Building Seafile-Client on windows with using cygwin - makefile

I try to building seafile-client on windows with using cygwin. When i call ./configure command it detect build system as Linux
...
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for WIN32... no
checking for Mac... no
checking for Linux... compile in linux
checking for uuid_generate in -luuid... yes
found library uuid
...
it configure successfuly but when i call the make command it occur a lot of error. I guess it's because of it detect the build system as linux, but i think it must be windows. How can i do for solve this?
make error output:
Making all in daemon
make[2]: Entering directory '/cygdrive/c/msys/1.0/home/seafile-6.2.4/daemon'
gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/local/share/seafile\" -DPACKAGE_DATA_DIR=\""/usr/local/share/seafile"\" -DSEAFILE_CLIENT -I../include -I../lib -I../lib -I../common -D_REENTRANT -I/usr/local/include -I/usr/local/include/searpc -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -Wall -g -O2 -MT http-tx-mgr.o -MD -MP -MF .deps/http-tx-mgr.Tpo -c -o http-tx-mgr.o http-tx-mgr.c
http-tx-mgr.c: 'http_get' işlevinde:
http-tx-mgr.c:741:91: hata: expected ')' before 'USER_AGENT_OS'
headers = curl_slist_append (headers, "User-Agent: Seafile/"SEAFILE_CLIENT_VERSION" ("USER_AGENT_OS")");
^~~~~~~~~~~~~
http-tx-mgr.c: 'http_put' işlevinde:
http-tx-mgr.c:865:91: hata: expected ')' before 'USER_AGENT_OS'
headers = curl_slist_append (headers, "User-Agent: Seafile/"SEAFILE_CLIENT_VERSION" ("USER_AGENT_OS")");
^~~~~~~~~~~~~
http-tx-mgr.c: 'http_post' işlevinde:
http-tx-mgr.c:982:91: hata: expected ')' before 'USER_AGENT_OS'
headers = curl_slist_append (headers, "User-Agent: Seafile/"SEAFILE_CLIENT_VERSION" ("USER_AGENT_OS")");
^~~~~~~~~~~~~
Üst düzeyde:
http-tx-mgr.c:507:1: UYARI: 'load_ca_bundle' defined but not used [-Wunused-function]
load_ca_bundle (CURL *curl)
^~~~~~~~~~~~~~
make[2]: *** [Makefile:581: http-tx-mgr.o] Error 1
make[2]: Leaving directory '/cygdrive/c/msys/1.0/home/seafile-6.2.4/daemon'
make[1]: *** [Makefile:444: all-recursive] Error 1
make[1]: Leaving directory '/cygdrive/c/msys/1.0/home/seafile-6.2.4'
make: *** [Makefile:376: all] Error 2
this code written for cross-compile and contains many definition like below:
...
#ifdef WIN32
#include <windows.h>
#include <wincrypt.h>
#endif
...
#ifndef SEAFILE_CLIENT_VERSION
#define SEAFILE_CLIENT_VERSION PACKAGE_VERSION
#endif
#ifdef WIN32
#define USER_AGENT_OS "Windows NT"
#endif
#ifdef __APPLE__
#define USER_AGENT_OS "Apple OS X"
#endif
#ifdef __linux__
#define USER_AGENT_OS "Linux"
#endif
#if defined __FreeBSD__ || defined __NetBSD__ || defined __OpenBSD__ || defined __DragonFly__
#define USER_AGENT_OS "BSD"
#endif
...

