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tidygraph lazy loading fails #16

Closed tdhock closed 8 months ago

tdhock commented 8 months ago

when checking akc

/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fvisibility=hidden -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vendor/cigraph/src/io/graphml.c -o vendor/cigraph/src/io/graphml.o
vendor/cigraph/src/io/graphml.c:46:10: fatal error: libxml/globals.h: No such file or directory
   46 | #include <libxml/globals.h>
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/th798/R/R-devel/etc/Makeconf:191: vendor/cigraph/src/io/graphml.o] Error 1
ERROR: compilation failed for package 'igraph'
* removing '/tmp/th798/7451013/R-devel/19/library/igraph'
...
ERROR: dependency 'igraph' is not available for package 'tidygraph'
* removing '/tmp/th798/7451013/R-devel/19/library/tidygraph'
...
* installing *source* package 'tidygraph' ...
** package 'tidygraph' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
g++ -std=gnu++17 -I"/home/th798/R/R-4.3.2/include" -DNDEBUG  -I'/tmp/th798/7451013/R-4.3.2/19/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/th798/R/R-4.3.2/include" -DNDEBUG  -I'/tmp/th798/7451013/R-4.3.2/19/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -g -O2  -c get_paths.cpp -o get_paths.o
g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o tidygraph.so cpp11.o get_paths.o
installing to /tmp/th798/7451013/R-4.3.2/19/library/00LOCK-tidygraph/00new/tidygraph/libs
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'igraph' 1.5.1 is being loaded, but >= 2.0.0 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'tidygraph'

root problem is that igraph was updated yesterday, https://cloud.r-project.org/web/packages/igraph/ 2.0.1.1 published 2024-01-30 no similar issues on https://github.com/igraph/rigraph/issues?q=globals+ yet. nor on https://r.igraph.org/articles/installation-troubleshooting is there a mis-match between system/conda libxml version, and version that igraph expects?

tdhock commented 8 months ago

https://github.com/igraph/rigraph/blob/1bd2bf79/src/vendor/cigraph/CHANGELOG.md says current master: Compatibility with libxml2 version 2.12. Previous version: 0.10.6 - 2023-07-13 Compatibility with libxml2 2.11. Looks like conda libxml2 on monsoon is older

th798@wind:~$ ls .conda/envs/emacs1/lib/libxml2.so*
.conda/envs/emacs1/lib/libxml2.so
.conda/envs/emacs1/lib/libxml2.so.2
.conda/envs/emacs1/lib/libxml2.so.2.9.14
tdhock commented 8 months ago

fresh conda install libxml2 gives me libxml2-2.10.4 R CMD INSTALL igraph gives missing include which can be fixed by removing quotes, see below

