3
Cygwin을 사용하여 Windows 7 시스템에 커프 링크 2.0.1을 설치하려고합니다. Make 명령까지 모든 설치 단계를 완료했지만 make 명령은 어떤 이유로 실패합니다. 나는 왜 누군가가 저에게 말할 수 있는지 궁금 해서요. 나는 부스트 버전 1.50Cygwin에서 커프스 링크를 설치하는 방법
먼저 사용하고, 여기에 내가 구성 파일을 실행할 때 발생하는 내용은 다음과 같습니다
Benjamin [email protected] /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 :
Benjamin [email protected] /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.
여기에 내가 그것을 만들려고하면 어떻게 무엇을 cygwin과 나에게 필요한 몇 가지 생물 정보학 프로그램에 관해서는 여전히 아마추어인데, 그래서 당신이 줄 수있는 도움을 주시면 감사하겠습니다.
당신이 sqrtl 기능 누락 된 것 같습니다
루트로'make'를 실행 해 보셨습니까? – Steve
나는 당신이 무슨 뜻인지 모르겠다. 어떻게 당신은 뿌리로 달리는가? 다시 한 번 나는 유닉스에서 꽤 큰 아마추어이며, 그 라인이 나에게 무엇을해야할 지에 대해 말하지 않았다. –
불행히도 Cygwin 쉘에 대한 경험은 제한적이지만 필자가 읽은 것에서는 관리자로 실행하는 것이 가치가 있습니다. 바로 가기를 마우스 오른쪽 단추로 클릭하고 관리자 권한으로 실행을 클릭 할 수 있습니다. 그런 다음'./configure' ..와'make' 단계를 다시 시도하십시오. – Steve