Related

cross-compile iperf from x86_64 for ARM64 target

I want to cross compile iperf-2.0.5 from my x86_64 ubuntu linux machine for a ARM64 target. Therefore I installed the cross compiler:
sudo apt install gcc make gcc-aarch64-linux-gnu binutils-aarch64-linux-gnu g++-aarch64-linux-gnu
then I tried to configure:
./configure --build=aarch64-unknown-linux-gnu --host=x86_64-unknown-linux-gnu --enable-static --disable-shared
which gives me this warning: configure: WARNING: unrecognized options: --enable-static, --disable-shared
apart from this warning i'm not getting any errors but I'm not sure how to verify that the build and host parameters are selected correctly.
When I run make I get the following error.
make all-recursive
make[1]: Entering directory '/home/recherma/Documents/iperf-2.0.5'
Making all in compat
make[2]: Entering directory '/home/recherma/Documents/iperf-2.0.5/compat'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -I../include -Wall -O2 -MT delay.o -MD -MP -MF ".deps/delay.Tpo" -c -o delay.o delay.cpp; \
then mv -f ".deps/delay.Tpo" ".deps/delay.Po"; else rm -f ".deps/delay.Tpo"; exit 1; fi
In file included from /usr/include/c++/9/stdlib.h:36,
from ../include/headers.h:78,
from ../include/Timestamp.hpp:63,
from delay.cpp:53:
/usr/include/c++/9/cstdlib:151:11: error: ‘::malloc’ has not been declared
151 | using ::malloc;
| ^~~~~~
In file included from ../include/headers.h:78,
from ../include/Timestamp.hpp:63,
from delay.cpp:53:
/usr/include/c++/9/stdlib.h:65:12: error: ‘std::malloc’ has not been declared
65 | using std::malloc;
| ^~~~~~
In file included from /usr/include/c++/9/cmath:42,
from /usr/include/c++/9/math.h:36,
from ../include/headers.h:85,
from ../include/Timestamp.hpp:63,
from delay.cpp:53:
/usr/include/c++/9/bits/cpp_type_traits.h:214:12: error: redefinition of ‘struct std::__is_integer<int>’
214 | struct __is_integer<int>
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/cpp_type_traits.h:138:12: note: previous definition of ‘struct std::__is_integer<int>’
138 | struct __is_integer<bool>
| ^~~~~~~~~~~~~~~~~~
make[2]: *** [Makefile:273: delay.o] Error 1
make[2]: Leaving directory '/home/recherma/Documents/iperf-2.0.5/compat'
make[1]: *** [Makefile:252: all-recursive] Error 1
make[1]: Leaving directory '/home/recherma/Documents/iperf-2.0.5'
make: *** [Makefile:190: all] Error 2
So I guess the configuration failed. Does anyone know now to configure it correctly?
EDIT:
I think --host should be changed to aarch64-unknown-linux-gnu. But this changes nothing and I get the exact same errors.
Try removing DAST_CHECK_BOOL from configure.ac and try reconfigure again.
If that didn't help, after configure, comment #define bool int in config.h and try rebuild.

Problem installing ndless-sdk: error building genzehn

I am trying to install Ndless sdk on my Windows computer (with CygWin). I run
.../Ndless/ndless-sdk/toolchain/build_toolchain.sh
and I fixed all the problems with that. After that, according to the instructions, I went in the (top) Ndless directory and ran "make". It got stuck at this point and whatever I did, I could not get it to compile "genzehn"
.../Ndless/ndless-sdk/tools/genzehn/genzehn.cpp
What should I do?
The log(both stdout and stderr for make in "Ndless"):
https://pastebin.com/fpH6Mf2v
make all in genzehn...
make[3]: Entering directory '/Ndless/ndless-sdk/tools/genzehn'
g++ -Wall -Wextra -std=c++11 -I elfio-3.2 genzehn.cpp -lboost_program_options -lz -o ../../bin/genzehn || g++ -Wall -Wextra -std=c++11 -I elfio-3.2 genzehn.cpp -lboost_program_options-mt -lz -o ../../bin/genzehn
In file included from genzehn.cpp:12:
zehn.h:1:1: error: expected unqualified-id before ‘.’ token
1 | ../../include/zehn.h
| ^
genzehn.cpp: In function ‘int main(int, char**)’:
genzehn.cpp:96:9: error: ‘Zehn_header’ was not declared in this scope; did you mean ‘gz_header’?
96 | Zehn_header header;
| ^~~~~~~~~~~
| gz_header

