2.14/build/src/modules' make[3]: Entering directory `/home/markleeds/R/2.14/build/src/modules/internet' mkdir -p -- /usr/local/lib/R/modules make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/internet' make[3]: Entering directory `/home/markleeds/R/2.14/build/src/modules/lapack' make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/lapack' make[3]: Entering directory `/home/markleeds/R/2.14/build/src/modules/vfonts' make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/vfonts' make[3]: Entering directory `/home/markleeds/R/2.14/build/src/modules/X11' make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/X11' make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/modules' make[2]: Entering directory `/home/markleeds/R/2.14/build/src/library' mkdir -p -- /usr/local/lib/R/library installing packages ... building HTML index ... make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/library' make[1]: Leaving directory `/home/markleeds/R/2.14/build/src' make[1]: Entering directory `/home/markleeds/R/2.14/build/tests' make[1]: Nothing to be done for `install'. make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests' make[1]: Entering directory `/home/markleeds/R/2.14/build/po' installing translations: mkdir -p -- /usr/local/lib/R/share/locale/en/LC_MESSAGES en mkdir -p -- /usr/local/lib/R/share/locale/en_GB/LC_MESSAGES en_GB mkdir -p -- /usr/local/lib/R/share/locale/es/LC_MESSAGES es mkdir -p -- /usr/local/lib/R/share/locale/fr/LC_MESSAGES fr mkdir -p -- /usr/local/lib/R/share/locale/de/LC_MESSAGES de mkdir -p -- /usr/local/lib/R/share/locale/it/LC_MESSAGES it mkdir -p -- /usr/local/lib/R/share/locale/ja/LC_MESSAGES ja mkdir -p -- /usr/local/lib/R/share/locale/ko/LC_MESSAGES ko mkdir -p -- /usr/local/lib/R/share/locale/nn/LC_MESSAGES nn mkdir -p -- /usr/local/lib/R/share/locale/pt_BR/LC_MESSAGES pt_BR mkdir -p -- /usr/local/lib/R/share/locale/ru/LC_MESSAGES ru mkdir -p -- /usr/local/lib/R/share/locale/tr/LC_MESSAGES tr mkdir -p -- /usr/local/lib/R/share/locale/zh_CN/LC_MESSAGES zh_CN mkdir -p -- /usr/local/lib/R/share/locale/zh_TW/LC_MESSAGES zh_TW On Sun, Nov 6, 2011 at 11:43 PM, Mark Leeds <markleeds2@gmail.com> wrote:> Hi Everyone: Gavin's been so generous and patient that I figured I'd give > him a break and send this snag to the list. When I do get this working, I > will send an "How to build R from the tarball " instructions message to > this list for posterity's sake ( and myself and anyone else who doesn't > know how to build R from the tarball ). > > So, here's my latest snag: Gavin got me through the configure and the > make. So, then I did make check and I get below. But, since that error > didn't seem that serious, I figured I'd see whether R would run anyway. The > output of the R command is below what's below. It's expecting a file in > /usr/lib/R I think ? But maybe the fact that the tests don't complete > successfully causes that. I looked to see if I have an ENVIRONMENT variable > for R in my > .bashrc but it doesn't have one. Thanks for all the help. From past > experiences, I knew it was going to be a long road and it has been but I'm > getting close. > > > Mark > > END OF make check OUTPUT > > #========================================================================================================> make[2]: Entering directory `/home/markleeds/R/2.14/build/tests' > running regression tests ... > make[3]: Entering directory `/home/markleeds/R/2.14/build/tests' > running code in '../../tests/reg-tests-1a.R' ... OK > running code in '../../tests/reg-tests-1b.R' ... OK > running code in '../../tests/reg-tests-2.R' ... OK > comparing 'reg-tests-2.Rout' to '../../tests/reg-tests-2.Rout.save' ... > OK > running code in '../../tests/reg-examples1.R' ... OK > running code in '../../tests/reg-examples2.R' ... OK > running code in '../../tests/reg-packages.R' ...make[3]: *** > [reg-packages.Rout] Error 1 > make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests' > make[2]: *** [test-Reg] Error 2 > make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests' > make[1]: *** [test-all-basics] Error 1 > make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests' > make: *** [check] Error 2 > > # THEN TRY TO RUN R > > #=================================================================================================> > :~/R/2.14/build> R > /usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory > :~/R/2.14/build> ^C > :~/R/2.14/build> > >[[alternative HTML version deleted]]
Gavin Simpson
2011-Nov-07 09:35 UTC
[R-sig-Fedora] still working on building R from source
On Sun, 2011-11-06 at 18:43 -0500, Mark Leeds wrote:> Hi Everyone: Gavin's been so generous and patient that I figured I'd give > him a break and send this snag to the list. When I do get this working, I > will send an "How to build R from the tarball " instructions message to > this list for posterity's sake ( and myself and anyone else who doesn't > know how to build R from the tarball ).I would question whether configure or make really did complete correctly. Something went wrong if checking the compiled app failed. You haven't shown us the conclusion of the configure step - it prints out a list of capabilities and compilation options etc. Can you show that. Also, can you show the configure arguments - i.e. how you called configure? Finally, can you show the last 10 or so lines of the output from make? If you configured R as per my emails, you shouldn't need to go anywhere near the root filesystem. I don't bother installing R I just run it from the build DIR, which is in my ~/ I also build from svn which I find easier to maintain as I only need a svn update path/to/sources to get the latest patches. You could also try again with a make distclean or make clean (I forget which is really required here) before you re-run configure, just to make sure it has picked up the correct/new information. HTH G> So, here's my latest snag: Gavin got me through the configure and the > make. So, then I did make check and I get below. But, since that error > didn't seem that serious, I figured I'd see whether R would run anyway. The > output of the R command is below what's below. It's expecting a file in > /usr/lib/R I think ? But maybe the fact that the tests don't complete > successfully causes that. I looked to see if I have an ENVIRONMENT variable > for R in my > .bashrc but it doesn't have one. Thanks for all the help. From past > experiences, I knew it was going to be a long road and it has been but I'm > getting close. > > > Mark > > END OF make check OUTPUT > #========================================================================================================> make[2]: Entering directory `/home/markleeds/R/2.14/build/tests' > running regression tests ... > make[3]: Entering directory `/home/markleeds/R/2.14/build/tests' > running code in '../../tests/reg-tests-1a.R' ... OK > running code in '../../tests/reg-tests-1b.R' ... OK > running code in '../../tests/reg-tests-2.R' ... OK > comparing 'reg-tests-2.Rout' to '../../tests/reg-tests-2.Rout.save' ... OK > running code in '../../tests/reg-examples1.R' ... OK > running code in '../../tests/reg-examples2.R' ... OK > running code in '../../tests/reg-packages.R' ...make[3]: *** > [reg-packages.Rout] Error 1 > make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests' > make[2]: *** [test-Reg] Error 2 > make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests' > make[1]: *** [test-all-basics] Error 1 > make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests' > make: *** [check] Error 2 > > # THEN TRY TO RUN R > #=================================================================================================> > :~/R/2.14/build> R > /usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory > :~/R/2.14/build> ^C > :~/R/2.14/build> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Fedora mailing list > R-SIG-Fedora at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%