jmbono
commented
9 months ago Just an update in case anyone else is encountering this issue. I was able to install salmon using these instructions: CONDA_SUBDIR=osx-64 conda create -n rosetta conda activate rosetta conda env config vars set CONDA_SUBDIR=osx-64 conda install salmon
I am encountering two issues when I follow the instructions for installing salmon 1.10.1:https://salmon.readthedocs.io/en/latest/building.html#installation I am installing on a mac studio (M2 max) running Ventura.
The first issue I run into is that my understanding of the instructions suggests that I should be in the "build" directory when I run cmake. However, if I do that it returns an error about CMakeLists.txt not being in that location. I noticed that is in the salmon directory so I ran cmake from there and it seemed to work fine. But, I'm not sure if that is leading to the problems I am having downstream.
The second issue is when I run make I get an error associated with configuring liblzma (error 77). I have pasted the console log below. I appreciate any suggestions and apologize if I missed something obvious.
This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake.
It was created by XZ Utils configure 5.2.2, which was generated by GNU Autoconf 2.69. Invocation command line was
$ /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/configure --prefix=/Users/jeremybono/Downloads/salmon-1.10.1/external/install CC=/Library/Developer/CommandLineTools/usr/bin/cc CXX=/Library/Developer/CommandLineTools/usr/bin/c++ CFLAGS= CPPFLAGS= LDFLAGS=
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Platform.
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hostname = Jeremys-Mac-Studio.local uname -m = arm64 uname -r = 22.6.0 uname -s = Darwin uname -v = Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020
/usr/bin/uname -p = arm /bin/uname -X = unknown
/bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = Mach kernel version: Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 Kernel configured for up to 12 processors. 12 processors are physically available. 12 processors are logically available. Processor type: arm64e (ARM64E) Processors active: 0 1 2 3 4 5 6 7 8 9 10 11 Primary memory available: 64.00 gigabytes Default processor set: 650 tasks, 3562 threads, 12 processors Load average: 1.14, Mach factor: 10.84 /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown
PATH: /Users/jeremybono/miniforge3/bin PATH: /Users/jeremybono/miniforge3/condabin PATH: /opt/homebrew/bin PATH: /opt/homebrew/sbin PATH: /usr/local/bin PATH: /System/Cryptexes/App/usr/bin PATH: /usr/bin PATH: /bin PATH: /usr/sbin PATH: /sbin PATH: /Users/jeremybono/Downloads/bbmap PATH: /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin PATH: /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin PATH: /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
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Core tests.
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configure:5259: error: in
/Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2': configure:5261: error: C compiler cannot create executables Seeconfig.log' for more details----------------
Cache variables.
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ac_cv_build=arm-apple-darwin22.6.0 ac_cv_env_CCASFLAGS_set= ac_cv_env_CCASFLAGS_value= ac_cv_env_CCAS_set= ac_cv_env_CCAS_value= ac_cv_env_CC_set=set ac_cv_env_CC_value=/Library/Developer/CommandLineTools/usr/bin/cc ac_cv_env_CFLAGS_set=set ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set=set ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_LT_SYS_LIBRARY_PATH_set= ac_cv_env_LT_SYS_LIBRARY_PATH_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_host=arm-apple-darwin22.6.0 ac_cv_path_install='/usr/bin/install -c' ac_cv_prog_AWK=awk ac_cv_prog_ac_ct_CC=/Library/Developer/CommandLineTools/usr/bin/cc ac_cv_prog_make_make_set=yes am_cv_make_support_nested_variables=yes gl_cv_posix_shell=/bin/sh
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Output variables.