CMake failing to detect pthreads due to warnings

I get an error when making a project with CMake:
-- Could NOT find Threads (missing: Threads_FOUND)
The error log shows that CMake tripped up over something truly banal:
/usr/bin/cc -std=c11 -D_GNU_SOURCE -Wall -Wextra -Wpointer-arith -Wundef -Wvla -Wwrite-strings -Werror -Wno-error=extra -Wno-error=deprecated-declarations -Wno-error=sign-compare -Wno-error=strict-aliasing -Wno-error=type-limits -Wno-unused-parameter -Wno-error=unused-variable -Wno-error=undef -Wno-error=uninitialized -Wlogical-op -Wno-error=maybe-uninitialized -Waggregate-return -Wnested-externs -Wold-style-definition -Wstrict-prototypes -march=native -o CMakeFiles/cmTryCompileExec2533162744.dir/CheckIncludeFiles.c.o -c /mnt/shared/fooproj/build/release/CMakeFiles/CMakeTmp/CheckIncludeFiles.c
/mnt/shared/fooproj/build/release/CMakeFiles/CMakeTmp/CheckIncludeFiles.c:5:5:
error: function declaration isn’t a prototype [-Werror=strict-prototypes]
int main(){return 0;}
^
/mnt/shared/fooproj/build/release/CMakeFiles/CMakeTmp/CheckIncludeFiles.c:
In function ‘main’:
/mnt/shared/fooproj/build/release/CMakeFiles/CMakeTmp/CheckIncludeFiles.c:5:5:
error: old-style function definition [-Werror=old-style-definition]
cc1: all warnings being treated as errors
[...]
Source:
/* */
#include <pthread.h>
int main(){return 0;}
This really should be no reason for CMake to think Threads doesn't exist. How do I go about fixing this?
I believe this is CMake bug 15058 which I just reported.
The test that CMake is using to check the include file uses an old-style C function definition. If -Wold-style-definition -Werror is in effect, gcc will barf on this.
I included a patch in the bug report linked above, but for a quick fix, find the file Modules/CheckIncludeFiles.cmake in your CMake installation (possibly in /usr/share/cmake or similar), find the line
"${CMAKE_CONFIGURABLE_FILE_CONTENT}\n\nint main(){return 0;}\n")
and change int main() to int main(void).
Issue seems to be still there.
I try to compile the lates nominatim. seems i got the same error.
Determining if the pthread_create exist failed with the following output:
Change Dir: /home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/make" "cmTC_b87d8/fast"
/usr/bin/make -f CMakeFiles/cmTC_b87d8.dir/build.make CMakeFiles/cmTC_b87d8.dir/build
make[1]: Entering directory '/home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_b87d8.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTC_b87d8.dir/CheckSymbolExists.c.o -c /home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_b87d8
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_b87d8.dir/link.txt --verbose=1
/usr/bin/cc -rdynamic CMakeFiles/cmTC_b87d8.dir/CheckSymbolExists.c.o -o cmTC_b87d8
CMakeFiles/cmTC_b87d8.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0x1b): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_b87d8.dir/build.make:97: recipe for target 'cmTC_b87d8' failed
make[1]: *** [cmTC_b87d8] Error 1
make[1]: Leaving directory '/home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_b87d8/fast' failed
make: *** [cmTC_b87d8/fast] Error 2
File /home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>
int main(int argc, char** argv)
{
(void)argv;
#ifndef pthread_create
return ((int*)(&pthread_create))[argc];
#else
(void)argc;
return 0;
#endif
}
Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/make" "cmTC_eb9e3/fast"
/usr/bin/make -f CMakeFiles/cmTC_eb9e3.dir/build.make CMakeFiles/cmTC_eb9e3.dir/build
make[1]: Entering directory '/home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_eb9e3.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_eb9e3.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.9/Modules/CheckFunctionExists.c
Linking C executable cmTC_eb9e3
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_eb9e3.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CMakeFiles/cmTC_eb9e3.dir/CheckFunctionExists.c.o -o cmTC_eb9e3 -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_eb9e3.dir/build.make:97: recipe for target 'cmTC_eb9e3' failed
make[1]: *** [cmTC_eb9e3] Error 1
make[1]: Leaving directory '/home/mikelaptop/Desktop/nominatim/290102/Nominatim/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_eb9e3/fast' failed
make: *** [cmTC_eb9e3/fast] Error 2
Edit: cmake -lpthread .. seems to fix this

