I cant install subversion with MacPorts on mountain lion. It fails installting db46, here the log:
UPDATE: I also opened a ticket at macports: https://trac.macports.org/ticket/35570
:debug:main db46 has no conflicts
:debug:main Executing org.macports.main (db46)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:main Skipping completed org.macports.archivefetch (db46)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (db46)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (db46)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (db46)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (db46)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.configure (db46)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Tue Aug 7 14:51:37 CEST 2012
:notice:build ---> Building db46
:debug:build Executing org.macports.build (db46)
:debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.8'
:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/work/db-4.6.21/build_unix" && /usr/bin/make -j4 -w all'
:debug:build Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/work/db-4.6.21/build_unix" && /usr/bin/make -j4 -w all
:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/work/db-4.6.21/build_unix'
:info:build /bin/sh ./libtool --mode=compile /usr/bin/clang -c -pipe -O2 -arch x86_64 -I../dist/.. -I/opt/local/include ../dist/../db_dump185/db_dump185.c
:info:build /bin/sh ./libtool --mode=link /usr/bin/clang -pipe -O2 -arch x86_64 -o db_upgrade -L/opt/local/lib -arch x86_64 \
:info:build db_upgrade.lo util_sig.lo libdb-4.6.la -lpthread
:info:build /bin/sh ./libtool --mode=compile /usr/bin/clang -c -I. -I../dist/.. -I/opt/local/include -pipe -O2 -arch x86_64 ../dist/../db_verify/db_verify.c
:info:build /usr/bin/clang -c -pipe -O2 -arch x86_64 -I../dist/.. -I/opt/local/include ../dist/../db_dump185/db_dump185.c -fno-common -DPIC -o .libs/db_dump185.o
:info:build /usr/bin/clang -c -I. -I../dist/.. -I/opt/local/include -pipe -O2 -arch x86_64 ../dist/../db_verify/db_verify.c -fno-common -DPIC -o .libs/db_verify.o
:info:build ../dist/../db_dump185/db_dump185.c:211:13: warning: implicit declaration of function 'dbopen' is invalid in C99 [-Wimplicit-function-declaration]
:info:build if ((dbp = dbopen(argv[0], O_RDONLY, 0, DB_BTREE, NULL)) == NULL) {
:info:build ^
:info:build ../dist/../db_dump185/db_dump185.c:211:11: warning: incompatible integer to pointer conversion assigning to 'DB *' (aka 'struct __db *') from 'int';
:info:build if ((dbp = dbopen(argv[0], O_RDONLY, 0, DB_BTREE, NULL)) == NULL) {
:info:build ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:info:build ../dist/../db_dump185/db_dump185.c:212:12: warning: incompatible integer to pointer conversion assigning to 'DB *' (aka 'struct __db *') from 'int';
:info:build if ((dbp =
:info:build ^
:info:build ../dist/../db_dump185/db_dump185.c:228:24: error: no member named 'seq' in 'struct __db'
:info:build while (!(rval = dbp->seq(dbp, &key, &data, R_NEXT))) {
:info:build ~~~ ^
:info:build ../dist/../db_dump185/db_dump185.c:228:46: error: use of undeclared identifier 'R_NEXT'
:info:build while (!(rval = dbp->seq(dbp, &key, &data, R_NEXT))) {
:info:build ^
:info:build ../dist/../db_dump185/db_dump185.c:233:24: error: no member named 'seq' in 'struct __db'
:info:build while (!(rval = dbp->seq(dbp, &key, &data, R_NEXT))) {
:info:build ~~~ ^
:info:build ../dist/../db_dump185/db_dump185.c:233:46: error: use of undeclared identifier 'R_NEXT'
:info:build while (!(rval = dbp->seq(dbp, &key, &data, R_NEXT))) {
:info:build ^
:info:build ../dist/../db_dump185/db_dump185.c:261:18: error: no member named 'internal' in 'struct __db'
:info:build hash185p = dbp->internal;
:info:build ~~~ ^
:info:build ../dist/../db_dump185/db_dump185.c:263:19: error: no member named 'internal' in 'struct __db'
:info:build hash186p = dbp->internal;
:info:build ~~~ ^
:info:build ../dist/../db_dump185/db_dump185.c:288:13: error: no member named 'internal' in 'struct __db'
:info:build btp = dbp->internal;
:info:build ~~~ ^
:info:build 3 warnings and 7 errors generated.
:info:build make: *** [db_dump185.lo] Error 1
:info:build make: *** Waiting for unfinished jobs....
