I am trying to compile til parameter estimation tool PEST (http://www.pesthomepage.org/) for linux.
According to the PEST-manual I did:
make -f pest.mak all
but I get following error message:
gfortran -c -O3 -static pestdata.for
gfortran -c -O3 -static pest.for
gfortran -c -O3 -static pestsub2.for
gfortran -c -O3 -static writall.for
gfortran -c -O3 -static pardef.for
gfortran -c -O3 -static readpest.for
gfortran -c -O3 -static runpest.for
gfortran -static -o pest \
pest.o pestsub1.o pestsub2.o dercalc.o modrun.o writall.o \
linpos.o lapack1.o writsig.o common.o \
pgetcl.o pestwait.o writint.o pardef.o\
drealrd.o space.o optwt.o cgsolve.o compress.o \
readpest.o runpest.o lsqr.o orthog.o ms_stubs.o pestdata.o
/bin/ld: cannot find -lgfortran
/bin/ld: cannot find -lm
/bin/ld: cannot find -lquadmath
/bin/ld: cannot find -lm
/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make: *** [pest] Error 1
After goggling I have tried different things, but without results. Can somebody please help
me?
Regards Tanja
Solutions to a problem shouldn't be hidden in comments, which is why I write this answer.
The make output shows that the Makefile tries to link statically.
That requires the libraries that can be linked statically, notably libm.a, libgfortran.a, libquadmath.a and libc.a
A possible solution is to remove the -static flag in the final step.
The resulting executable will of course need the shared objects (libm.so and friends) in order to be able to run. In most situations that's not a problem though.
Related
Info:
Linux watvde0453 3.10.0-1062.1.1.el7.x86_64 #1 SMP Fri Sep 13 22:55:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
GNU Make 4.2.1
Built for x86_64-pc-linux-gnu
Hi
I have been playing around with a make file to allow builds of shared, static libraries and an exe (and also to get some sort of understanding about how it works) and came across some behavior I do not understand.
I was trying to separate out the flags used for lib / exe into separate variables, but when using a line to compile and link all in one it looks like only the CFLAGS variable is being included for the compile step.
When using the following makefile:
LIBCFLAGS := -fPIC
CFLAGS := -O3 -g -Wall -Werror
CC := gcc
SRCS=hashfunction.c hashtable.c hashtablelinkedlist.c
OBJS=hashfunction.o hashtable.o hashtablelinkedlist.o
LIBSO = lib$(NAME).so
libso: $(OBJS)
$(CC) $(LIBCFLAGS) $(CFLAGS) -shared -o $(LIBSO) $(OBJS)
I get the following output when running the make command for libso:
$ make libso
gcc -O3 -g -Wall -Werror -c -o hashfunction.o hashfunction.c
gcc -O3 -g -Wall -Werror -c -o hashtable.o hashtable.c
gcc -O3 -g -Wall -Werror -c -o hashtablelinkedlist.o hashtablelinkedlist.c
gcc -fPIC -O3 -g -Wall -Werror -shared -o lib.so hashfunction.o hashtable.o hashtablelinkedlist.o
/tools/oss/packages/x86_64-centos7/binutils/default/bin/ld: hashtable.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
hashtable.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make: *** [Makefile:12: libso] Error 1
I can get it all working by sticking all the flags in CFLAGS, but I was wondering if anyone could explain what make is doing underneath ?
It looks like the $(LIBCFLAGS) is being ignored for the implicit compile lines, but $(CFLAGS) is not. Is CFALGS used implicitly by make for all compilations ?
You can see all the built-in rules make knows about by running make -p -f/dev/null. There you'll see:
%.o: %.c
# recipe to execute (built-in):
$(COMPILE.c) $(OUTPUT_OPTION) $<
which is the built-in rule make uses to create a .o file from a .c file. Looking elsewhere in the output you'll see:
COMPILE.c = $(CC) $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
so these are the variables make uses to compile .c files into .o files.
I'm trying to run my c++ (written in clion) program in linux. When I try to compile it in the terminal using "make" command, I get this error:
"makefile:5: *** missing separator. Stop."
I already checked that there tabs and not 4 spaces in my makefile.
Anyone has an idea?
Thanks!
