Document HOMEBREW_ARCH issues #1

drbenmorgan · 2019-01-17T15:28:01Z

Bug reports:

The move to gcc-7 (and further) on Linux can cause issues if there is a mismatch between this and the host CPU and system binutils versions. This is caused by Homebrew using -march=native for from-source builds on a Host CPU that supports ISAs the system binutils cannot assemble. With that flag, GCC will generate assembly that the used (system) binutils cannot assemble, causing "no such instruction set" errors.

For supported platforms, we have:

CentOS6: binutils 2.20.51
CentOS7: binutils: 2.27-34
Ubuntu 16.04LTS: binutils 2.26.1
Ubuntu 18.04LTS: binutils 2.30

So this is mostly going to affect CentOS 6 systems in the short term. We'll need to keep track of GCC vs Binutils recommendations, plus the minimum CPU features we can expect. We should probably recommend ~~the use of HOMEBREW_CORE=core2 for now~~ brew install binutils --cc=gcc-7 --env=std, and update this as and when we can mostly guarantee more modern chips and systems with sufficient binutils.

This will also affect Docker containers as those will need to be built on a host with a CPU supporting only the oldest set of features we want to support.

Note that the use of HOMEBREW_ARCH is no longer supported, so we need to build with the std env, or build a bottle at the same time (as bottles are built with core2 arch).

The text was updated successfully, but these errors were encountered:

drbenmorgan · 2019-01-17T15:28:59Z

@pfranchini, I've just noted the issue we looked at this afternoon here. If you have further failure (or success!) please post them here.

pfranchini · 2019-01-17T15:45:48Z

I have built on CentOS6 with HOMEBREW_CORE=core2 but I got errors coming from assembler.

drbenmorgan · 2019-01-17T15:54:48Z

Hi @pfranchini, could you run and post the logs here of:

$ brew config

$ brew doctor

please? Please also run, for each of the formula that fail:

$ brew gist-logs <nameofformula>

and post the resulting link here. I think it's now binutils failing, so try:

$ brew gist-logs binutils

pfranchini · 2019-01-17T17:08:09Z

[pfranchi@lx00 brew]$ brew config
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
HOMEBREW_VERSION: >=1.7.1 (shallow or no git repository)
ORIGIN: https://github.com/Linuxbrew/brew.git
HEAD: 6613974e73714c7137ad869834cb6590cde638a4
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 51b678e4a0af8d9bc027f4ae4fb86b5b885c81c7
Core tap last commit: 9 hours ago
HOMEBREW_PREFIX: /vols/build/snemo/brew
HOMEBREW_REPOSITORY: /vols/build/snemo/brew
HOMEBREW_CELLAR: /vols/build/snemo/brew/Cellar
HOMEBREW_CACHE: /home/hep/pfranchi/.cache/Homebrew
HOMEBREW_TEMP: /vols/build/snemo/tmp
HOMEBREW_ARCH: core
HOMEBREW_BUILD_FROM_SOURCE: 1
HOMEBREW_LOGS: /home/hep/pfranchi/.cache/Homebrew/Logs
HOMEBREW_NO_ANALYTICS_THIS_RUN: 1
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_SYSTEM_CURL_TOO_OLD: 1
CPU: 40-core 64-bit broadwell
Homebrew Ruby: 2.3.7 => /vols/build/snemo/brew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: N/A
Git: 1.7.1 => /usr/bin/git
Curl: 7.63.0 => /vols/build/snemo/brew/opt/curl/bin/curl
Java: 1.7.0_201
Kernel: Linux 2.6.32-754.9.1.el6.x86_64 x86_64 GNU/Linux
OS: CentOS release 6.10 (Final) (Final)
Host glibc: 2.12
/usr/bin/gcc: 4.4.7
glibc: N/A
gcc: N/A
xorg: N/A
[pfranchi@lx00 brew]$ brew doctor
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: You have HOMEBREW_BUILD_FROM_SOURCE set. This environment variable is
intended for use by Homebrew developers. If you are encountering errors,
please try unsetting this. Please do not file issues if you encounter
errors when using this environment variable.