:info:build /usr/bin/clang -c -I. -I../dist/.. -I/opt/local/include -pipe -O2 -arch x86_64 ../dist/../db_verify/db_verify.c -o db_verify.o >/dev/null 2>&1
:info:build /usr/bin/clang -pipe -O2 -arch x86_64 -o .libs/db_upgrade -arch x86_64 .libs/db_upgrade.o .libs/util_sig.o -L/opt/local/lib ./.libs/libdb-4.6.dylib -lpthread
:info:build creating db_upgrade
:info:build /bin/sh ./libtool --mode=execute true db_upgrade
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/work/db-4.6.21/build_unix'
:info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/work/db-4.6.21/build_unix" && /usr/bin/make -j4 -w all
:info:build Exit code: 2
:error:build org.macports.build for port db46 returned: command execution failed
:debug:build Error code: CHILDSTATUS 4210 2
:debug:build Backtrace: command execution failed
while executing
"system -nice 0 $fullcmdstring"
("eval" body line 1)
invoked from within
"eval system $notty $nice \$fullcmdstring"
invoked from within
"command_exec build"
(procedure "portbuild::build_main" line 8)
invoked from within
"$procedure $targetname"
:info:build Warning: targets not executed for db46: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port db46 for details:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_databases_db46/db46/main.log
admins-MacBook-Pro:config admin$
There was an older version of db.h in /opt/local/include/. After deletion of the file the problem was fixed.
Related
I am trying to run a make file in MacOS sierra, but it seems to have trouble with the header of the Zlib (see below).
I have tried to install a separate version with brew and pass the directory of the brew zlib installation in the configure file.
./configure --prefix=/usr/local/etherlab --with-xml-prefix=/usr/local/opt/libxml2 --with-zlib-dir=/usr/local/opt/zlib CXXFLAGS=-std=c++11
However, when I run make I got the error
$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in proto
make[2]: Nothing to be done for `all'.
Making all in lib
Making all in LibDLS
make[3]: Nothing to be done for `all'.
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/etherlab/include -Wall -I/usr/local/include -I/usr/local/opt/zlib/include -I/usr/local/opt/libxml2/include/libxml2 -std=c++11 -MT libdls_la-ZLib.lo -MD -MP -MF .deps/libdls_la-ZLib.Tpo -c -o libdls_la-ZLib.lo `test -f 'ZLib.cpp' || echo './'`ZLib.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/etherlab/include -Wall -I/usr/local/include -I/usr/local/opt/zlib/include -I/usr/local/opt/libxml2/include/libxml2 -std=c++11 -MT libdls_la-ZLib.lo -MD -MP -MF .deps/libdls_la-ZLib.Tpo -c ZLib.cpp -fno-common -DPIC -o .libs/libdls_la-ZLib.o
ZLib.cpp:22:10: warning: non-portable path to file '<ZLib.h>'; specified path differs in case from file name on disk
[-Wnonportable-include-path]
#include <zlib.h>
^~~~~~~~
<ZLib.h>
In file included from ZLib.cpp:22:
./zlib.h:42:17: error: unknown type name 'string'; did you mean 'std::string'?
EZLib(const string &pmsg) : Exception(pmsg) {};
^~~~~~
std::string
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iosfwd:194:65: note:
'std::string' declared here
typedef basic_string<char, char_traits<char>, allocator<char> > string;
^
ZLib.cpp:90:5: error: unknown type name 'uLongf'
uLongf out_size;
^
ZLib.cpp:104:17: error: use of undeclared identifier 'uLongf'
out_size = (uLongf) (src_size * 1.01 + 12 + 0.5);
^
ZLib.cpp:117:28: error: use of undeclared identifier 'Bytef'
comp_ret = ::compress((Bytef *) _out_buf, &out_size,
^
ZLib.cpp:117:35: error: expected expression
comp_ret = ::compress((Bytef *) _out_buf, &out_size,
^
ZLib.cpp:118:34: error: unknown type name 'Bytef'
(const Bytef *) src, src_size);
^
ZLib.cpp:117:16: error: no member named 'compress' in the global namespace; did you mean simply 'compress'?
