I cannot compile ORBIT2:
make[3]: Entering directory `/home/software/orbit2/ORBit2-2.14.19/linc2/src'
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../linc2/include -I../../linc2/include -pthread -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -Wall -Wunused -Wmissing-prototypes -Wmissing-declarations -DG_DISABLE_DEPRECATED -D_GNU_SOURCE -g -O2 -Werror-implicit-function-declaration -MT linc.lo -MD -MP -MF .deps/linc.Tpo -c -o linc.lo linc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../linc2/include -I../../linc2/include -pthread -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -Wall -Wunused -Wmissing-prototypes -Wmissing-declarations -DG_DISABLE_DEPRECATED -D_GNU_SOURCE -g -O2 -Werror-implicit-function-declaration -MT linc.lo -MD -MP -MF .deps/linc.Tpo -c linc.c -fPIC -DPIC -o .libs/linc.o
linc.c: In function ‘link_init’:
linc.c:199:2: error: implicit declaration of function ‘g_thread_supported’
linc.c:200:3: error: implicit declaration of function ‘g_thread_init’
linc.c:204:2: warning: ‘g_type_init’ is deprecated (declared at /usr/local/include/glib-2.0/gobject/gtype.h:667)
linc.c:262:3: error: implicit declaration of function ‘g_cond_new’
linc.c:262:18: warning: assignment makes pointer from integer without a cast
linc.c:263:23: warning: assignment makes pointer from integer without a cast
linc.c: In function ‘link_mutex_new’:
linc.c:324:3: error: implicit declaration of function ‘g_mutex_new’
linc.c:324:3: warning: return makes pointer from integer without a cast
linc.c: In function ‘link_exec_set_io_thread’:
linc.c:463:3: error: implicit declaration of function ‘g_thread_create_full’
linc.c:464:4: error: ‘G_THREAD_PRIORITY_NORMAL’ undeclared (first use in this function)
linc.c:464:4: note: each undeclared identifier is reported only once for each function it appears in
linc.c: In function ‘link_mainloop_handle_input’:
linc.c:94:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
The bug has been reported and apparently fixed here, in october 2013:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=707456
But the fix does not appear to have been committed upstream (latest release 2010):
ftp://ftp.gnome.org/pub/gnome/sources/ORBit2/2.14
nor on the git repository (only 3 commits since early 2013):
https://git.gnome.org/browse/ORBit2/
But I cannot find the patch that fixes the issue.
The problem is also set as 'fixed' here:
https://bugs.archlinux.org/task/39138
but again, there is the patch?
I don't understand how those distributions work. It's frustrating that a fix appears to have been found, but I cannot find it.
I don't understand the content of the orbit2-NMU.patch in the debian issue.
Apart from changes to the debian package the only change i can spot is removing "-DG_DISABLE_DEPRECATED" from CPPFLAGS in linc2/src/Makefile.am
Try it!
Related
The project I am attempting compile is not in any way complex, and references nothing but the standard library and one self-contained library (everything compiles fine on another system). As indicated by the title, it can't even link against something in the standard library, due to things in there not having been compiled with -fPIC, supposedly. I didn't build it myself, nor do I want to, and reinstalling things with apt didn't seem to resolve the "recompile with -fPIC" issue.
I will say that I think one possible source of the issue is due to gcc-multilib or something being installed earlier, but I think that was purged. I don't know, maybe something was overwritten or a conflict arose. Might not even be related. Any ideas?
