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igraph / rigraph

igraph R package
https://r.igraph.org
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Installation Error in offline machine: make: *** [core/io/dl-parser.o] Error 1 #573

Closed tedmoorman closed 2 years ago

tedmoorman commented 2 years ago

Describe the bug Installation fails to install igraph on offline machine. Here is a portion of relevant code, rest is in attachment. Also tried to build with the development version, but received error about a missing DESCRIPTION file.

To reproduce

R CMD INSTALL igraph_1.3.4.tar.gz
#or 
install.packages("igraph")
...
g++ -std=c++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fPIC  -O3 -march=native -Wno-ignored-attributes -c core/hrg/hrg.cc -o core/hrg/hrg.o
g++ -std=c++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fPIC  -O3 -march=native -Wno-ignored-attributes -c core/hrg/hrg_types.cc -o core/hrg/hrg_types.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/internal/glpk_support.c -o core/internal/glpk_support.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/internal/hacks.c -o core/internal/hacks.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/internal/lsap.c -o core/internal/lsap.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/internal/qsort.c -o core/internal/qsort.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/internal/qsort_r.c -o core/internal/qsort_r.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/internal/zeroin.c -o core/internal/zeroin.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/io/dimacs.c -o core/io/dimacs.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/io/dl-lexer.c -o core/io/dl-lexer.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/io/dl-parser.c -o core/io/dl-parser.o
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/io/dl.c -o core/io/dl.o
yy.tab.c: In function ‘yytnamerr’:
yy.tab.c:1088:3: warning: implicit declaration of function ‘stpcpy’ [-Wimplicit-function-declaration]
yy.tab.c:1088:34: error: invalid operands to binary - (have ‘int’ and ‘char *’)
yy.tab.c: In function ‘yysyntax_error’:
yy.tab.c:1147:13: warning: assignment makes pointer from integer without a cast [enabled by default]
yy.tab.c:1163:12: warning: assignment makes pointer from integer without a cast [enabled by default]
gcc -std=c99  -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.2.9019\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -O3 -march=native  -c core/io/dot.c -o core/io/dot.o
src/core/io/dl-lexer.c: In function ‘igraph_dl_yy_init_buffer’:
src/core/io/dl-lexer.c:1879:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
make: *** [core/io/dl-parser.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘igraph’
* removing ‘/R/x86_64-pc-linux-gnu-library/4.0/igraph’

Version information

tedmoorman commented 2 years ago

See fix in #212