comp_ret = ::compress((Bytef *) _out_buf, &out_size,
^~~~~~~~~~
compress
ZLib.cpp:88:12: note: 'compress' declared here
void ZLib::compress(const char *src, unsigned int src_size)
^
ZLib.cpp:120:21: error: use of undeclared identifier 'Z_OK'
if (comp_ret != Z_OK) // Fehler beim Komprimieren
^
ZLib.cpp:123:25: error: use of undeclared identifier 'Z_BUF_ERROR'
if (comp_ret == Z_BUF_ERROR) err << " (BUFFER ERROR)";
^
ZLib.cpp:155:5: error: unknown type name 'uLongf'
uLongf zlib_out_size = out_size;
^
ZLib.cpp:173:32: error: use of undeclared identifier 'Bytef'
uncomp_ret = ::uncompress((Bytef *) _out_buf, &zlib_out_size,
^
ZLib.cpp:173:39: error: expected expression
uncomp_ret = ::uncompress((Bytef *) _out_buf, &zlib_out_size,
^
ZLib.cpp:174:38: error: unknown type name 'Bytef'
(const Bytef *) src, src_size);
^
ZLib.cpp:173:18: error: no member named 'uncompress' in the global namespace; did you mean simply 'uncompress'?
uncomp_ret = ::uncompress((Bytef *) _out_buf, &zlib_out_size,
^~~~~~~~~~~~
uncompress
ZLib.cpp:150:12: note: 'uncompress' declared here
void ZLib::uncompress(const char *src, unsigned int src_size,
^
ZLib.cpp:176:23: error: use of undeclared identifier 'Z_OK'
if (uncomp_ret != Z_OK) // Fehler beim Dekomprimieren
^
ZLib.cpp:179:27: error: use of undeclared identifier 'Z_BUF_ERROR'
if (uncomp_ret == Z_BUF_ERROR) {
^
1 warning and 16 errors generated.
make[3]: *** [libdls_la-ZLib.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Digging a bit more I found that I could try to add
#include <string>
#include <cstring>
to the header zlib.h but this does not work either.
What else can I do to solve this issue?.
I'm using bitbake 1.32.0, Yocto 2.2.2 (Poky) trying to add protobuf-c to my build. I keep getting a build failure on protobuf_2.6.1 (protobuf-c depends on protobuf).
I can manually download the Protobuf source code and cross-compile it without any problems. But for some reason Yocto can't build it.
During the Yocto build process, libprotobuf-lite.so links okay, but libprotobuf.so fails linking due to these errors:
| /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libc_nonshared.a(elf-init.oS): In function `__libc_csu_init':
| /usr/src/debug/glibc/2.24-r0/git/csu/elf-init.c:87: undefined reference to `__init_array_end'
| /usr/src/debug/glibc/2.24-r0/git/csu/elf-init.c:87: undefined reference to `__init_array_start'
| /home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/libexec/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0/ld: .libs/libprotobuf.so.9.0.1: hidden symbol `__init_array_end' isn't defined
| /home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/libexec/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0/ld: final link failed: Bad value
I have tried looking through the .o files that are part of libprotobuf.so but are not included in libprotobuf-lite.so, to see if anything directly references the missing symbols, but I haven't found anything useful yet.
For a while I thought the culprit was -nostdlib. But then I saw libprotobuf-lite compiles just fine with that flag, and the -lc and -lgcc flags are included in the link command.
The recipe is a very straightforward autotools setup.
SUMMARY = "Protocol Buffers - structured data serialisation mechanism"
DESCRIPTION = "Protocol Buffers are a way of encoding structured data in an \
efficient yet extensible format. Google uses Protocol Buffers for almost \
all of its internal RPC protocols and file formats."
HOMEPAGE = "https://github.com/google/protobuf"
SECTION = "console/tools"
LICENSE = "BSD-3-Clause"
PACKAGE_BEFORE_PN = "${PN}-compiler"
DEPENDS = "zlib"
RDEPENDS_${PN}-compiler = "${PN}"
RDEPENDS_${PN}-dev += "${PN}-compiler"
LIC_FILES_CHKSUM =
"file://LICENSE;md5=af6809583bfde9a31595a58bb4a24514"
SRCREV = "bba83652e1be610bdb7ee1566ad18346d98b843c"
PV = "2.6.1+git${SRCPV}"
SRC_URI = "git://github.com/google/protobuf.git"
EXTRA_OECONF += " --with-protoc=echo"
inherit autotools
S = "${WORKDIR}/git"
FILES_${PN}-compiler = "${bindir} ${libdir}/libprotoc${SOLIBS}"
BBCLASSEXTEND = "native nativesdk"
Here is the more complete error statement:
