Getting a very strange error with a new install of R from source on x86; make[3]: Leaving directory `/tmp/R.INSTALL.r20887/cluster/src' ** R ** data ** moving datasets to lazyload DB Error in factor(c(1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1), : invalid labels; length 2 should be 1 or 1 Execution halted ERROR: lazydata failed for package 'cluster' ** Removing '/home/dylan/src/R-2.3.1/library/cluster' make[2]: *** [cluster.ts] Error 1 make[2]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' make: *** [stamp-recommended] Error 2 note that i am using the GCC flags: CFLAGS=-march=opteron -ffast-math CXXFLAGS=-march=opteron -ffast-math any ideas? -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341
On Wed, 20 Sep 2006, Dylan Beaudette wrote:> Getting a very strange error with a new install of R from source on x86; > > make[3]: Leaving directory `/tmp/R.INSTALL.r20887/cluster/src' > ** R > ** data > ** moving datasets to lazyload DB > Error in factor(c(1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1), : > invalid labels; length 2 should be 1 or 1 > Execution halted > ERROR: lazydata failed for package 'cluster' > ** Removing '/home/dylan/src/R-2.3.1/library/cluster' > make[2]: *** [cluster.ts] Error 1 > make[2]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' > make[1]: *** [recommended-packages] Error 2 > make[1]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' > make: *** [stamp-recommended] Error 2 > > note that i am using the GCC flags: > CFLAGS=-march=opteron -ffast-math > CXXFLAGS=-march=opteron -ffast-mathWe do request you do not do so in the R-admin manual. From the gcc man page: This option should never be turned on by any -O option since it can result in incorrect output for programs which depend on an exact implementation of IEEE or ISO rules/specifications for math func- tions. R is such a program. -- Brian D. Ripley, ripley at stats.ox.ac.uk 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, UK Fax: +44 1865 272595
Dylan Beaudette <dylan.beaudette at gmail.com> writes:> Getting a very strange error with a new install of R from source on x86; > > make[3]: Leaving directory `/tmp/R.INSTALL.r20887/cluster/src' > ** R > ** data > ** moving datasets to lazyload DB > Error in factor(c(1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1), : > invalid labels; length 2 should be 1 or 1 > Execution halted > ERROR: lazydata failed for package 'cluster' > ** Removing '/home/dylan/src/R-2.3.1/library/cluster' > make[2]: *** [cluster.ts] Error 1 > make[2]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' > make[1]: *** [recommended-packages] Error 2 > make[1]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' > make: *** [stamp-recommended] Error 2 > > note that i am using the GCC flags: > CFLAGS=-march=opteron -ffast-math > CXXFLAGS=-march=opteron -ffast-math > > any ideas?Don't do that.... Seriously! -ffast-math will allow the compiler to break IEEE math specifications, which in turn will break R all over the place. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907