This is my makefile:
CFLAGS := -c -Wall -Weffc++ -g -std=c++11 -Iinclude
LDFLAGS := -lboost_system
all: StompBookClubClient
g++ -pthread -o bin/StompBookClubClient bin/ConnectionHandler.o bin/Book.o bin/keyboardInputSend.o bin/socketReader.o bin/User.o $(LDFLAGS)
StompBookClubClient: bin/StompBookClubClient bin/ConnectionHandler.o bin/Book.o bin/keyboardInputSend.o bin/socketReader.o bin/User.o
bin/Book.o: src/Stomp/Book.cpp
g++ -pthread $(CFLAGS) -o bin/Book.o src/Book.cpp
bin/ConnectionHandler.o: src/Stomp/ConnectionHandler.cpp
g++ -pthread $(CFLAGS) -o bin/ConnectionHandler.o src/ConnectionHandler.cpp
bin/keyboardInputSend.o: src/Stomp/keyboardInputSend.cpp
g++ -pthread $(CFLAGS) -o bin/keyboardInputSend.o src/keyboardInputSend.cpp
bin/socketReader.o: src/Stomp/socketReader.cpp
g++ -pthread $(CFLAGS) -o bin/socketReader.o src/socketReader.cpp
bin/StompBookClubClient.o: src/Stomp/StompBookClubClient.cpp
g++ -pthread $(CFLAGS) -o bin/StompBookClubClient.o src/StompBookClubClient.cpp
bin/User.o: src/Stomp/User.cpp
g++ -pthread $(CFLAGS) -o bin/User.o src/User.cpp
.PHONY: clean
clean:
rm -f bin/*
I already checked that there tabs and not 4 spaces in my makefile.
Check it a bit harder. The Makefile you pasted here has 4 spaces on line 5 and produces exactly the error you are seeing. If I replace them by a tab, the next error occurs on line 10, and so on.
This is not an answer but I do not have sufficient points to comment and hence answering.
Apart from 'tab' issue ,you get a similar error if ':'(colon) is missed after the rule name.
Ex makefile:
helloworld.o
g++ helloworld.cc -o helloworld.o;
Error:
Makefile:1: *** missing separator. Stop.
Solution:
Colon after helloworld.o like below
helloworld.o:
g++ helloworld.cc -o helloworld.o;
I have a new c++ project built with autoconf, automake and libtool. Functionality is divided up into support libraries and user binaries. There is also a set of unittests binaries which link against these libraries, are built and run at make check time, but are not installed.
I said the the project is new. I'm actually just now getting around to extracting the first library that should be installed. Until now the (small amount of) written code was just compiled directly into a unittests.
My attempted Makefile.am snippet looks like this:
lib_LTLIBRARIES += libfoo.la
libfoo_la_SOURCES = foo.cc
In make check, I get this:
/bin/bash ./libtool --tag=CXX --mode=link g++ -Wall -Wextra -Werror -ansi -fprofile-arcs -ftest-coverage -g -O0 -fprofile-arcs -ftest-coverage -L/usr/local/lib -Wl,-rpath /usr/local/lib -o libfoo.la -rpath /usr/local/lib foo.lo -lboost_thread-mt -lboost_system-mt -pthread
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.6.1/crtbeginS.o .libs/foo.o -L/usr/local/lib -lboost_thread-mt -lboost_system-mt -L/usr/lib/gcc/x86_64-linux-gnu/4.6.1 -L/usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.6.1/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../../x86_64-linux-gnu/crtn.o -fprofile-arcs -O0 -fprofile-arcs -Wl,-rpath -pthread -pthread -Wl,-soname -Wl,libfoo.so.0 -o .libs/libfoo.so.0.0.0
/usr/bin/ld: cannot find libfoo.so.0: No such file or directory
collect2: ld returned 1 exit status
Notice the missing library is precisely the one I'm trying to compile.
(The library is not libfoo, but I am able to reproduce the same error with this stub library. The Makefile.am and error lines above are literal and unedited.)
If I change the automake lines to
check_LTLIBRARIES += libfoo.la
libfoo_la_SOURCES = foo.cc
then the compile looks like this:
/bin/bash ./libtool --tag=CXX --mode=link g++ -Wall -Wextra -Werror -ansi -fprofile-arcs -ftest-coverage -g -O0 -fprofile-arcs -ftest-coverage -L/usr/local/lib -Wl,-rpath /usr/local/lib -o libfoo.la foo.lo -lboost_thread-mt -lboost_system-mt -pthread
libtool: link: ar cru .libs/libfoo.a .libs/foo.o
libtool: link: ranlib .libs/libfoo.a
libtool: link: ( cd ".libs" && rm -f "libfoo.la" && cp -p "../libfoo.la" "libfoo.la" )
..and everything works fine (except my library isn't installed, being in check_.)
Notice the only difference in the command lines is some additional arguments in the 2nd one:
... -Wl,-rpath /usr/local/lib -o libfoo.la -rpath /usr/local/lib foo.lo -lboost_thread-mt ...
I don't know offhand if this new argument shouldn't be there, but it does appear to be causing the problem. Does anyone know what I'm missing?