| arm-agl-linux-gnueabi-libtool: link: arm-agl-linux-gnueabi-g++ -march=armv7-a -marm -mfpu=neon -mfloat-abi=softfp -mcpu=cortex-a9 --sysroot=/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4 -fPIC -DPIC -shared -nostdlib /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/Scrt1.o /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/crti.o /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/arm-agl-linux-gnueabi/6.2.0/crtbeginS.o google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o google/protobuf/stubs/.libs/common.o google/protobuf/stubs/.libs/once.o google/protobuf/stubs/.libs/stringprintf.o google/protobuf/.libs/extension_set.o google/protobuf/.libs/generated_message_util.o google/protobuf/.libs/message_lite.o google/protobuf/.libs/repeated_field.o google/protobuf/.libs/wire_format_lite.o google/protobuf/io/.libs/coded_stream.o google/protobuf/io/.libs/zero_copy_stream.o google/protobuf/io/.libs/zero_copy_stream_impl_lite.o google/protobuf/stubs/.libs/strutil.o google/protobuf/stubs/.libs/substitute.o google/protobuf/stubs/.libs/structurally_valid.o google/protobuf/.libs/descriptor.o google/protobuf/.libs/descriptor.pb.o google/protobuf/.libs/descriptor_database.o google/protobuf/.libs/dynamic_message.o google/protobuf/.libs/extension_set_heavy.o google/protobuf/.libs/generated_message_reflection.o google/protobuf/.libs/message.o google/protobuf/.libs/reflection_ops.o google/protobuf/.libs/service.o google/protobuf/.libs/text_format.o google/protobuf/.libs/unknown_field_set.o google/protobuf/.libs/wire_format.o google/protobuf/io/.libs/gzip_stream.o google/protobuf/io/.libs/printer.o google/protobuf/io/.libs/strtod.o google/protobuf/io/.libs/tokenizer.o google/protobuf/io/.libs/zero_copy_stream_impl.o google/protobuf/compiler/.libs/importer.o google/protobuf/compiler/.libs/parser.o -lpthread -lz -L/home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/lib/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0 -L/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/lib -L/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/arm-agl-linux-gnueabi/6.2.0 -L/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libstdc++.so -lm /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libssp_nonshared.a -lc -lgcc_s -lgcc /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/arm-agl-linux-gnueabi/6.2.0/crtendS.o /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/crtn.o -march=armv7-a -marm -mfpu=neon -mfloat-abi=softfp -mcpu=cortex-a9 --sysroot=/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4 -pthread -O2 -g -fstack-protector-strong -Wl,-O1 -Wl,--hash-style=gnu -Wl,--as-needed -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libprotobuf.so.9 -o .libs/libprotobuf.so.9.0.1
| arm-agl-linux-gnueabi-libtool: link: arm-agl-linux-gnueabi-g++ -march=armv7-a -marm -mfpu=neon -mfloat-abi=softfp -mcpu=cortex-a9 --sysroot=/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4 -fPIC -DPIC -shared -nostdlib /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/Scrt1.o /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/crti.o /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/arm-agl-linux-gnueabi/6.2.0/crtbeginS.o google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o google/protobuf/stubs/.libs/common.o google/protobuf/stubs/.libs/once.o google/protobuf/stubs/.libs/stringprintf.o google/protobuf/.libs/extension_set.o google/protobuf/.libs/generated_message_util.o google/protobuf/.libs/message_lite.o google/protobuf/.libs/repeated_field.o google/protobuf/.libs/wire_format_lite.o google/protobuf/io/.libs/coded_stream.o google/protobuf/io/.libs/zero_copy_stream.o google/protobuf/io/.libs/zero_copy_stream_impl_lite.o -lpthread -lz -L/home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/lib/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0 -L/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/lib -L/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/arm-agl-linux-gnueabi/6.2.0 -L/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libstdc++.so -lm /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libssp_nonshared.a -lc -lgcc_s -lgcc /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/arm-agl-linux-gnueabi/6.2.0/crtendS.o /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/crtn.o -march=armv7-a -marm -mfpu=neon -mfloat-abi=softfp -mcpu=cortex-a9 --sysroot=/home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4 -pthread -O2 -g -fstack-protector-strong -Wl,-O1 -Wl,--hash-style=gnu -Wl,--as-needed -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libprotobuf-lite.so.9 -o .libs/libprotobuf-lite.so.9.0.1
| ERROR: oe_runmake failed
| /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libc_nonshared.a(elf-init.oS): In function `__libc_csu_init':
| /usr/src/debug/glibc/2.24-r0/git/csu/elf-init.c:87: undefined reference to `__init_array_end'
| /usr/src/debug/glibc/2.24-r0/git/csu/elf-init.c:87: undefined reference to `__init_array_start'
| /home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/libexec/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0/ld: .libs/libprotobuf-lite.so.9.0.1: hidden symbol `__init_array_end' isn't defined
| /home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/libexec/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0/ld: final link failed: Bad value
| collect2: error: ld returned 1 exit status
| make[3]: *** [libprotobuf-lite.la] Error 1
| make[3]: *** Waiting for unfinished jobs....