Warning: An outdated version (1.7.1) of Git was detected in your PATH.
Git 2.7.0 or newer is required for Homebrew.
Please upgrade:
  brew install git

Warning: Your Homebrew's prefix is not /home/linuxbrew/.linuxbrew.
You can install Homebrew anywhere you want but some bottles (binary packages)
can only be used with a standard prefix and some formulae (packages)
may not build correctly with a non-standard prefix.

pfranchini · 2019-01-17T17:09:00Z

Have to figure how to make brew gist-logs work

drbenmorgan · 2019-01-17T17:11:20Z

Thanks! Only thing I can spot in the config output is that HOMEBREW_ARCH is core rather than core2. However, don't change that until we get the gist-logs working to confirm that's the issue or something else.

pfranchini · 2019-01-17T17:13:01Z

Was a later try.

pfranchini · 2019-01-18T11:46:19Z

I have got it here:
https://gist.github.com/pfranchini/e24e5b1a8e69fe832e2aa20593c30b90

drbenmorgan · 2019-01-18T12:09:04Z

Thanks! It does look as if the superenv isn't set correctly, as this line:

https://gist.github.com/pfranchini/e24e5b1a8e69fe832e2aa20593c30b90#file-02-make-cc-L2

Shows it's adding -march=native to the flags. Let's try the following:

$ brew install binutils --env=std --cc=gcc-7

as it looks like the HOMEBREW_ARCH variable isn't supported any more... The std env should however default to core2 or close. If we can get binutils installed through this, that should give a sufficient bootstrap to then install everything else with native...

pfranchini · 2019-01-18T14:20:44Z

From a fresh session:

export HOMEBREW_BUILD_FROM_SOURCE=1
export HOMEBREW_NO_AUTO_UPDATE=1
[pfranchi@lx00 snemo]$ brew install binutils --env=std --cc=gcc-7
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
==> Downloading https://ftp.gnu.org/gnu/binutils/binutils-2.31.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/57a8c61605f9ae31b3f1fa1d01466aebf29785b0f0e119d23488dfc3e1a6dea4--binutils-2.31.1.tar.gz
==> ./configure --with-sysroot=/ --enable-deterministic-archives --prefix=/vols/build/snemo/brew/Cellar/binutils/2.31.1_2 --infodir=/vols/build/snemo/
==> make
Last 15 lines from /home/hep/pfranchi/.cache/Homebrew/Logs/binutils/02.make:
checking whether canonicalize_file_name must be declared... no
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getpagesize... (cached) yes
checking for working mmap... yes
checking for working strncmp... yes
configure: updating cache ./config.cache
configure: creating ./config.status
config.status: creating Makefile
config.status: creating testsuite/Makefile
config.status: creating config.h
config.status: executing default commands
make[1]: Leaving directory `/tmp/binutils-20190118-187980-60gbzf/binutils-2.31.1'
make: *** [all] Error 2

drbenmorgan · 2019-01-22T14:54:28Z

O.k., I think we need to start from scratch here... So try:

$ brew rm --force $(brew ls)
$ brew install binutils --build-from-source

Let's just see if that works before going further. The above should try and build binutils with the system compiler/binutils (which should be o.k.). That should work.

pfranchini · 2019-01-25T15:02:15Z

Unfortunately it did not....