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ACLOCAL='${SHELL} /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/build-aux/missing aclocal-1.15' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_CFLAGS='' AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' AM_DEFAULT_VERBOSITY='1' AM_V='$(V)' AR='' AS='' AUTOCONF='${SHELL} /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/build-aux/missing autoconf' AUTOHEADER='${SHELL} /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/build-aux/missing autoheader' AUTOMAKE='${SHELL} /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/build-aux/missing automake-1.15' AWK='awk' CC='/Library/Developer/CommandLineTools/usr/bin/cc' CCAS='' CCASDEPMODE='' CCASFLAGS='' CCDEPMODE='' CFLAGS='' CFLAG_VISIBILITY='' COND_ASM_X86_64_FALSE='' COND_ASM_X86_64_TRUE='#' COND_ASM_X86_FALSE='' COND_ASM_X86_TRUE='#' COND_CHECK_CRC32_FALSE='#' COND_CHECK_CRC32_TRUE='' COND_CHECK_CRC64_FALSE='#' COND_CHECK_CRC64_TRUE='' COND_CHECK_SHA256_FALSE='#' COND_CHECK_SHA256_TRUE='' COND_DECODER_ARMTHUMB_FALSE='#' COND_DECODER_ARMTHUMB_TRUE='' COND_DECODER_ARM_FALSE='#' COND_DECODER_ARM_TRUE='' COND_DECODER_DELTA_FALSE='#' COND_DECODER_DELTA_TRUE='' COND_DECODER_IA64_FALSE='#' COND_DECODER_IA64_TRUE='' COND_DECODER_LZMA1_FALSE='#' COND_DECODER_LZMA1_TRUE='' COND_DECODER_LZMA2_FALSE='#' COND_DECODER_LZMA2_TRUE='' COND_DECODER_LZ_FALSE='#' COND_DECODER_LZ_TRUE='' COND_DECODER_POWERPC_FALSE='#' COND_DECODER_POWERPC_TRUE='' COND_DECODER_SIMPLE_FALSE='#' COND_DECODER_SIMPLE_TRUE='' COND_DECODER_SPARC_FALSE='#' COND_DECODER_SPARC_TRUE='' COND_DECODER_X86_FALSE='#' COND_DECODER_X86_TRUE='' COND_DOC_FALSE='#' COND_DOC_TRUE='' COND_ENCODER_ARMTHUMB_FALSE='#' COND_ENCODER_ARMTHUMB_TRUE='' COND_ENCODER_ARM_FALSE='#' COND_ENCODER_ARM_TRUE='' COND_ENCODER_DELTA_FALSE='#' COND_ENCODER_DELTA_TRUE='' COND_ENCODER_IA64_FALSE='#' COND_ENCODER_IA64_TRUE='' COND_ENCODER_LZMA1_FALSE='#' COND_ENCODER_LZMA1_TRUE='' COND_ENCODER_LZMA2_FALSE='#' COND_ENCODER_LZMA2_TRUE='' COND_ENCODER_LZ_FALSE='#' COND_ENCODER_LZ_TRUE='' COND_ENCODER_POWERPC_FALSE='#' COND_ENCODER_POWERPC_TRUE='' COND_ENCODER_SIMPLE_FALSE='#' COND_ENCODER_SIMPLE_TRUE='' COND_ENCODER_SPARC_FALSE='#' COND_ENCODER_SPARC_TRUE='' COND_ENCODER_X86_FALSE='#' COND_ENCODER_X86_TRUE='' COND_FILTER_ARMTHUMB_FALSE='#' COND_FILTER_ARMTHUMB_TRUE='' COND_FILTER_ARM_FALSE='#' COND_FILTER_ARM_TRUE='' COND_FILTER_DELTA_FALSE='#' COND_FILTER_DELTA_TRUE='' COND_FILTER_IA64_FALSE='#' COND_FILTER_IA64_TRUE='' COND_FILTER_LZMA1_FALSE='#' COND_FILTER_LZMA1_TRUE='' COND_FILTER_LZMA2_FALSE='#' COND_FILTER_LZMA2_TRUE='' COND_FILTER_LZ_FALSE='#' COND_FILTER_LZ_TRUE='' COND_FILTER_POWERPC_FALSE='#' COND_FILTER_POWERPC_TRUE='' COND_FILTER_SIMPLE_FALSE='#' COND_FILTER_SIMPLE_TRUE='' COND_FILTER_SPARC_FALSE='#' COND_FILTER_SPARC_TRUE='' COND_FILTER_X86_FALSE='#' COND_FILTER_X86_TRUE='' COND_GNULIB_FALSE='' COND_GNULIB_TRUE='' COND_INTERNAL_SHA256_FALSE='' COND_INTERNAL_SHA256_TRUE='' COND_LZMADEC_FALSE='#' COND_LZMADEC_TRUE='' COND_LZMAINFO_FALSE='#' COND_LZMAINFO_TRUE='' COND_LZMALINKS_FALSE='#' COND_LZMALINKS_TRUE='' COND_MAIN_DECODER_FALSE='#' COND_MAIN_DECODER_TRUE='' COND_MAIN_ENCODER_FALSE='#' COND_MAIN_ENCODER_TRUE='' COND_SCRIPTS_FALSE='#' COND_SCRIPTS_TRUE='' COND_SHARED_FALSE='' COND_SHARED_TRUE='' COND_SMALL_FALSE='' COND_SMALL_TRUE='#' COND_SYMVERS_FALSE='' COND_SYMVERS_TRUE='#' COND_THREADS_FALSE='' COND_THREADS_TRUE='' COND_W32_FALSE='' COND_W32_TRUE='#' COND_XZDEC_FALSE='#' COND_XZDEC_TRUE='' COND_XZ_FALSE='#' COND_XZ_TRUE='' CPP='' CPPFLAGS='' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' DLLTOOL='' DSYMUTIL='' DUMPBIN='' ECHO_C='\c' ECHO_N='' ECHO_T='' EGREP='' EXEEXT='' FGREP='' GETOPT_H='' GETTEXT_MACRO_VERSION='' GMSGFMT='' GMSGFMT_015='' GREP='' HAVE_VISIBILITY='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' INTLLIBS='' INTL_MACOSX_LIBS='' LD='' LDFLAGS='' LIBICONV='' LIBINTL='' LIBOBJS='' LIBS='' LIBTOOL='' LIPO='' LN_EXEEXT='$(EXEEXT)' LN_S='ln -s' LTLIBICONV='' LTLIBINTL='' LTLIBOBJS='' LT_SYS_LIBRARY_PATH='' MAKEINFO='${SHELL} /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/build-aux/missing makeinfo' MANIFEST_TOOL='' MKDIR_P='build-aux/install-sh -c -d' MSGFMT='' MSGFMT_015='' MSGMERGE='' NM='' NMEDIT='' OBJDUMP='' OBJEXT='' OTOOL64='' OTOOL='' PACKAGE='xz' PACKAGE_BUGREPORT='lasse.collin@tukaani.org' PACKAGE_NAME='XZ Utils' PACKAGE_STRING='XZ Utils 5.2.2' PACKAGE_TARNAME='xz' PACKAGE_URL='http://tukaani.org/xz/' PACKAGE_VERSION='5.2.2' PATH_SEPARATOR=':' POSIX_SHELL='/bin/sh' POSUB='' PREFERABLY_POSIX_SHELL='/bin/sh' PTHREAD_CC='' PTHREAD_CFLAGS='' PTHREAD_LIBS='' RANLIB='' RC='' SED='' SET_MAKE='' SHELL='/bin/sh' STRIP='' USE_NLS='' VERSION='5.2.2' XGETTEXT='' XGETTEXT_015='' XGETTEXT_EXTRA_OPTIONS='' ac_ct_AR='' ac_ct_CC='/Library/Developer/CommandLineTools/usr/bin/cc' ac_ct_DUMPBIN='' amEXEEXT_FALSE='' am__EXEEXT_TRUE='' amfastdepCCAS_FALSE='' amfastdepCCAS_TRUE='' am__fastdepCC_FALSE='' amfastdepCC_TRUE='' aminclude='include' amisrc='' amleading_dot='.' am__nodep='_no' amquote='' amtar='$${TAR-tar} chof - "$$tardir"' amuntar='$${TAR-tar} xf -' ax_pthread_config='' bindir='${exec_prefix}/bin' build='arm-apple-darwin22.6.0' build_alias='' build_cpu='arm' build_os='darwin22.6.0' build_vendor='apple' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='arm-apple-darwin22.6.0' host_alias='' host_cpu='arm' host_os='darwin22.6.0' host_vendor='apple' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2/build-aux/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/Users/jeremybono/Downloads/salmon-1.10.1/external/install' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' xz=''
-----------
confdefs.h.
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/ confdefs.h /
define PACKAGE_NAME "XZ Utils"
define PACKAGE_TARNAME "xz"
define PACKAGE_VERSION "5.2.2"
define PACKAGE_STRING "XZ Utils 5.2.2"
define PACKAGE_BUGREPORT "lasse.collin@tukaani.org"
define PACKAGE_URL "http://tukaani.org/xz/"
define NDEBUG 1
define HAVE_ENCODER_LZMA1 1
define HAVE_ENCODER_LZMA2 1
define HAVE_ENCODER_DELTA 1
define HAVE_ENCODER_X86 1
define HAVE_ENCODER_POWERPC 1
define HAVE_ENCODER_IA64 1
define HAVE_ENCODER_ARM 1
define HAVE_ENCODER_ARMTHUMB 1
define HAVE_ENCODER_SPARC 1
define HAVE_DECODER_LZMA1 1
define HAVE_DECODER_LZMA2 1
define HAVE_DECODER_DELTA 1
define HAVE_DECODER_X86 1
define HAVE_DECODER_POWERPC 1
define HAVE_DECODER_IA64 1
define HAVE_DECODER_ARM 1
define HAVE_DECODER_ARMTHUMB 1
define HAVE_DECODER_SPARC 1
define HAVE_MF_HC3 1
define HAVE_MF_HC4 1
define HAVE_MF_BT2 1
define HAVE_MF_BT3 1
define HAVE_MF_BT4 1
define HAVE_CHECK_CRC32 1
define HAVE_CHECK_CRC64 1
define HAVE_CHECK_SHA256 1
define ASSUME_RAM 128
define PACKAGE "xz"
define VERSION "5.2.2"
configure: exit 77 "5.2.2"
configure: exit 77
Steps and data to reproduce the behavior: salmon-1.10.1/cmake -DFETCH_BOOST=TRUE make
Additional context Add any other context about the problem here.