PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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Attempting fresh install throws igraph exception #83

Closed gtng92 closed 7 years ago

gtng92 commented 7 years ago
tng92@Langley:~/Desktop/Kaphi$ R CMD INSTALL pkg
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘Kaphi’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c blank.cpp -o blank.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -Iigraph/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dQAL-6.3.c -o dQAL-6.3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -Iigraph/include -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kernel.c -o kernel.o
In file included from kernel.c:18:0:
igraph/include/igraph.h:31:28: fatal error: igraph_version.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'kernel.o' failed
make: *** [kernel.o] Error 1
ERROR: compilation failed for package ‘Kaphi’
* removing ‘/usr/local/lib/R/site-library/Kaphi’
* restoring previous ‘/usr/local/lib/R/site-library/Kaphi’
0ldM4j0r commented 7 years ago

I got same thing on the mac mini, so this isn't a linux only issue.

ArtPoon commented 7 years ago

User is required to compile a local version of igraph (based on Rosemary's fork of their repo), which has some modifications for thread safety. If user followed installation instructions then this problem should not arise.