As above. I am running an ubuntu 20.04 LT desktop on a university research computer on which I do not have administrator rights. install.packages(‘igraph’) runs for quite a while, but then abends (on several attempts) with the final command and error message as i give below. Oddly, I have had no problem installing igraph 2.0.1.1 on an ubuntu 22.04 container on my home pc. Even more oddly, the admin folks have been able to install igraph with no problem on their desktop that they tell me is identically set up as mine. The admins note that I have installed the R package reticulate and run reticulate::install_python(), which sets up a library that may include the same packages that R igraph may be requiring. They speculate that this may be setting up a mapping of the ubuntu packages that conflicts with what is expected by igraph. This is beyond me. But I am hoping that you can help me get igraph 2.0.1.1 installed.
Many thanks for any help that you can give me to get igraph 2.0.0.1 successfully installed!
Larry Hunsicker
Following what szhorvat requested in response to springc’s message of Aug 2023 " Unable to install igraph on Mac for R, I am attaching the following setup information:
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.6 LTS
Release: 20.04
Codename: focaluname -a
Linux idas-research-hunsickerl 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxwhich R
/opt/R/bin/RR --version
R version 4.3.1 (2023-06-16) – “Beagle Scouts”
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
Licenses - GNU Project - Free Software Foundation.R CMD config --all
CC = gcc
CFLAGS = -g -O2
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CC17 = gcc -std=gnu17
C17FLAGS = -g -O2
CC23 = gcc -std=gnu2x
C23FLAGS = -g -O2
CC90 = gcc -std=gnu90
C90FLAGS = -g -O2
CC99 = gcc -std=gnu99
C99FLAGS = -g -O2
CXX = g++ -std=gnu++17
CXXFLAGS = -g -O2
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11STD = -std=gnu++11
CXX11FLAGS = -g -O2
CXX11PICFLAGS = -fpic
CXX14 = g++
CXX14STD = -std=gnu++14
CXX14FLAGS = -O3 -march=native -mtune=native -fPIC
CXX14PICFLAGS = -fpic
CXX17 = g++
CXX17STD = -std=gnu++17
CXX17FLAGS = -g -O2
CXX17PICFLAGS = -fpic
CXX20 =
CXX20STD =
CXX20FLAGS =
CXX20PICFLAG =
CXX23 =
CXX23STD =
CXX23FLAGS =
CXX23PICFLAGS =
DYLIB_EXT = .so
DYLIB_LD = gcc
DYLIB_LDFLAGS = -shared -fopenmp
FC = gfortran
FFLAGS = -g -O2
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
FCFLAGS = -g -O2
SAFE_FFLAGS = -g -O2 -msse2 -mfpmath=sse
OBJC =
OBJCFLAGS =
JAVA = /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
JAVAC = /usr/lib/jvm/java-8-openjdk-amd64/bin/javac
JAVAH = /usr/lib/jvm/java-8-openjdk-amd64/bin/javah
JAR = /usr/lib/jvm/java-8-openjdk-amd64/bin/jar
JAVA_HOME = /usr/lib/jvm/java-8-openjdk-amd64
JAVA_LIBS = -L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm
JAVA_CPPFLAGS = -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux
LDFLAGS = -L/usr/local/lib
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++ -std=gnu++17
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX11LD = g++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = g++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = g++ -std=gnu++17
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD =
SHLIB_CXX20LDFLAGS = -shared
SHLIB_CXX23LD =
SHLIB_CXX23LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS = -I/usr/include/tcl8.6 -I/usr/include/tcl8.6
TCLTK_LIBS = -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-linux-gnu -ltk8.6 -lX11 -lXss -lXext
BLAS_LIBS = -L/opt/R/lib/R/lib -lRblas
LAPACK_LIBS = -L/opt/R/lib/R/lib -lRlapack
MAKE = make
LIBnn = lib
AR = ar
NM = /usr/bin/nm -B
RANLIB = ranlib
LTO =
LTO_FC =
LTO_LD =The following variables are defunct
CPP CXXCPP
gcc --version
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.g++ --version
g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.~/.R$ more Makevars
CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=g++CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=g++
Final output just before the install.packages("igraph) abended:
gcc -I"/opt/R/lib/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -I"/opt/conda/include/libxml2 -I/opt/conda/include" -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/home/hunsickerl/R/x86_64-pc-linux-gnu-library/4.3/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -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.