| /home/cjholmes/gen4/build/tmp/sysroots/imx6dlleargen4/usr/lib/libc_nonshared.a(elf-init.oS): In function `__libc_csu_init':
| /usr/src/debug/glibc/2.24-r0/git/csu/elf-init.c:87: undefined reference to `__init_array_end'
| /usr/src/debug/glibc/2.24-r0/git/csu/elf-init.c:87: undefined reference to `__init_array_start'
| /home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/libexec/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0/ld: .libs/libprotobuf.so.9.0.1: hidden symbol `__init_array_end' isn't defined
| /home/cjholmes/gen4/build/tmp/sysroots/x86_64-linux/usr/libexec/arm-agl-linux-gnueabi/gcc/arm-agl-linux-gnueabi/6.2.0/ld: final link failed: Bad value
| collect2: error: ld returned 1 exit status
| make[3]: *** [libprotobuf.la] Error 1
| make[3]: Leaving directory `/home/cjholmes/gen4/build/tmp/work/cortexa9-neon-agl-linux-gnueabi/protobuf/2.6.1+gitAUTOINC+bba83652e1-r0/build/src'
| make[2]: *** [all] Error 2
| make[2]: Leaving directory `/home/cjholmes/gen4/build/tmp/work/cortexa9-neon-agl-linux-gnueabi/protobuf/2.6.1+gitAUTOINC+bba83652e1-r0/build/src'
| make[1]: *** [all-recursive] Error 1
| make[1]: Leaving directory `/home/cjholmes/gen4/build/tmp/work/cortexa9-neon-agl-linux-gnueabi/protobuf/2.6.1+gitAUTOINC+bba83652e1-r0/build'
| make: *** [all] Error 2
| WARNING: /home/cjholmes/gen4/build/tmp/work/cortexa9-neon-agl-linux-gnueabi/protobuf/2.6.1+gitAUTOINC+bba83652e1-r0/temp/run.do_compile.121250:1 exit 1 from 'exit 1'
| ERROR: Function failed: do_compile (log file is located at /home/cjholmes/gen4/build/tmp/work/cortexa9-neon-agl-linux-gnueabi/protobuf/2.6.1+gitAUTOINC+bba83652e1-r0/temp/log.do_compile.121250)
I could really use some pointers on what to look at next. This has eaten a lot of hours already.
I am trying to install a linear solver called PDSLin on ubuntu16.04 LTS machine. I installed all the dependencies but when running make for PDSLin I got those warnings and errors. I do not understand from where -c in gcc -c come from and whether it is the reason of not identifying "superlu_options_t" variable.
(cd src; make lib;)
make[1]: Entering directory '/home/afrah/pdslin/src'
(make all; cd slu; make lib)
make[2]: Entering directory '/home/afrah/pdslin/src'
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_graph.c
pdslin_graph.c: In function ‘a_plus_at_CompRow_loc_with_diag’:
pdslin_graph.c:51:26: warning: variable ‘sz_tcolind_loc’ set but not used [-Wunused-but-set-variable]
int_t sz_tcolind_send, sz_tcolind_loc, sz_tcolind_recv;
^
pdslin_graph.c: In function ‘perm_snodes’:
pdslin_graph.c:898:22: warning: passing argument 1 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, m_rowptr, m_colind, &numflag, options,
^
// similar warnings
pdslin_graph.c:1034:9: warning: variable ‘numflag’ set but not used [-Wunused-but-set-variable]
int numflag;
^
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_wrapper.c
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_perm.c
pdslin_perm.c: In function ‘comp_perm’:
pdslin_perm.c:113:24: warning: passing argument 1 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, rowptr_l, colind_l, &numflag, options,
^
In file included from pdslin_perm.c:14:0:
/home/afrah/SuperLU_DIST_5.1.2/SRC/parmetis.h:102:13: note: expected ‘idx_t * {aka long int *}’ but argument is of type ‘int *’
int __cdecl ParMETIS_V3_NodeND(
^
pdslin_perm.c:113:30: warning: passing argument 2 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, rowptr_l, colind_l, &numflag, options,
^
In file included from pdslin_perm.c:14:0:
/home/afrah/SuperLU_DIST_5.1.2/SRC/parmetis.h:102:13: note: expected ‘idx_t * {aka long int *}’ but argument is of type ‘int *’
int __cdecl ParMETIS_V3_NodeND(
^
pdslin_perm.c:113:40: warning: passing argument 3 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, rowptr_l, colind_l, &numflag, options,
^
// warnings
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_util.c
In file included from pdslin_util.c:11:0:
/home/afrah/pdslin/include/pdslin_slu.h:49:24: error: unknown type name ‘superlu_options_t’
void get_perm_c_dist_t(superlu_options_t *options, int_t pnum, int_t ispec, S
^