Running Ubuntu 18.04
g++ -I inc -I /usr/include/mono-2.0 -MMD -MF dep/Nonsense.d -std=c++17 -O3 -fno-stack-protector -fno-unroll-loops -fomit-frame-pointer -Wno-ignored-optimization-argument -c -o obj/Nonsense.o src/Nonsense.cpp
g++ -I inc -I /usr/include/mono-2.0 -MMD -MF dep/Socket.d -std=c++17 -O3 -fno-stack-protector -fno-unroll-loops -fomit-frame-pointer -Wno-ignored-optimization-argument -c -o obj/Socket.o src/Socket.cpp
g++ -shared -flto -o libNonsense.so obj/Nonsense.o obj/Socket.o -Llib -lenet
/usr/bin/x86_64-linux-gnu-ld: obj/Socket.o: relocation R_X86_64_PC32 against symbol `_ZTISt13runtime_error##GLIBCXX_3.4' can not be used when making a shared object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
makefile:22: recipe for target 'libNonsense.so' failed
make: *** [libNonsense.so] Error 1
Apparently, it is compulsory to compile with the -fPIC flag in 64bits platform. If you are making a 32-bits project with linkink with 32-bits library; you don't need -fPIC.
Indeed, without -fPIC, the dynamic linker recalculates adresses for global variables and functions (which are not known in advance in the step of compilation). However, in a 64-bits system, it is not possible to use this technique as it is required to guess in advance the size of adress.
PIC (Position Independent Code), a more sophisticated and complicated process is used. https://eli.thegreenplace.net/2011/11/11/position-independent-code-pic-in-shared-libraries-on-x64 for explanations.
As the error message says, you need to recompile with -fPIC. Your current compiler command does not show the -fPIC option:
g++ -I inc -I /usr/include/mono-2.0 -MMD -MF dep/Socket.d -std=c++17 -O3 -fno-stack-protector -fno-unroll-loops -fomit-frame-pointer -Wno-ignored-optimization-argument -c -o obj/Socket.o src/Socket.cpp
Same for -flto by the way—this flag also has to be specified when compiling in order to be effective.
I have installed (GCC) 4.7.2 20121015 (Red Hat 4.7.2-5) already and jave also installed yum install gcc-gfortran . (Package gcc-gfortran-4.4.7-18.el6.x86_64)
But I'm getting error like :
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [quadprog.so] Error 1
Please help me in installing -lgfortran. It seems like I need to install "Fortran -dev package providing the Fortran library". I do not know how to do that in RedHat/CentOS. Please help. I'm facing hard time in doing this.
I have tried installing libgfortran using:
yum install libgfortran
But it says:
Package libgfortran-4.4.7-18.el6.x86_64 already installed and latest version
Nothing to do
(Running in an interactive session, skipping clean step.)
More Info:
I tried installing package quadprog for R and below are the logs:
install.packages('https://cran.cnr.berkeley.edu/src/contrib/quadprog_1.5-5.tar.gz',dependencies = TRUE,repos = NULL,type ="source")
Installing package into '/usr/lib64/R/library'
(as 'lib' is unspecified)
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/quadprog_1.5-5.tar.gz'
Content type 'application/x-gzip' length 33651 bytes (32 KB)
==================================================
downloaded 32 KB
* installing *source* package 'quadprog' ...
** package 'quadprog' successfully unpacked and MD5 sums checked
** libs
gfortran -m64 -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules -c aind.f -o aind.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c init.c -o init.o
gfortran -m64 -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules -ffloat-store -c -o solve.QP.compact.o solve.QP.compact.f
solve.QP.compact.f:254.3:
72 if (nvl .EQ. 0) then
1
Warning: Label 72 at (1) defined but not used
solve.QP.compact.f:302.2:
7 t1inf = .FALSE.
1
Warning: Label 7 at (1) defined but not used
solve.QP.compact.f: In function 'qpgen1':
solve.QP.compact.f:94: warning: 'it1' may be used uninitialized in this function
solve.QP.compact.f:98: warning: 't1' may be used uninitialized in this function
gfortran -m64 -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules -ffloat-store -c -o solve.QP.o solve.QP.f
solve.QP.f:245.3:
72 if (nvl .EQ. 0) then
1
Warning: Label 72 at (1) defined but not used
solve.QP.f:293.2:
7 t1inf = .FALSE.
