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Estou tentando instalar o igraph for R (3.2.3), que está instalado em um sistema CentOS 5.11. A cauda do erro se parece com:
foreign-graphml.c:65: warning: excess elements in struct initializer
foreign-graphml.c:65: warning: (near initialization for ‘blankEntityStruct’)
foreign-graphml.c: In function ‘igraph_read_graph_graphml’:
foreign-graphml.c:1330: error: ‘XML_PARSE_HUGE’ undeclared (first use in this function)
foreign-graphml.c:1330: error: (Each undeclared identifier is reported only once
foreign-graphml.c:1330: error: for each function it appears in.)
make: *** [foreign-graphml.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/usr/lib64/R/library/igraph’
The downloaded source packages are in
‘/tmp/RtmpBDaixr/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("igraph") :
installation of package ‘igraph’ had non-zero exit status
XML_PARSE_HUGE ficou preso em mim. O Quick Google descobriu que não aparece até a libxml2 2.7.3 ( link ). Parece que eu preciso construir uma versão mais recente para a máquina que foi encontrada neste site antes no link abaixo.
Instale o libxml2 2.7.X no CentOS 5.X
Quando executo a instalação para ele com
yum localinstall --nogpgcheck /usr/src/redhat/RPMS/x86_64/libxml2-2.7.8-1.x86_64.rpm
Eu entendo isso na cauda
Error: Missing Dependency: libxml2.so.2 is needed by package eel2-2.16.1-1.el5.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package evolution-data-server-1.12.3-18.el5.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package 1:gnome-utils-2.16.0-5.el5.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package libxslt-1.1.17-4.el5_8.3.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package 7:kdenetwork-3.5.4-13.el5_6.1.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package gnome-media-2.16.1-3.el5.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package gnome-pilot-2.0.13-16.i386 (installed)
Error: Missing Dependency: libxml2.so.2 is needed by package 1:control-center-2.16.0-16.el5.i386 (installed)
You could try using --skip-broken to work around the problem
You could try running: package-cleanup --problems
package-cleanup --dupes
rpm -Va --nofiles --nodigest
Eu pensei que talvez queira um pacote de 32 bits em vez
rpmbuild --target i386 -ba /usr/src/redhat/SPECS/libxml2.spec
yum localinstall --nogpgcheck /usr/src/redhat/RPMS/i386/libxml2-2.7.8-1.i386.rpm
Qual caudas
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package gtkhtml2-2.11.0-3.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package nautilus-2.16.2-10.el5.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package libgnome-java-2.12.4-3.fc6.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package nautilus-cd-burner-2.16.0-7.el5.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package gnome-spell-1.0.7-3.1.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package 1:gnome-utils-2.16.0-5.el5.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package gok-1.2.0-2.el5.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package libglade-java-2.12.5-3.fc6.x86_64 (installed)
Error: Missing Dependency: libxml2.so.2()(64bit) is needed by package evolution-webcal-2.7.1-6.x86_64 (installed)
You could try using --skip-broken to work around the problem
You could try running: package-cleanup --problems
package-cleanup --dupes
rpm -Va --nofiles --nodigest
Estou um pouco nervoso ao tentar usar o --skip-broken e o package-cleanup, já que preciso ter um patch de migração sólido para / das alterações (está em uma máquina de produção) e não sou tão versado em Tudo isso como eu deveria ser. Eu posso ter que girar uma VM para bater. Em última análise, tudo o que estou procurando é o pacote R igraph em execução no sistema. Alguém tem alguma ideia?
A solução foi derivada de uma postagem da Radek Simko:
wget ftp://xxmlsoft.org/libxml2/libxml2-2.7.8.tar.gz
tar -xvf libxml2-2.7.8.tar.gz
cd libxml2-2.7.8
./configure
make
sudo make install
Era simples compilar a partir da fonte para uma instalação. Eu poderia então:
install.packages("igraph")
Em R com sucesso.