/home/afrah/pdslin/include/pdslin_slu.h:70:24: error: unknown type name ‘superlu_options_t’
int_t pdslin_symbfact( superlu_options_t *options, /* input options */
^
pdslin_util.c: In function ‘a_plus_at’:
pdslin_util.c:116:9: warning: variable ‘nnz_loc’ set but not used [-Wunused-but-set-variable]
int_t nnz_loc; /* number of local nonzeros in matrix A */
^
pdslin_util.c:107:26: warning: variable ‘sz_tcolind_loc’ set but not used [-Wunused-but-set-variable]
int_t sz_tcolind_send, sz_tcolind_loc, sz_tcolind_recv;
^
pdslin_util.c: In function ‘pdslin_print_stat’:
pdslin_util.c:1047:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘long long int’ [-Wformat=]
printf( " domain dim : (%.2lf, %.2lf ) %ld / %ld, %ld\n",
^
pdslin_util.c:1047:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘long long int’ [-Wformat=]
pdslin_util.c:1047:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘long long int’ [-Wformat=]
pdslin_util.c:1049:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘long long int’ [-Wformat=]
printf( " domain nnz : (%.2lf, %.2lf ) %ld / %ld, %ld\n",
^
// warnings
makefile:103: recipe for target 'pdslin_util.o' failed
make[2]: *** [pdslin_util.o] Error 1
make[2]: Leaving directory '/home/afrah/pdslin/src'
make[2]: Entering directory '/home/afrah/pdslin/src/slu'
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC get_perm_c.c
get_perm_c.c:49:11: error: unknown type name ‘superlu_options_t’
superlu_options_t *options,
^
get_perm_c.c:167:19: error: unknown type name ‘superlu_options_t’
get_perm_c_dist_t(superlu_options_t *options, int_t pnum, int_t ispec, SuperM
^
makefile:41: recipe for target 'get_perm_c.o' failed
make[2]: *** [get_perm_c.o] Error 1
make[2]: Leaving directory '/home/afrah/pdslin/src/slu'
makefile:46: recipe for target 'lib' failed
make[1]: *** [lib] Error 2
make[1]: Leaving directory '/home/afrah/pdslin/src'
makefile:8: recipe for target 'all' failed
make: *** [all] Error 2
This is my makefile:
#
# top directory make.inc
#
# on hopper: % module load cray-petsc which also loads cray-tpsl, including pt-schotch and parmetis.
########################################################################
# home directory, where the software is located
TOP = /home/afrah/pdslin
INCLUDEDIR =/usr/include
########################################################################
# hybrid solver library name
LIB = $(TOP)/lib/libhybrid.a
########################################################################
# Libraries:
#
# MPI/BLAS libraries
L_MPI = /usr/share/mpich-install/lib/libmpi.a -llibmpi
I_MPI = -I/usr/share/mpich-install/include
L_BLAS = -llibblas -lliblapack
########################################################################
# make utility
MAKE = make
########################################################################
# archiver and flags to build the library
ARCH = /usr/bin/ar
ARCHFLAGS = -cr
RANLIB = /usr/bin/ranlib
########################################################################
# C compiler and flags
CC = gcc
FLAGS = -Wall -DWITH_HIPS -DWITH_PETSC
FLAGS = -Wall -DWITH_HIPS -DWITH_PETSC
########################################################################
# fortran compiler and flags
FC = mpif90
FLIB = -pgf90libs
FFLAGS = -fast
FFLAGS = -g
########################################################################
# linker used to link example program with the library
#LINKER = /usr/share/mpich-install/bin/mpicc -Wl,--allow-multiple-definition
LINKER = CC -Wl,--allow-multiple-definition
########################################################################
# C++ compiler (this is not needed for your standard compilation)
CPP = mpicxx
####################################################################
#L_PPART = -L/usr/share/parmetis/lib/libparmetis -lparmetis
#I_PPART = -I/usr/local/include
L_PPART = -L/usr/local/lib -llibscotch -llibptscotch \
-L/usr/local/lib -lptscotcherr -llibscotchmetis -lptscotchparmetis
I_PPART = -DSCOTCH_ORDER -I/usr/local/include
#------------------------------------------------------#
# Metis Library, and its header files
L_METIS = -L/usr/share/parmetis/lib/libmetis -lmetis