1
Warning: Label 7 at (1) defined but not used
solve.QP.f: In function 'qpgen2':
solve.QP.f:85: warning: 'it1' may be used uninitialized in this function
solve.QP.f:89: warning: 't1' may be used uninitialized in this function
gfortran -m64 -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules -c util.f -o util.o
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lgfortran -lm -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [quadprog.so] Error 1
ERROR: compilation failed for package 'quadprog'
* removing '/usr/lib64/R/library/quadprog'
Warning message:
In install.packages("https://cran.cnr.berkeley.edu/src/contrib/quadprog_1.5-5.tar.gz", :
installation of package '/tmp/Rtmpry5XTG/downloaded_packages/quadprog_1.5-5.tar.gz' had non-zero exit status
Edits :
bash-4.1# rpm -ql libgfortran
/usr/lib64/libgfortran.so.3
/usr/lib64/libgfortran.so.3.0.0
You showed us this:
# type -a gcc
gcc is /opt/centos/devtoolset-1.1/root/usr/bin/gcc
gcc is /usr/bin/gcc'
It means that you have installed Red Hat Developer Toolset and enabled it for this shell, using scl enable or a similar command. Do you still need it? If not, I suggest to disable it.
If you need DTS, you will have to install the Fortran compiler from DTS 1.1, using:
yum install devtoolset-1.1-gcc-gfortran
(Or download it directly from here, which seems to be the repository from where you got your DTS compiler.)
This will install the Fortran compiler which is compatible with the gcc compiler you have configured. Without that, the system Fortran compiler and the DTS gcc are used together, which does not work because the DTS gcc command (used for linking in the build process you quoted) is not able to locate the libgfortran.so library from the system Fortran compiler.
Alternatively, you can bring the two compilers into sync by deinstalling the DTS compiler:
yum install devtoolset-1.1-gcc-gfortran
The following compile line was looking for libgfortran at /usr/lib64/R/lib but the library is not there. Hence, the linker error.
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lgfortran -lm -L/usr/lib64/R/lib -lR
As we could not locate and modify the makefile. We created a symbolic link /usr/lib64/R/lib/libgfortran.so to /usr/lib64/libgfortran.so.3 and rerun the installation steps and it resolves the linker error.
This is a work around that we follow which resolves the issue
why am I getting "fatal error: asm/early_ioremap.h: No such file or directory" while building simple hello world kernel driver for x86_64 with Linux 4.4.15 libraries using gcc-4.8.5? gcc is searching for asm/early_ioremap.h which is not available in Linux 4.4.15.
any idea how can i fix this?
/opt/gcc-4.8.5-glibc-2.21-p8/x86_64-linux-gnu/bin/x86_64-linux-gnu-gcc -M -MP -MT '/home/obj/src/kernel/hello_world/hello.o' -MT '/home/obj/src/kernel/hello_world/hello.d' -MT 'hello.E' -MT 'hello.S' -I/home/src/kernel/hello_world -I/home/obj/src/kernel/linux-4.4.15/include -I/home/src/inc -I/home/obj/src/kernel/linux-4.4.15/arch/x86/include -D__KERNEL__ -DMODULE -DPACKET_LEAK_TRACING -DSIZEOF_CPU_REGISTER=8 -DNUM_DEV_CF=0 -DNUM_DEV_USB=0 -mtune=nocona -march=nocona -m64 -pipe -std=gnu89 -g -nostdinc -isystem /opt/gcc-4.8.5-glibc-2.21-p8/x86_64-linux-gnu/lib/gcc/x86_64-linux-gnu/4.8.5/include -O2 -fno-strict-aliasing -fno-common -ffreestanding -Wall -Wstrict-prototypes -Wno-trigraphs -Wmissing-format-attribute -Wdisabled-optimization -Wwrite-strings -Wimplicit-int -Wmissing-braces -Wmissing-noreturn -Wundef -Wmissing-field-initializers -Wmissing-declarations -Wmissing-prototypes -Wno-unused-parameter -Winline -mcmodel=kernel -fno-omit-frame-pointer -fno-stack-protector -mno-red-zone -fno-asynchronous-unwind-tables -imacros generated/autoconf.h hello.c -I/home/obj/src/kernel/linux-4.4.15/include/uapi/ -I/home/obj/src/kernel/linux-4.4.15/arch/x86/include/uapi/
In file included from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/realmode.h:5:0,
from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/acpi.h:33,
from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/fixmap.h:19,
from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/apic.h:12,
from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/smp.h:12,
from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/mmzone_64.h:10,
from /home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/mmzone.h:4,
from /home/obj/src/kernel/linux-4.4.15/include/linux/mmzone.h:856,
from /home/obj/src/kernel/linux-4.4.15/include/linux/gfp.h:5,
from /home/obj/src/kernel/linux-4.4.15/include/linux/kmod.h:22,
from /home/obj/src/kernel/linux-4.4.15/include/linux/module.h:13,
from hello.c:1:
/home/obj/src/kernel/linux-4.4.15/arch/x86/include/asm/io.h:43:31: fatal error: asm/early_ioremap.h: No such file or directory
#include <asm/early_ioremap.h>
^
compilation terminated.
