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Error compiling from source on macOS #382

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pat-s opened this issue Mar 26, 2020 · 9 comments
Closed

Error compiling from source on macOS #382

pat-s opened this issue Mar 26, 2020 · 9 comments

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@pat-s
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pat-s commented Mar 26, 2020

Compilers tested:

  • openMP enabled clang7
  • default clang (macOS 10.15.4)

The same goes for the previous version (1.2.4) so it looks like a generic problem.
I know that I could just install the binary but I would like to solve this for the source installation way.

Details 
Installing package into ‘/Users/pjs/Library/R/3.6/library’
(as ‘lib’ is unspecified)
trying URL 'https://ftp.fau.de/cran/src/contrib/igraph_1.2.5.tar.gz'
Content type 'application/x-gzip' length 2726569 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... ccache /usr/local/clang7/bin/clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether ccache /usr/local/clang7/bin/clang accepts -g... yes
checking for ccache /usr/local/clang7/bin/clang option to accept ISO C89... none needed
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether ccache /usr/local/clang7/bin/clang++ accepts -g... yes
checking how to run the C++ preprocessor... ccache /usr/local/clang7/bin/clang++ -E
checking for rintf... yes
checking for finite... yes
checking for expm1... yes
checking for rint... yes
checking for log2... yes
checking for logbl... yes
checking for snprintf... yes
checking for log1p... yes
checking for round... yes
checking for fmin... yes
checking for stpcpy... yes
checking how to run the C preprocessor... ccache /usr/local/clang7/bin/clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether stpcpy is declared... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking net/if.h usability... yes
checking net/if.h presence... yes
checking for net/if.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking net/if_dl.h usability... yes
checking net/if_dl.h presence... yes
checking for net/if_dl.h... yes
checking sys/sockio.h usability... yes
checking sys/sockio.h presence... yes
checking for sys/sockio.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking for struct sockaddr.sa_len... yes
checking for xml2-config... /usr/bin/xml2-config
checking for xmlSAXUserParseFile in -lxml2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for __gmpz_add in -lgmp... no
checking for glp_read_mps in -lglpk... no
configure: creating ./config.status
config.status: creating src/Makevars.tmp
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
gfortran  -fPIC  -Wall -g -O2  -c AMD/Source/amd.f -o AMD/Source/amd.o
f951: Warning: Nonconforming tab character in column 1 of line 422 [-Wtabs]
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_1.c -o AMD/Source/amd_1.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_2.c -o AMD/Source/amd_2.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_aat.c -o AMD/Source/amd_aat.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_control.c -o AMD/Source/amd_control.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_defaults.c -o AMD/Source/amd_defaults.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_dump.c -o AMD/Source/amd_dump.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_global.c -o AMD/Source/amd_global.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_info.c -o AMD/Source/amd_info.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_order.c -o AMD/Source/amd_order.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_post_tree.c -o AMD/Source/amd_post_tree.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_postorder.c -o AMD/Source/amd_postorder.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_preprocess.c -o AMD/Source/amd_preprocess.o
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c AMD/Source/amd_valid.c -o AMD/Source/amd_valid.o
gfortran  -fPIC  -Wall -g -O2  -c AMD/Source/amdbar.f -o AMD/Source/amdbar.o
f951: Warning: Nonconforming tab character in column 1 of line 422 [-Wtabs]
ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c CHOLMOD/Check/cholmod_check.c -o CHOLMOD/Check/cholmod_check.o
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:174:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:174:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:176:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", " , ") ;
        ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:176:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", " , ") ;
        ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:178:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", ")") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:178:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", ")") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:182:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [CHOLMOD/Check/cholmod_check.o] Error 1
@szhorvat
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I know it's not very helpful, I just wanted to note that it did compile for me on macOS 10.14 with clang 9.0 from MacPorts (but I doubt that this has much to do with the different compiler).

@gaborcsardi
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That does not look like a supported fortran compiler.

@pat-s
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pat-s commented Mar 27, 2020

The error starts in line

ccache /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.5\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c CHOLMOD/Check/cholmod_check.c -o CHOLMOD/Check/cholmod_check.o

The gfortran call is one line above.

I am using clang7 and gfortran6.1 as recommended here.

(The same occurs without ccache). What compilers are you using?

@gaborcsardi
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Oh, right! Sry, my mistake.

❯ R CMD config CC
clang

❯ clang -v
Apple clang version 11.0.0 (clang-1100.0.33.17)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

But CRAN is apparently also able to compile it with their compilers. Maybe it only fails with new SDKs, e.g. on Catalina?

@pat-s
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pat-s commented Mar 27, 2020

Seems like its related to Catalina.
I can't get it to compile no matter which CC compiler I use (with or without linking to the SDKs).

  • clang7 (CRAN)
  • gcc9
  • clang (apple default)

There is only sparse/no information about such issue for Catalina and I feel a bt lost here.

Apparently CRAN has no access to a Catalina machine and only runs/tests on El Capitan/Sierra. I am somewhat worried about the overall situation.
Sure, there are binaries but that cannot be the final solution when source installations are in an unknown state for the latest release of an OS... (not mentioning all of the implications for R-devel builds during CI runs)

@szhorvat
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szhorvat commented Mar 27, 2020 •
edited
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Just curious if you can compile the C interface alone, with the same toolchain (no Fortran needed for that). Instructions: https://igraph.org/c/#cinstall

If you don't want to fuss with dependencies, pass --disable-graphml to ./configure. Then no dependencies need to be installed. The error you saw came from a part of the code that is not related to GraphML anyway.

@pat-s
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pat-s commented Mar 28, 2020

Thanks for helping!

The following works

(default clang)

./configure --disable-graphml CFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' CC='/usr/bin/clang'

(custom clang7)

./configure --disable-graphml CFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' CC='/usr/local/clang7/clang'

CFLAGS here is important - otherwise I end up with

checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/Users/pjs/igraph':
configure: error: cannot run C compiled programs.

I have CFLAGS set in ~/.R/Makevars and can see that it is used (as shown in the first post)

@pat-s
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pat-s commented Apr 1, 2020

Turns out SDK 10.15 is the problem. Using 10.13 solves the problem

# install SDK10.13
wget https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX10.13.sdk.tar.xz
tar fvxz MacOSX10.13.sdk.tar.xz
sudo mv MacOSX10.13.sdk /Library/Developer/CommandLineTools/SDKs/
rm -rf MacOSX10.13*

~/.R/Makevars

CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk

We will need to have some discussion about this on R-SIG-MAC how to proceed further.

@pat-s pat-s closed this as completed Apr 1, 2020
@Colelyman
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In case you need another point of reference, I wasn't able to install the package using SDK 10.15 either. However, I was able to successfully install it using 10.14.

@lcolladotor lcolladotor mentioned this issue Feb 12, 2021
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@gaborcsardi @Colelyman @szhorvat @pat-s