search for: colamd

...m /usr/include/limits.h:145, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:122, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/syslimits.h:7, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:11, from colamd.c:677: /usr/include/bits/local_lim.h:36:26 error: linux/limits.h: No such file or directory make: *** [colamd.o] Error 1 ERROR: compilation failed for package 'lpSolve' ======================================================================== The first things that I tried was to figure out...

...*source* package 'Matrix' ... ** libs gcc -std=gnu99 -I/usr/local/R-devel/include -I./UFconfig -I/usr/local/include -fpic -g -O2 -c CHMfactor.c -o CHMfactor.o [..snip..] gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include -fpic -g -O2 -c colamd_global.c -o colamd_global.o gcc -std=gnu99 -I/usr/local/R-devel/include -I../Include -I../../UFconfig -I/usr/local/include -fpic -g -O2 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd_l.o # colamd.o ( cd Source ; make lib ) gcc -std=gnu99 -I/usr/l...

...(see the complete attached r_log.tar.gz) cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -I../UFc cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -I../UFc ar -rucs ../COLAMD.a colamd.o colamd_global.oM ( cd Source ; make lib )M Error expanding embedded variable.M *** Error code 2M M Stop in /tmp/R.INSTALL.IuAhvE/Matrix/src/AMD.M *** Error code 1M M Stop in /tmp/R.INSTALL.IuAhvE/Matrix/src.M ERROR: compilation failed for package 'Matrix'M ** Removing '/usr/l...

...sr/local/lib/R/include -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -D__NO_MATH_INLINES -fpic -O2 -fno-strict-aliasing -pipe -march=prescott -c colamd.c -o colamd.o cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -D__NO_MATH_INLINES...

Hi! I want to use R for network analysis and have tried to install the 'igraph' package. Unfortunately, the installation is aborted by an error: --snip-- gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -DUSING_R -I. -Ics -Iglpk -Iglpk/amd -Iglpk/colamd -I/usr/local/include -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DNDEBUG -DPACKAGE_VERSION=\"0.6\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-prote...

...e.c -o Csparse.o ... numerous lines deleted ... gcc -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -fPIC -g -O2 -c triplet_to_col.c -o triplet_to_col.o f77 -fPIC -g -O2 -c zpotf2.f -o zpotf2.o f77 -fPIC -g -O2 -c zpotrf.f -o zpotrf.o touch CHOLMOD.stamp UMFPACK.stamp COLAMD.stamp CCOLAMD.stamp AMD.stamp Metis.stamp LDL.stamp gmake[1]: Entering directory `/tmp/R.INSTALL.WMODs1/Matrix/src/CHOLMOD' ( cd Lib ; make ) make: don't know how to make w. Stop gmake[1]: *** [library] Error 2 I am running: > version _ platform i386-...

...Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o SPQR.a CHOLMOD.a COLAMD.a AMD.a -L/usr/local/apps/R/R-2.8.1/lib64/R/lib -lRlapack -lRblas -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lpthread -lm -pgf90libs /usr/lib64/crt1.o(.text+0x21): In function `_start': ../sysdeps/x86_64/elf/start.S:109: undefined reference to `main'...

...on and gcc 4.9's link time optimzation, because of its practice of building part of it as archive first. Specifically it builds some bundled libraries as archive first, the symbols of which are then entirely invisible in gcc 4.9. The Matrix package also does this awful practice, with CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a . One way of fixing R is: diff --git a/src/main/Makefile.in b/src/main/Makefile.in index 908b7ab..ce015b4 100644 --- a/src/main/Makefile.in +++ b/src/main/Makefile.in @@ -86,7 +86,7 @@ ALL_CPPFLAGS = $(ZLIB_CPPFLAGS) $(BZLIB_CPPFLAGS) $(PCRE_CPPFLAGS) \ R_ZLIBS = @BU...

...Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRlapack -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRblas -lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfui -lfsu -lsunmath -lmtsk -lm ld: fatal: file CHMfactor.o: wrong ELF class: ELFCLASS64 ld: fatal: File process...

...HMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o CHOLMOD.a COLAMD.a AMD.a -L/home/user/R/R-devel/lib -lRlapack -L/home/user/R/R-devel/lib -lRblas -R/opt/sun/sunstudio12/lib/amd64:/opt/sun/sunstudio12/lib/amd64:/opt/sun/lib/rtlibs/amd64:/opt/sun/lib/rtlibs/amd64 -L/opt/sun/sunstudio12/rtlibs/amd64 -L/opt/sun/sunstudio12/prod/lib/amd64 -lfui -lfai -lfsu -lmtsk -lpt...

..._valid.o arpack.o array.o atlas.o attributes.o basic_query.o bfgs.o bigint.o bignum.o bipartite.o blas.o bliss.o bliss_eqrefhash.o bliss_graph.o bliss_heap.o bliss_orbit.o bliss_partition.o bliss_timer.o bliss_utils.o cattributes.o centrality.o cliques.o clustertool.o cocitation.o cohesive_blocks.o colamd.o community.o complex.o components.o conversion.o cores.o cs_add.o cs_amd.o cs_chol.o cs_cholsol.o cs_compress.o cs_counts.o cs_cumsum.o cs_dfs.o cs_dmperm.o cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o cs_house.o cs_ipvec.o cs_leaf.o cs_...

Hello, In the src folder of my R package I have a.cc b.cc f/g/x.cc my Makevars.in has all: $(SHLIB) upon installing only, a.o and b.o is build and the final dll is comprised of a.o and b.o How can I instruct $(SHLIB) to pick up its source files from all subdirectories (or maybe a subset, though here it will be all) in src ? Much thanks Saptarshi

...front.o' Current working directory /tmp/R.INSTALL.KwaqDb/Matrix/src/SPQR/Lib *** Error code 1 make: Fatal error: Command failed for target `library' Current working directory /tmp/R.INSTALL.KwaqDb/Matrix/src/SPQR *** Error code 1 The following command caused the error: for d in SPQR CHOLMOD COLAMD AMD; do \ (cd ${d} && CFLAGS="-O -I/opt/SUNWspro/prod/include" CXXFLAGS="-O -I/opt/SUNWspro/prod/include" MkInclude="/home/choid/bin/R281/lib/R/etc/Makeconf" make library) || exit 1; \ done make: Fatal error: Command failed for target `sublibs' ERROR: com...

The bulk is on my forums - the final post for today is: Results to date: A. It looks like I am going to need a newer compiler for C - xlc/xlC V11 apparently does not understand this code: "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) Syntax error. I will have to check if R-devel has different code before asking for assistence. +2139 #ifdef