gcc is searching for asm/early_ioremap.h which is not available in Linux 4.4.15.
any idea how can i fix this?
I think you've answered your own question; either you figure out where the functionality contained in that header file has moved, or with what it has been replaced, or you use a Linux 4.4.15-compatible hello world module, or you use an older kernel.
Personally, I'd go for trying out another example that is supposed to work with recent versions of Linux.
I've faced a very similar error just recently trying to build a module from the kernel to an out-of-tree output by specifying the O= flag.
It seems to be that this is the part causing the failure for me
make \
-j1 \
-C /lib/modules/4.17.9-041709-generic/build \
M=/home/kbingham/sources/linux/drivers/media/usb/uvc \
O=/tmp/build-uvc \
V=1 \
modules
fails,
with the error:
/usr/src/linux-headers-4.17.9-041709-generic/arch/x86/include/asm/io.h:44:10: fatal error: asm/early_ioremap.h: No such file or directory
#include <asm/early_ioremap.h>
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
whilst
make \
-j1 \
-C /lib/modules/4.17.9-041709-generic/build \
M=/home/kbingham/sources/linux/drivers/media/usb/uvc \
V=1 \
modules
suceeds.
I'm trying to install node.js, so I've cloned the repo and ./configure it. However, when I run make I get this ridiculous infinite loop of errors:
make -C out BUILDTYPE=Release V=1
make[1]: Entering directory `/home/ubuntu/nodejs/node/out'
g++ '-DOPENSSL_NO_SSL2=1' '-DV8_TARGET_ARCH_X64' '-DENABLE_DEBUGGER_SUPPORT' -I../deps/v8/src -pthread -Wall -Wextra -Wno-unused-parameter -m64 -fno-strict-aliasing -m64 -O3 -ffunction-sections -fdata-sections -fno-tree-vrp -fno-omit-frame-pointer -fdata-sections -ffunction-sections -O3 -fno-rtti -fno-exceptions -MMD -MF /home/ubuntu/nodejs/node/out/Release/.deps//home/ubuntu/nodejs/node/out/Release/obj.target/v8_base.x64/deps/v8/src/runtime.o.d.raw -c -o /home/ubuntu/nodejs/node/out/Release/obj.target/v8_base.x64/deps/v8/src/runtime.o ../deps/v8/src/runtime.cc
In file included from ../deps/v8/src/v8.h:52:0,
from ../deps/v8/src/runtime.cc:31:
../deps/v8/src/../include/v8.h: In member function ‘void v8::ReturnValue<T>::Set(uint32_t)’:
../deps/v8/src/../include/v8.h:5816:31: warning: typedef ‘I’ locally defined but not used [-Wunused-local-typedefs]
typedef internal::Internals I;
^
In file included from ../deps/v8/src/v8globals.h:32:0,
from ../deps/v8/src/v8.h:53,
from ../deps/v8/src/runtime.cc:31:
../deps/v8/src/v8utils.h: In function ‘void v8::internal::CopyWords(T*, const T*, size_t)’:
../deps/v8/src/checks.h:271:22: warning: typedef ‘__StaticAssertTypedef__131’ locally defined but not used [-Wunused-local-typedefs]
SEMI_STATIC_JOIN(__StaticAssertTypedef__, __LINE__)
^
../deps/v8/src/checks.h:261:39: note: in definition of macro ‘SEMI_STATIC_JOIN_HELPER’
#define SEMI_STATIC_JOIN_HELPER(a, b) a##b
^
../deps/v8/src/checks.h:271:5: note: in expansion of macro ‘SEMI_STATIC_JOIN’
SEMI_STATIC_JOIN(__StaticAssertTypedef__, __LINE__)
^
../deps/v8/src/checks.h:319:30: note: in expansion of macro ‘STATIC_CHECK’
#define STATIC_ASSERT(test) STATIC_CHECK(test)
This seems to be a bug but I have g++4.8.1 gcc-4.8.1 which are the latest versions that I know of. Please let me know how I can fix this. Thanks.