Some more details:
On osx lion, this works fine (and the command lines are different.) This error manifests on
ubuntu 12.04, possibly other linuxes.
noinst_LTLIBRARIES and EXTRA_LTLIBRARIES work like check_LTLIBRARIES: no extra arguments, and it links. It seems libtool 'convenience' libraries are specifically the ones without these arguments.
automake 1.11.1
autoconf 2.68
libtool 2.4
EDIT
(Manually) dropping -Wl,-rpath /usr/local/lib from the arguments also fixes the problem.
I did it to myself. While bringing in autoconf support for boost, I encountered a bug described here. My work-around followed the suggestion of one post:
diff --git a/m4/boost.m4 b/m4/boost.m4
index 3d4e47c..9dd0c43 100644
--- a/m4/boost.m4
+++ b/m4/boost.m4
## -403,7 +403,7 ## dnl generated only once above (before we start the for loops).
LDFLAGS=$boost_save_LDFLAGS
LIBS=$boost_save_LIBS
if test x"$Boost_lib" = xyes; then
- Boost_lib_LDFLAGS="-L$boost_ldpath -Wl,-R$boost_ldpath"
+ Boost_lib_LDFLAGS="-L$boost_ldpath -Wl,-rpath $boost_ldpath"
Boost_lib_LDPATH="$boost_ldpath"
break 6
else
The -rpath introduced here is the same one apparently causing the issue. If I revert this change, the problem goes away (I am of course left with the first issue, but that's another story.)
I have a set of kernel source files in ~linux/fs/wrapfs/. Besides, there is also a source file present for a user level program. I want to build that user level program while the kernel gets compiled by running "make" in ~/linux folder i.e in the top level kernel directory.
So, I tried adding following in ~/linux/fs/wrapfs/Makefile:
EXTRA_CFLAGS += prog
prog:
gcc -Wall -Werror prog.c -o prog -lssl -lcrypto
But, then everytime I do "make" in ~/linux, I get following error:
gcc: prog: No such file or directory
I then tried changing it to following but nothing helped:
EXTRA_CFLAGS += prog
all:
gcc -Wall -Werror prog.c -o prog -lssl -lcrypto
EXTRA_CFLAGS += prog
prog:
gcc -Wall -Werror ./fs/wrapfs/prog.c -o ./fs/wrapfs/prog -lssl -lcrypto
Please suggest how can this be solved.
You should not be trying to pass prog in CFLAGS, extra or otherwise.
I have built OpenSSL from source (an intentionally old version; built with ./config && make && make test) and would prefer to use what I have built without doing make install to link against my program.
The command that's failing is:
gcc -Wall -Wextra -Werror -static -Lopenssl/openssl-0.9.8k/ -lssl -lcrypto
-Iopenssl/openssl-0.9.8k/include -o myApp source1.o source2.o common.o`
And I receive a series of errors similar to:
common.c:(.text+0x1ea): undefined reference to `SSL_write'
This makes me think there's something funky with my OpenSSL. If I omit -Lopenssl/openssl-0.9.8k/ from my command, the error changes to being unable to:
/usr/bin/ld: cannot find -lssl
/usr/bin/ld: cannot find -lcrypto
Am I compiling OpenSSL incorrectly? Or how should I best resolve this?
Silly "Linux-isms" strike again! Apparently, I need to change my command such that the -L and -l stuff is at the end like (despite what man gcc seems to indicate):
gcc -Wall -Wextra -Werror -static -o myApp source1.o source2.o common.o -Lopenssl/openssl-0.9.8k/ -lssl -lcrypto -Iopenssl/openssl-0.9.8k/include
Why don't you want to use make install? It can copy generated binaries in the directory you want if you previously passed it to ./configure --prefix $HOME/target_library_install_directory
If you used this trick with every library you build and install, you could then add the target directory to the LIBRARY_PATH environment variable and avoid using -L option.
If you use Autotools, or you are building an Autools project like cURL, then you should be able to use pkg-config. The idea is the Autotools package will read OpenSSL's package configuration and things will "just work" for you.
The OpenSSL package configuration library name is openssl.
You would use it like so in a makefile based project.
%.o: %.c
$(CC) -o $# -c `pkg-config --cflags openssl` $^
target: foo.o bar.o baz.o
$(CC) -o $# `pkg-config --libs openssl` $^
Also see How to use pkg-config in Make and How to use pkg-config to link a library statically.
Another approach is to use pkg-config to preserve compatibility. This is an example of makefile when needs to link OpenSSL.
CC = gcc
CFLAGS = \
-I. \
-D_GNU_SOURCE=1
LDFLAGS = `pkg-config --libs inih`
LDFLAGS += `pkg-config --libs libcurl`
LDFLAGS += `pkg-config --libs liburiparser`
LDFLAGS += `pkg-config --libs openssl`
# Executable
foo: foo.o
$(CC) -o $# $^ $(LDFLAGS)
foo.o: foo.c
$(CC) -c $(CFLAGS) $< -o $#