build.log

build.log (text/plain), 14.01 KB, created by Agostino Sarubbo on 2021-02-14 11:53:05 UTC

 * Package:    sci-chemistry/openbabel-2.4.1-r1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux openmp userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/647581f177918ef68d295bf65edcb18685cb235b  (Sun Feb 14 00:08:31 UTC 2021)
@@@@@ END @@@@@



emerge --info:
Portage 3.0.14 (python 3.9.1-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r7, 5.4.0-1029-aws x86_64)
=================================================================
System uname: Linux-5.4.0-1029-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.32
KiB Mem:    64359964 total,  23443060 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sun, 14 Feb 2021 00:08:31 +0000
sh bash 5.1_p4
ld GNU ld (Gentoo 2.35.2 p1) 2.35.2
app-shells/bash:          5.1_p4::gentoo
dev-lang/perl:            5.32.1::gentoo
dev-lang/python:          3.7.9-r2::gentoo, 3.8.7-r1::gentoo, 3.9.1-r1::gentoo
dev-util/cmake:           3.19.4::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.7-r1::gentoo
sys-apps/openrc:          0.42.1-r1::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.3-r1::gentoo
sys-devel/binutils:       2.35.2::gentoo
sys-devel/gcc:            10.2.0-r5::gentoo
sys-devel/gcc-config:     2.3.3::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.10::gentoo (virtual/os-headers)
sys-libs/glibc:           2.32-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-jobs: 1
    sync-rsync-extra-opts: 

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* GPL-2"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color"
DISTDIR="/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/distdir"
EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="C.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j16"
PKGDIR="/root/.packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU"
Unset:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS





emerge history:
2021-02-14T03:46:21 >>> dev-cpp/eigen-3.3.9
2021-02-14T03:46:22 >>> sci-libs/inchi-1.04



>>> Unpacking source...
>>> Unpacking openbabel-2.4.1.tar.gz to /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work
>>> Unpacking openbabel.png to /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work
unpack openbabel.png: file format not recognized. Ignoring.
>>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1 ...
 * Applying openbabel-2.3.2-gcc-6_and_7-backport.patch ...
 [ ok ]
 * Applying openbabel-2.4.1-gcc-8.patch ...
 [ ok ]
 * Hardcoded definition(s) removed in CMakeLists.txt:
 *     set(CMAKE_BUILD_TYPE RelWithDebInfo)
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build"
cmake -C /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DOPENBABEL_USE_SYSTEM_INCHI=ON -DENABLE_OPENMP=yes -DBUILD_GUI=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1
loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/gentoo_common_config.cmake
CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:16 (cmake_policy):
  The OLD behavior for policy CMP0005 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


CMake Deprecation Warning at CMakeLists.txt:18 (cmake_policy):
  The OLD behavior for policy CMP0042 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:426 (message):
  The package name passed to `find_package_handle_standard_args` (INCHI) does
  not match the name of the calling package (Inchi).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/modules/FindInchi.cmake:19 (find_package_handle_standard_args)
  CMakeLists.txt:149 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found INCHI: /usr/lib64/libinchi.so  
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.10") 
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES wxWidgets_INCLUDE_DIRS) 
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - not found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH):
  MATH cannot parse the expression: "x86_6410*10000 + x86_642*100 + x86_640":
  syntax error, unexpected exp_NUMBER, expecting $end (9).
Call Stack (most recent call first):
  cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION)
  CMakeLists.txt:248 (macro_ensure_version)


CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH):
  MATH cannot parse the expression: "x86_6410*10000 + x86_642*100 + x86_640":
  syntax error, unexpected exp_NUMBER, expecting $end (9).
Call Stack (most recent call first):
  cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION)
  CMakeLists.txt:249 (macro_ensure_version)


CMake Error at cmake/modules/MacroEnsureVersion.cmake:76 (MATH):
  MATH cannot parse the expression: "x86_6410*10000 + x86_642*100 + x86_640":
  syntax error, unexpected exp_NUMBER, expecting $end (9).
Call Stack (most recent call first):
  cmake/modules/MacroEnsureVersion.cmake:95 (NORMALIZE_VERSION)
  CMakeLists.txt:250 (macro_ensure_version)


-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success
-- Use std::shared_ptr in memory
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "0.29.2") 
-- Checking for module 'cairo'
--   No package 'cairo' found
-- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS) 
-- Could NOT find Cairo. PNG output will NOT be supported.
-- Looking for getopt
-- Looking for getopt - found
-- GUI will not be built
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) 
CMake Deprecation Warning at scripts/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fopenmp
C++             -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fopenmp
Linker flags:
Executable      -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 
Module          -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring incomplete, errors occurred!
See also "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/CMakeFiles/CMakeOutput.log".
See also "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build/CMakeFiles/CMakeError.log".
 * ERROR: sci-chemistry/openbabel-2.4.1-r1::gentoo failed (configure phase):
 *   cmake failed
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_configure
 *   environment, line 2659:  Called cmake-utils_src_configure
 *   environment, line  992:  Called die
 * The specific snippet of code:
 *       "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/openbabel-2.4.1-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-2.4.1-r1::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/openbabel-2.4.1-r1:20210214-024627.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1_build'
 * S: '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r1/work/openbabel-2.4.1'