There is an easier way than bringing old g++, as mentioned in V8 bug report discussion:
http://code.google.com/p/v8/issues/detail?id=2149
You could set additional flag for g++ before using make:
export CXX="g++ -Wno-unused-local-typedefs"
I've had problems with g++ 4.8 compiling v8 (which Node uses), and a bunch of other stuff, so I use 4.7. First install g++-4.7 using apt-get (which I trust you know how to do), and then:
CXX=g++-4.7 make [... etc...]
I need some help with a linker error I get during installation of an Rcpp package on a linux system where I don't have admin rights. In a nutshell, I get this error:
relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
I have a file solve.cpp that uses external library interp2d, which in turn has a GSL dependency. I specify my dependencies via [[Rcpp::depends(RcppArmadillo,RcppGSL)]] and in the DESCRIPTION. My Makevars is like the one from the RcppGSL package, with the addition of the linterp2d flag:
PKG_CPPFLAGS = -W $(GSL_CFLAGS) $(LOCAL_INCLUDE)
PKG_LIBS += $(GSL_LIBS) $(LOCAL_LIBS) -linterp2d $(RCPP_LDFLAGS)
where I define the environement variables
export LOCAL_INCLUDE="-I/data/uctpfos/local/include/"
export LOCAL_LIBS="-L/data/uctpfos/local/lib/"
on the system.
I do R CMD INSTALL bkPackage and see:
g++ -I/cm/shared/apps/R/3.0.1/lib64/R/include -DNDEBUG -W -I/cm/shared/apps/gsl/1.15/include -I/data/uctpfos/local/include -fPIC -I/usr/local/include -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppArmadillo/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppGSL/include" -fpic -O3 -fPIC -c RcppExports.cpp -o RcppExports.o
g++ -I/cm/shared/apps/R/3.0.1/lib64/R/include -DNDEBUG -W -I/cm/shared/apps/gsl/1.15/include -I/data/uctpfos/local/include -fPIC -I/usr/local/include -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppArmadillo/include" -I"/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/RcppGSL/include" -fpic -O3 -fPIC -c solve.cpp -o solve.o
The problems appears after that in the linking step:
g++ -shared -L/usr/local/lib64 -o bkPackage.so RcppExports.o solve.o -L/cm/shared/apps/gsl/1.15/lib -lgsl -lgslcblas -lm -L/data/uctpfos/local/lib -linterp2d -L/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/lib -lRcpp -Wl,-rpath,/data/uctpfos/R/x86_64-unknown-linux-gnu-library/3.0/Rcpp/lib
The error follows as:
/usr/bin/ld: /data/uctpfos/local/lib/libinterp2d.a(interp2d_spline.c.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/data/uctpfos/local/lib/libinterp2d.a: could not read symbols: Bad value
As you can see I compiled this with -fPIC, so that can't be it.
It's complaining that libinterp2d.a was not compiled with -fPIC; are you sure that was also compiled with -fPIC on?
Also, it seems you both have -fpic and -fPIC in your flags; you probably just want -fPIC. I think R actually ensures that's on by default.