Configure error installing salmon

Question

Configure error installing salmon

jmbono opened this issue 10 months ago · 1 comments

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=

---------

Platform.

---------

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

-----------

Core tests.

-----------

configure:2959: checking build system type
configure:2973: result: arm-apple-darwin22.6.0
configure:2993: checking host system type
configure:3006: result: arm-apple-darwin22.6.0
configure:3066: checking if debugging code should be compiled
configure:3082: result: no
configure:3122: checking which encoders to build
configure:3209: result: lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc
configure:3213: checking which decoders to build
configure:3305: result: lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc
configure:3644: checking which match finders to build
configure:3695: result: hc3 hc4 bt2 bt3 bt4
configure:3713: checking which integrity checks to build
configure:3755: result: crc32 crc64 sha256
configure:3792: checking if assembler optimizations should be used
configure:3816: result: no
configure:3847: checking if small size is preferred over speed
configure:3865: result: no
configure:3881: checking if threading support is wanted
configure:3907: result: yes, posix
configure:3940: checking how much RAM to assume if the real amount is unknown
configure:3955: result: 128 MiB
configure:4085: checking if library symbol versioning should be used
configure:4108: result: no
configure:4126: checking for a shell that conforms to POSIX
configure:4167: result: /bin/sh
configure:4208: checking for a BSD-compatible install
configure:4276: result: /usr/bin/install -c
configure:4287: checking whether build environment is sane
configure:4342: result: yes
configure:4493: checking for a thread-safe mkdir -p
configure:4532: result: build-aux/install-sh -c -d
configure:4539: checking for gawk
configure:4569: result: no
configure:4539: checking for mawk
configure:4569: result: no
configure:4539: checking for nawk
configure:4569: result: no
configure:4539: checking for awk
configure:4555: found /usr/bin/awk
configure:4566: result: awk
configure:4577: checking whether make sets $(MAKE)
configure:4599: result: yes
configure:4628: checking whether make supports nested variables
configure:4645: result: yes
configure:4771: checking whether ln -s works
configure:4775: result: yes
configure:4795: checking for style of include used by make
configure:4823: result: GNU
configure:4894: checking for gcc
configure:4921: result: /Library/Developer/CommandLineTools/usr/bin/cc
configure:5150: checking for C compiler version
configure:5159: /Library/Developer/CommandLineTools/usr/bin/cc --version >&5
Apple clang version 15.0.0 (clang-1500.0.40.1)
Target: arm64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
configure:5170: $? = 0
configure:5159: /Library/Developer/CommandLineTools/usr/bin/cc -v >&5
Apple clang version 15.0.0 (clang-1500.0.40.1)
Target: arm64-apple-darwin22.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
configure:5170: $? = 0
configure:5159: /Library/Developer/CommandLineTools/usr/bin/cc -V >&5
clang: error: argument to '-V' is missing (expected 1 value)
clang: error: no input files
configure:5170: $? = 1
configure:5159: /Library/Developer/CommandLineTools/usr/bin/cc -qversion >&5
clang: error: unknown argument '-qversion'; did you mean '--version'?
clang: error: no input files
configure:5170: $? = 1
configure:5190: checking whether the C compiler works
configure:5212: /Library/Developer/CommandLineTools/usr/bin/cc conftest.c >&5
ld: library 'System' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:5216: $? = 1
configure:5254: result: no
configure: failed program was:
| /* 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"
| / end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:5259: error: in /Users/jeremybono/Downloads/salmon-1.10.1/external/xz-5.2.2': configure:5261: error: C compiler cannot create executables See config.log' for more details

----------------

Cache variables.

----------------

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

-----------------

Output variables.

-----------------

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=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCCAS_FALSE=''
am__fastdepCCAS_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${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.

-----------

/* 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.

Answer 1 · 2024-02-20T19:24:03.000Z

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