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hall-lab
Make error: Error 2 on lumpy-sv
Hi, I am getting constant error during the installation of speedseq. I have git cloned the speedseq and tried the make command after installing all the dependencie
git clone --recursive https://github.com/hall-lab/speedseq.git
I have tried in both RHEL and Ubuntu. In both the case error is same. if I try to install lumpy-sv seperately by cloning from directly, there is now problem.
cp src/parallel/src/parallel bin make[1]: Leaving directory '/home/seqigib/Softwares/speedseq' make sv make[1]: Entering directory '/home/seqigib/Softwares/speedseq' make -C src/lumpy-sv make[2]: Entering directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv' configure.ac:26: warning: AC_INIT: not a literal: make2: Entering directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: 1.4 configure.ac:26: make2: Leaving directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: warning: AC_INIT: not a literal: make2: Entering directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: 1.4 configure.ac:26: make2: Leaving directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: warning: AC_INIT: not a literal: make2: Entering directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: 1.4 configure.ac:26: make2: Leaving directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: warning: AC_INIT: not a literal: make2: Entering directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' configure.ac:26: 1.4 configure.ac:26: make2: Leaving directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' cd lib/htslib && \ ./configure --disable-bz2 --disable-lzma --enable-libcurl ./configure: 4: ./configure: 1.4: not found ./configure: 5: ./configure: make2:: not found ./configure: line 4: 1.4: command not found ./configure: line 5: make2:: command not found ./configure: line 4: 1.4: command not found ./configure: line 5: make2:: command not found checking for gcc... gcc checking whether the C compiler works... no configure: error: in /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib':
configure: error: C compiler cannot create executables
See config.log' for more details Makefile:74: recipe for target 'htslib' failed make[2]: *** [htslib] Error 77 make[2]: Leaving directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv' Makefile:120: recipe for target 'lumpy' failed make[1]: *** [lumpy] Error 2 make[1]: Leaving directory '/home/seqigib/Softwares/speedseq' Makefile:23: recipe for target 'all' failed make: *** [all] Error 2
my gcc version is
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4)
Here is the config.log file `This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake.
It was created by HTSlib configure make2: Entering directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' 1.4 make2: Leaving directory '/home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib', which was generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure
---------
Platform.
---------
hostname = seqigib uname -m = x86_64 uname -r = 4.4.0-72-generic uname -s = Linux uname -v = #93-Ubuntu SMP Fri Mar 31 14:07:41 UTC 2017
/usr/bin/uname -p = unknown /bin/uname -X = unknown
/bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown
PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin PATH: /usr/games PATH: /usr/local/games PATH: /snap/bin PATH: /home/seqigib/Anoop_tools/bin
-----------
Core tests.
-----------
configure:2190: checking for gcc configure:2206: found /usr/bin/gcc configure:2217: result: gcc configure:2446: checking for C compiler version configure:2455: gcc --version >&5 gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:2466: $? = 0
configure:2455: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.4' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --pr
efix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-cloca
le=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-
browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-di
r=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=
m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4)
configure:2466: $? = 0
configure:2455: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2466: $? = 1
configure:2455: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:2466: $? = 1
configure:2486: checking whether the C compiler works
configure:2508: gcc conftest.c >&5
conftest.c:4:25: warning: missing terminating " character
#define PACKAGE_VERSION "make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib
^
conftest.c:5:1: error: expected identifier or '(' before numeric constant
1.4
^
conftest.c:6:82: warning: missing terminating " character
make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib"
^
conftest.c:6:1: error: missing terminating " character
make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib"
^
conftest.c:7:24: warning: missing terminating " character
#define PACKAGE_STRING "HTSlib make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib
^
conftest.c:9:82: warning: missing terminating " character
make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib"
^
conftest.c:9:1: error: missing terminating " character
make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib"
^
configure:2512: $? = 1
configure:2550: result: no
configure: failed program was:
| /* confdefs.h /
| #define PACKAGE_NAME "HTSlib"
| #define PACKAGE_TARNAME "htslib"
| #define PACKAGE_VERSION "make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib
| 1.4
| make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib"
| #define PACKAGE_STRING "HTSlib make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib
| 1.4
| make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE_URL "http://www.htslib.org/"
| / end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:2555: error: in /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib': configure:2557: error: C compiler cannot create executables See config.log' for more details
----------------
Cache variables.
----------------
ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PKG_CONFIG_LIBDIR_set= ac_cv_env_PKG_CONFIG_LIBDIR_value= ac_cv_env_PKG_CONFIG_PATH_set= ac_cv_env_PKG_CONFIG_PATH_value= ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_prog_ac_ct_CC=gcc
-----------------
Output variables.
-----------------
1.4 1.4 CC='gcc' CFLAGS='' CPP='' CPPFLAGS='' CRYPTO_LIBS='' DEFS='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='' EXEEXT='' GREP='' LDFLAGS='' LIBOBJS='' LIBS='' LTLIBOBJS='' OBJEXT='' PACKAGE_BUGREPORT='[email protected]' PACKAGE_NAME='HTSlib' PACKAGE_STRING='HTSlib make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib PACKAGE_TARNAME='htslib' PACKAGE_URL='http://www.htslib.org/' PACKAGE_VERSION='make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib PATH_SEPARATOR=':' PKG_CONFIG='' PKG_CONFIG_LIBDIR='' PKG_CONFIG_PATH='' PLATFORM='' PLUGIN_EXT='' RANLIB='' SHELL='/bin/bash' ac_ct_CC='gcc' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' enable_plugins='' exec_prefix='NONE' gcs='' host_alias='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' libcurl='' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib' mandir='${datarootdir}/man' oldincludedir='/usr/include' pc_requires='' pdfdir='${docdir}' plugindir='' pluginpath='' prefix='NONE' private_LIBS='' program_transform_name='s,x,x,' psdir='${docdir}' runstatedir='${localstatedir}/run' s3='' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' static_LDFLAGS='' static_LIBS='' sysconfdir='${prefix}/etc' target_alias=''
-----------
confdefs.h.
-----------
/* confdefs.h */ #define PACKAGE_NAME "HTSlib" #define PACKAGE_TARNAME "htslib" #define PACKAGE_VERSION "make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib 1.4 make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib" #define PACKAGE_STRING "HTSlib make2: Entering directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib 1.4 make2: Leaving directory /home/seqigib/Softwares/speedseq/src/lumpy-sv/lib/htslib" #define PACKAGE_BUGREPORT "[email protected]" #define PACKAGE_URL "http://www.htslib.org/"
configure: exit 77 ` Please help me to fix the same
Thanks in advance Shams
Thanks for bringing this to our attention. It looks like some of the recent updates to LUMPY conflict with our Makefile. I've modified the LUMPY submodule in speedseq to resolve this. Please try running the following:
cd /path/to/speedseq
git pull origin master
git submodule update --init --recursive
make sv