'glib.h' file not found on Max OSX 10.9

I'm trying to compile msg2pdf which is a tool to convert messages in mu4e (mu for Emacs) to pdf.
I'm receiving the following error :
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in .
CC msg2pdf.o
In file included from msg2pdf.c:20:
In file included from ../../lib/mu-msg.h:24:
../../lib/mu-flags.h:24:10: fatal error: 'glib.h' file not found
#include <glib.h>
^
1 error generated.
make[2]: *** [msg2pdf.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Oddly, I checked the Makefile and GLIB_CFLAGS seem to be pointing on the right folder (where brew installed it).
In fact, glib.h is located in /usr/local/Cellar/glib/2.40.0_1/include/glib-2.0.
GLIB_CFLAGS = -D_REENTRANT -I/usr/local/Cellar/glib/2.40.0_1/include/glib-2.0 -I/usr/local/Cellar/glib/2.40.0_1/lib/glib-2.0/include -I/usr/local/opt/gettext/include
GLIB_LIBS = -L/usr/local/Cellar/glib/2.40.0_1/lib -L/usr/local/opt/gettext/lib -lgio-2.0 -lgobject-2.0 -lglib-2.0 -lintl
How can I succeed compiling the file? Is there any command line "hack" I can use while calling
make?
Edit
Here are the files in the directory
https://github.com/flexdec/temp
Edit 2
This is the output when using make V=1
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in .
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../lib -DICONDIR='""' -Wall -Wextra -Wno-unused-parameter -Wdeclaration-after-statement -g -O2 -MT msg2pdf.o -MD -MP -MF .deps/msg2pdf.Tpo -c -o msg2pdf.o msg2pdf.c
In file included from msg2pdf.c:20:
In file included from ../../lib/mu-msg.h:24:
../../lib/mu-flags.h:24:10: fatal error: 'glib.h' file not found
#include <glib.h>
^
1 error generated.
make[2]: *** [msg2pdf.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Edit 3
The new error I get using make V=1 now that GLIB_CFLAGS issue is fixed
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in .
gcc -DHAVE_CONFIG_H -I. -I../.. -I../../lib -D_REENTRANT -I/usr/local/Cellar/glib/2.40.0_1/include/glib-2.0 -I/usr/local/Cellar/glib/2.40.0_1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -DICONDIR='""' -Wall -Wextra -Wno-unused-parameter -Wdeclaration-after-statement -g -O2 -MT msg2pdf.o -MD -MP -MF .deps/msg2pdf.Tpo -c -o msg2pdf.o msg2pdf.c
msg2pdf.c:24:10: fatal error: 'gtk/gtk.h' file not found
#include <gtk/gtk.h>
^
1 error generated.
make[2]: *** [msg2pdf.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
make V=1 instead of make will tell you what the C compiler command looks like (instead of just "CC msg2pdf.o")—check that and make sure it includes the flags you need.
Based on a quick look at your Makefile.am, you are including $(GTK_CFLAGS) and $(WEBKIT_CFLAGS) in your AM_CPPFLAGS but not $(GLIB_CFLAGS).
You need to run ./configure in mu's top-level directory on the machine where you want to compile it. configure will tell you about any missing dependencies. Optional components (such as msg2pdf) are skipped if their dependencies are not there.
Then, after configure succeeds, do a 'make'.
In any case, if configure has run successfully, the top-level 'make' should succeed as well (that's why we have configure!), otherwise please file a bug.