(igraph) th798@cn25:/tmp/th798/7475594/RtmpQlPKF7/downloaded_packages$ R CMD INSTALL igraph_igraph/
* installing to library '/projects/genomic-ml/R/4.2.3'
* installing *source* package 'igraph' ...
** package 'igraph' successfully unpacked and MD5 sums checked
** using staged installation
libxml2 include directory: /home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include
/usr/bin/cp -f src/Makevars.new src/Makevars
** libs
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c simpleraytracer.cpp -o simpleraytracer.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c rinterface_extra.c -o rinterface_extra.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c rrandom.c -o rrandom.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c rinterface.c -o rinterface.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c cpprinterface.cpp -o cpprinterface.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c lazyeval.c -o lazyeval.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c init.cpp -o init.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/second.f -o vendor/arpack/second.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o
/usr/bin/gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2  -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/version.c -o vendor/cigraph/src/version.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/eigenvector.c -o vendor/cigraph/src/centrality/eigenvector.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/truss.cpp -o vendor/cigraph/src/centrality/truss.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack.cpp -o vendor/cigraph/src/centrality/prpack.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/pagerank.c -o vendor/cigraph/src/centrality/pagerank.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/closeness.c -o vendor/cigraph/src/centrality/closeness.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/hub_authority.c -o vendor/cigraph/src/centrality/hub_authority.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/coreness.c -o vendor/cigraph/src/centrality/coreness.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/centralization.c -o vendor/cigraph/src/centrality/centralization.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/betweenness.c -o vendor/cigraph/src/centrality/betweenness.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/centrality_other.c -o vendor/cigraph/src/centrality/centrality_other.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_utils.cpp -o vendor/cigraph/src/centrality/prpack/prpack_utils.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_base_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_base_graph.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_result.cpp -o vendor/cigraph/src/centrality/prpack/prpack_result.o
/usr/bin/g++ -std=gnu++14 -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/centrality/prpack/prpack_solver.cpp -o vendor/cigraph/src/centrality/prpack/prpack_solver.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/glet.c -o vendor/cigraph/src/cliques/glet.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/maximal_cliques.c -o vendor/cigraph/src/cliques/maximal_cliques.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/cliquer_wrapper.c -o vendor/cigraph/src/cliques/cliquer_wrapper.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/cliques.c -o vendor/cigraph/src/cliques/cliques.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/cliquer/cliquer.c -o vendor/cigraph/src/cliques/cliquer/cliquer.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/cliquer/reorder.c -o vendor/cigraph/src/cliques/cliquer/reorder.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/cliques/cliquer/cliquer_graph.c -o vendor/cigraph/src/cliques/cliquer/cliquer_graph.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/community/voronoi.c -o vendor/cigraph/src/community/voronoi.o
/usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/community/optimal_modularity.c -o vendor/cigraph/src/community/optimal_modularity.o
In file included from vendor/cigraph/src/community/optimal_modularity.c:32:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: glpk.h: No such file or directory
 #include <glpk.h>
          ^~~~~~~~
compilation terminated.
make: *** [/packages/r/4.2.3-5aaqx6d/rlib/R/etc/Makeconf:169: vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package 'igraph'
* removing '/projects/genomic-ml/R/4.2.3/igraph'
(igraph) th798@cn25:/tmp/th798/7475594/RtmpQlPKF7/downloaded_packages$ cd igraph_igraph/src/
(igraph) th798@cn25:/tmp/th798/7475594/RtmpQlPKF7/downloaded_packages/igraph_igraph/src$ /usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/community/optimal_modularity.c -o vendor/cigraph/src/community/optimal_modularity.o
In file included from vendor/cigraph/src/community/optimal_modularity.c:32:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: glpk.h: No such file or directory
 #include <glpk.h>
          ^~~~~~~~
compilation terminated.
(igraph) th798@cn25:/tmp/th798/7475594/RtmpQlPKF7/downloaded_packages/igraph_igraph/src$ /usr/bin/gcc -I"/packages/r/4.2.3-5aaqx6d/rlib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/projects/genomic-ml/R/4.2.3/cpp11/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/cigraph/src/community/optimal_modularity.c -o vendor/cigraph/src/community/optimal_modularity.o
(igraph) th798@cn25:/tmp/th798/7475594/RtmpQlPKF7/downloaded_packages/igraph_igraph/src$
tdhock commented 8 months ago

globals.h does exist, under ~/.conda/envs/emacs1/include/libxml2/libxml/globals.h so actually version is not the problem.

tdhock commented 8 months ago

deleting the quotes for globals.h fixes the problem, just like it did for glpk.h not found above. problem is in Makevars:

PKG_CPPFLAGS=-DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" \
    -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= \
    -DPRPACK_IGRAPH_SUPPORT \
    -DHAVE_GFORTRAN=1 \
    -D_GNU_SOURCE=1

In Makevars.in we have similar:

So @cflags@ is expanded to -I"/home/th798/.conda/envs/igraph/include/libxml2 -I/home/th798/.conda/envs/igraph/include" which would work if there were no quotes, where do these come from?

tdhock commented 8 months ago

upstreadm says they will fix