I_METIS = -I/usr/share/parmetis/include
#------------------------------------------------------#
# SuperLU_DIST library, and its header files (hopper: module load superlu_dist)
# SLUDIST = /global/common/hopper2/acts/SuperLU/SuperLU_DIST/2.5
# L_SLUDIST = -L$(SLUDIST)/craypgi-xe6_O/lib -lsuperlu_dist_2.5
# I_SLUDIST = -DDEBUGlevel=0 -DPRNTlevel=1 -DAdd_ -DUSE_VENDOR_BLAS -I$(SLUDIST)/SRC
SLUDIST = /home/afrah/SuperLU_DIST_5.1.2
I_SLUDIST = -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I$(SLUDIST)/SRC
L_SLUDIST = -L$(SLUDIST)/lib -llibsuperlu_dist.so
#------------------------------------------------------#
# Petsc library, and its header files
# double version
I_PETSC = -I/home/afrah/petsc/include \
-I/home/afrah/petsc/arch-linux2-c-debug/include
L_PETSC = -L/home/afrah/petsc/arch-linux2-c-debug/lib -llibpetsc
#------------------------------------------------------#
# Other optional libraries
# serial SuperLU
L_SLU = -L/home/afrah/SuperLU_5.2.0/lib -llibsuperlu_5.2.a
I_SLU = -I/home/afrah/SuperLU_5.2.0/SRC
########################################################################
########################################################################
# accumulate all includes and libraries
INC = -I$(TOP)/include $(I_SLU) -I$(INCLUDEDIR) $(I_SLUDIST) $(I_PPART) $(I_METIS) $(I_MPI) $(I_PETSC)
LIBS = $(LIB) $(L_SLU) $(L_SLUDIST) $(L_PPART) $(L_METIS) $(L_BLAS) $(L_MPI) $
(L_PETSC)
ZLIBS = $(LIB) $(L_SLUDIST) $(L_PPART) $(L_METIS) $(L_BLAS) $(L_MPI) $(L_SLU) $(L_PETSC)
I'm using Mac OS X 10.9. I have already installed graphviz 2.36.0.
After downloading pygraphviz 1.2, I modified in setup.py the variables "library_path" and "include_path":
library_path='/usr/local/lib/graphviz'
include_path='/usr/local/include/graphviz'
When I try to install graphviz with python setup.py install, I get the following message:
library_path=/usr/local/lib/graphviz
include_path=/usr/local/include/graphviz
running install
running build
running build_py
running build_ext
building 'pygraphviz._graphviz' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/usr/local/include/graphviz -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.9-intel-2.7/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:2040:11: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
pygraphviz/graphviz_wrap.c:2043:11: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
pygraphviz/graphviz_wrap.c:2829:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
len = strlen(val);
~ ^~~~~~~~~~~
pygraphviz/graphviz_wrap.c:2855:12: warning: incompatible pointer to integer conversion returning 'Agsym_t *' (aka 'struct Agsym_s *') from a function with result type 'int' [-Wint-conversion]
return agattr(g, kind, name, val);
^~~~~~~~~~~~~~~~~~~~~~~~~~
pygraphviz/graphviz_wrap.c:2847:15: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
len = strlen(val);
~ ^~~~~~~~~~~
pygraphviz/graphviz_wrap.c:4806:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
~~~~~~~~~~ ^ ~~~~~~~~~~
6 warnings generated.
pygraphviz/graphviz_wrap.c:2040:11: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
pygraphviz/graphviz_wrap.c:2043:11: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
pygraphviz/graphviz_wrap.c:2855:12: warning: incompatible pointer to integer conversion returning 'Agsym_t *' (aka 'struct Agsym_s *') from a function with result type 'int' [-Wint-conversion]
return agattr(g, kind, name, val);
^~~~~~~~~~~~~~~~~~~~~~~~~~
pygraphviz/graphviz_wrap.c:4806:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
~~~~~~~~~~ ^ ~~~~~~~~~~
4 warnings generated.
cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F. build/temp.macosx-10.9-intel-2.7/pygraphviz/graphviz_wrap.o -L/usr/local/lib/graphviz -L/usr/local/lib/graphviz -lcgraph -lcdt -o build/lib.macosx-10.9-intel-2.7/pygraphviz/_graphviz.so
ld: library not found for -lcgraph
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'cc' failed with exit status 1
Does anybody know how I can fix this?
Make sure your XCode is updated to the latest version and then try this:
xcode-select --install
When prompted install the command line tools. Then try rebuilding.