How to install Cufflinks on Cygwin

I'm attempting to install cufflinks 2.0.1 on my Windows 7 system using Cygwin. I have done all of the installation steps up to the Make command, but that make command keeps on failing for some reason. I was wondering if anyone could tell me why. I'm using Boost version 1.50
First, here's what happens when I run the configure file:
Benjamin S#BenjaminS-HP /cygdrive/c/analysistools/cufflinks-2.0.1
$ ./configure --prefix=/cygdrive/c/analysistools/cufflinks --with-boost=/cygdrive/c/AnalysisTools/boost --with-bam=/cygdrive/c/analysistools/samtools/samtools
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.exe
checking for suffix of executables... .exe
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.6
checking for python platform... cygwin
checking for python script directory... ${prefix}/lib/python2.6/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... i686-pc-cygwin
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking how to run the C preprocessor... gcc -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 if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... i686-pc-cygwin
checking if gcc accepts -m64... no
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... no
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- cufflinks 2.0.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include
GCC version: gcc (GCC) 4.5.3
Host System type: i686-pc-cygwin
Install prefix: /cygdrive/c/analysistools/cufflinks
Install eprefix: ${prefix}
See config.h for further configuration information.
Then here is what happens when I try to make it:
Benjamin S#BenjaminS-HP /cygdrive/c/analysistools/cufflinks-2.0.1
$ make
make all-recursive
make[1]: Entering directory `/cygdrive/c/analysistools/cufflinks-2.0.1'
Making all in src
make[2]: Entering directory `/cygdrive/c/analysistools/cufflinks-2.0.1/src'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT clustering.o -MD -MP -MF .deps/clustering.Tpo -c -o clustering.o clustering.cpp
g++: unrecognized option '-pthread'
mv -f .deps/clustering.Tpo .deps/clustering.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT differential.o -MD -MP -MF .deps/differential.Tpo -c -o differential.o differential.cpp
g++: unrecognized option '-pthread'
In file included from differential.h:29:0,
from differential.cpp:18:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
In file included from differential.cpp:18:0:
differential.h: In constructor ‘FPKMContext::FPKMContext(double, double, double, double, const CountPerReplicateTable&, double, const FPKMPerReplicateTable&, double, AbundanceStatus, const StatusPerReplicateTable&)’:
differential.h:142:21: warning: ‘FPKMContext::status’ will be initialized after
differential.h:139:29: warning: ‘StatusPerReplicateTable FPKMContext::status_per_rep’
differential.h:131:2: warning: when initialized here
differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:212:31: warning: unused variable ‘s2’
differential.cpp: In member function ‘void TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:240:31: warning: unused variable ‘s2’
differential.cpp: In function ‘SampleDifference get_ds_tests(const AbundanceGroup&, const AbundanceGroup&, bool)’:
differential.cpp:790:16: warning: unused variable ‘name’
differential.cpp: In function ‘void test_differential(const std::string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, Tests&, Tracking&, bool)’:
differential.cpp:1771:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1772:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1814:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1815:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1856:83: warning: comparison between signed and unsigned integer expressions
differential.cpp:1857:83: warning: comparison between signed and unsigned integer expressions
mv -f .deps/differential.Tpo .deps/differential.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
g++: unrecognized option '-pthread'
In file included from common.cpp:28:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
mv -f .deps/common.Tpo .deps/common.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp
g++: unrecognized option '-pthread'
mv -f .deps/assemble.Tpo .deps/assemble.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp
g++: unrecognized option '-pthread'
mv -f .deps/tokenize.Tpo .deps/tokenize.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -pthread -I/cygdrive/c/AnalysisTools/boost/include -I/cygdrive/c/analysistools/samtools/samtools/include -I/usr/local/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp
g++: unrecognized option '-pthread'
In file included from abundances.cpp:35:0:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:152:50: warning: unused variable ‘s2’
abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector<MateHit>&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<MateHit>&, std::vector<double>&, bool)’:
abundances.cpp:769:28: warning: comparison between signed and unsigned integer expressions
abundances.cpp: In function ‘long double solve_beta(long double, long double, long double)’:
abundances.cpp:1227:145: error: ‘sqrtl’ was not declared in this scope
abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’:
abundances.cpp:1780:24: warning: unused variable ‘fpkm’
abundances.cpp: In function ‘void calculate_assignment_probs(const Eigen::VectorXd&, const Eigen::MatrixXd&, const Eigen::VectorXd&, Eigen::MatrixXd&)’:
abundances.cpp:2205:58: warning: comparison between signed and unsigned integer expressions
abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const std::vector<double>&, std::vector<double>&, bool)’:
abundances.cpp:3300:48: warning: comparison between signed and unsigned integer expressions
abundances.cpp:3302:52: warning: comparison between signed and unsigned integer expressions
In file included from abundances.cpp:36:0:
sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&) [with M = boost::numeric::ublas::matrix<double>]’:
abundances.cpp:117:45: instantiated from here
sampling.h:83:7: error: ‘sqrtl’ was not declared in this scope
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp: At global scope:
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:214:36: warning: ‘boost::system::posix_category’ defined but not used
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:215:36: warning: ‘boost::system::errno_ecat’ defined but not used
/cygdrive/c/AnalysisTools/boost/include/boost/system/error_code.hpp:216:36: warning: ‘boost::system::native_ecat’ defined but not used
Makefile:1444: recipe for target `abundances.o' failed
make[2]: *** [abundances.o] Error 1
make[2]: Leaving directory `/cygdrive/c/analysistools/cufflinks-2.0.1/src'
Makefile:290: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/analysistools/cufflinks-2.0.1'
Makefile:228: recipe for target `all' failed
make: *** [all] Error 2
I'm still a bit of an amateur when it comes to cygwin and several bioinformatics programs that require it for me, so I appreciate whatever help you can give.
It looks like you are missing the sqrtl function:
abundances.cpp:1227:145: error: ‘sqrtl’ was not declared in this scope
I do see this defined in Cygwin 1.7.16 in math.h as:
extern long double sqrtl _PARAMS((long double));
Are you running 1.7.16 of Cygwin? Check your /usr/include/math.h and see if sqrtl is defined.
However, I'd be careful running this in Cygwin. Officially cygwin says sqrtl isn't implemented, but I can build a test program to use it. I'm not seeing the results I'd expect, although my C is a bit rusty.

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