I've an OpenSUSE OS and want to compile GCC from scratch. I want to compile 4.9.1 version because of the c++11 support. I am following this guide here. I am using gcc version 4.8.3 for compilation. After executing make, I get following errors;
libtool: compile: /mnt/disk2/gccWork-Ozgur/4.9.1-objdir/./gcc/xgcc -shared-libgcc -B/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/./gcc -nostdinc++ -L/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/x86_64-unknown-linux-gnu/libstdc++-v3/src -L/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs -L/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/x86_64-unknown-linux-gnu/libstdc++-v3/libsupc++/.libs -B/mnt/disk2/gccWork-Ozgur/4.9.1-install/x86_64-unknown-linux-gnu/bin/ -B/mnt/disk2/gccWork-Ozgur/4.9.1-install/x86_64-unknown-linux-gnu/lib/ -isystem /mnt/disk2/gccWork-Ozgur/4.9.1-install/x86_64-unknown-linux-gnu/include -isystem /mnt/disk2/gccWork-Ozgur/4.9.1-install/x86_64-unknown-linux-gnu/sys-include -D_GNU_SOURCE -D_DEBUG -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -I. -I../../../../gcc-4.9.1/libsanitizer/sanitizer_common -I.. -I ../../../../gcc-4.9.1/libsanitizer/include -isystem ../../../../gcc-4.9.1/libsanitizer/include/system -Wall -W -Wno-unused-parameter -Wwrite-strings -pedantic -Wno-long-long -fPIC -fno-builtin -fno-exceptions -fno-rtti -fomit-frame-pointer -funwind-tables -fvisibility=hidden -Wno-variadic-macros -I../../libstdc++-v3/include -I../../libstdc++-v3/include/x86_64-unknown-linux-gnu -I../../../../gcc-4.9.1/libsanitizer/../libstdc++-v3/libsupc++ -DSANITIZER_LIBBACKTRACE -DSANITIZER_CP_DEMANGLE -I ../../../../gcc-4.9.1/libsanitizer/../libbacktrace -I ../libbacktrace -I ../../../../gcc-4.9.1/libsanitizer/../include -include ../../../../gcc-4.9.1/libsanitizer/libbacktrace/backtrace-rename.h -g -O2 -D_GNU_SOURCE -MT sanitizer_platform_limits_posix.lo -MD -MP -MF .deps/sanitizer_platform_limits_posix.Tpo -c ../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc -fPIC -DPIC -o .libs/sanitizer_platform_limits_posix.o
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:232:27: error: ‘PTRACE_GETSIGINFO’ was not declared in this scope
int ptrace_getsiginfo = PTRACE_GETSIGINFO;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:233:27: error: ‘PTRACE_SETSIGINFO’ was not declared in this scope
int ptrace_setsiginfo = PTRACE_SETSIGINFO;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:390:30: error: ‘EVIOCGREP’ was not declared in this scope
unsigned IOCTL_EVIOCGREP = EVIOCGREP;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:399:30: error: ‘EVIOCSREP’ was not declared in this scope
unsigned IOCTL_EVIOCSREP = EVIOCSREP;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:682:36: error: ‘FS_IOC_GETFLAGS’ was not declared in this scope
unsigned IOCTL_FS_IOC_GETFLAGS = FS_IOC_GETFLAGS;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:683:38: error: ‘FS_IOC_GETVERSION’ was not declared in this scope
unsigned IOCTL_FS_IOC_GETVERSION = FS_IOC_GETVERSION;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:684:36: error: ‘FS_IOC_SETFLAGS’ was not declared in this scope
unsigned IOCTL_FS_IOC_SETFLAGS = FS_IOC_SETFLAGS;
^
../../../../gcc-4.9.1/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc:685:38: error: ‘FS_IOC_SETVERSION’ was not declared in this scope
unsigned IOCTL_FS_IOC_SETVERSION = FS_IOC_SETVERSION;
^
make[4]: *** [sanitizer_platform_limits_posix.lo] Error 1
make[4]: Leaving directory `/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/x86_64-unknown-linux-gnu/libsanitizer/sanitizer_common'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/x86_64-unknown-linux-gnu/libsanitizer'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/mnt/disk2/gccWork-Ozgur/4.9.1-objdir/x86_64-unknown-linux-gnu/libsanitizer'
make[1]: *** [all-target-libsanitizer] Error 2
make[1]: Leaving directory `/mnt/disk2/gccWork-Ozgur/4.9.1-objdir'
make: *** [all] Error 2
Any help is appreciated. Thank you