pfranchi@lx00 brew]$ brew install binutils --build-from-source
==> Installing dependencies for curl: patchelf, zlib, binutils, linux-headers, glibc, m4, gmp, mpfr, libmpc, [email protected], gcc, openssl and pkg-config
==> Installing curl dependency: patchelf
==> Downloading https://linuxbrew.bintray.com/bottles/patchelf-0.9_1.x86_64_linux.bottle.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/db57574a8c5d4c51b86703f6616af7807a37eaa47e9fb7be610f04617dc29e2a--patchelf-0.9_1.x86_64_linux.bottle.tar.gz
==> Pouring patchelf-0.9_1.x86_64_linux.bottle.tar.gz
Updating Homebrew...
🍺  /vols/build/snemo/brew/Cellar/patchelf/0.9_1: 6 files, 1.1MB
==> Installing curl dependency: zlib
==> Downloading https://linuxbrew.bintray.com/bottles/zlib-1.2.11.x86_64_linux.bottle.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/e26d7f94e9190e27f35a0ca17586414d88d5bb82ae7927206a18556eab619109--zlib-1.2.11.x86_64_linux.bottle.tar.gz
==> Pouring zlib-1.2.11.x86_64_linux.bottle.tar.gz
🍺  /vols/build/snemo/brew/Cellar/zlib/1.2.11: 12 files, 399.7KB
==> Installing curl dependency: binutils
==> Downloading https://linuxbrew.bintray.com/bottles/binutils-2.31.1_2.x86_64_linux.bottle.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/8657fccf756b21f5ded48c04234e987f2c10e782d92b665109d2eb4d29d33b57--binutils-2.31.1_2.x86_64_linux.bottle.tar.gz
==> Pouring binutils-2.31.1_2.x86_64_linux.bottle.tar.gz
🍺  /vols/build/snemo/brew/Cellar/binutils/2.31.1_2: 4,638 files, 293.8MB
==> Installing curl dependency: linux-headers
==> Downloading https://linuxbrew.bintray.com/bottles/linux-headers-4.4.80.x86_64_linux.bottle.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/2dfc91a92fc1bd00ed90bcf9ec0b1649d3fd5c40a90b7589ae1c017713f6958d--linux-headers-4.4.80.x86_64_linux.bottle.tar.gz
==> Pouring linux-headers-4.4.80.x86_64_linux.bottle.tar.gz
🍺  /vols/build/snemo/brew/Cellar/linux-headers/4.4.80: 772 files, 3.6MB
==> Installing curl dependency: glibc
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/3c17421daad583cfd4fad587b8e1260f19385344f309d7ae11e0c2bb6b75d801--glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/vols/build/snemo/brew/Cellar/glibc/2.23 --enable-obsol
Last 15 lines from /home/hep/pfranchi/.cache/Homebrew/Logs/glibc/01.configure:                                                                        
checking for gnumsgfmt... no                                                                                                                          
checking for gmsgfmt... no                                                                                                                            
checking for msgfmt... msgfmt                                                                                                                         
checking version of msgfmt... 0.17, ok                                                                                                                
checking for makeinfo... makeinfo                                                                                                                     
checking version of makeinfo... 4.13, ok                                                                                                              
checking for sed... sed                                                                                                                               
checking version of sed... 4.2.1, ok                                                                                                                  
checking for gawk... gawk                                                                                                                             
checking version of gawk... 3.1.7, ok                                                                                                                 
checking if gcc -B/vols/build/snemo/brew/opt/binutils/bin/ is sufficient to build libc... no                                                          
checking for nm... nm                                                                                                                                 
configure: error: 
*** These critical programs are missing or too old: compiler
*** Check the INSTALL file for required versions.

READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."

==> Installing dependencies for git: glibc, m4, gmp, mpfr, libmpc, [email protected], gcc, pkg-config, gpatch, ncurses, gettext, bzip2, pcre2, openssl, curl, libbsd and expat
==> Installing git dependency: glibc
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/3c17421daad583cfd4fad587b8e1260f19385344f309d7ae11e0c2bb6b75d801--glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/vols/build/snemo/brew/Cellar/glibc/2.23 --enable-obsol
Last 15 lines from /home/hep/pfranchi/.cache/Homebrew/Logs/glibc/01.configure:
checking for gnumsgfmt... no
checking for gmsgfmt... no
checking for msgfmt... msgfmt
checking version of msgfmt... 0.17, ok
checking for makeinfo... makeinfo
checking version of makeinfo... 4.13, ok
checking for sed... sed
checking version of sed... 4.2.1, ok
checking for gawk... gawk
checking version of gawk... 3.1.7, ok
checking if gcc -B/vols/build/snemo/brew/opt/binutils/bin/ is sufficient to build libc... no
checking for nm... nm
configure: error: 
*** These critical programs are missing or too old: compiler
*** Check the INSTALL file for required versions.

READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."

error: unknown option `list'
usage: git tag [-a|-s|-u <key-id>] [-f] [-m <msg>|-F <file>] <tagname> [<head>]
   or: git tag -d <tagname>...
   or: git tag -l [-n[<num>]] [<pattern>]
   or: git tag -v <tagname>...

    -l                    list tag names
    -n[<n>]               print <n> lines of each tag message
    -d                    delete tags
    -v                    verify tags

Tag creation options
    -a                    annotated tag, needs a message
    -m <msg>              message for the tag
    -F <FILE>             message in a file
    -s                    annotated and GPG-signed tag
    -u <key-id>           use another key to sign the tag
    -f, --force           replace the tag if exists

Tag listing options
    --contains <commit>   print only tags that contain the commit

error: unknown option `list'
usage: git tag [-a|-s|-u <key-id>] [-f] [-m <msg>|-F <file>] <tagname> [<head>]
   or: git tag -d <tagname>...
   or: git tag -l [-n[<num>]] [<pattern>]
   or: git tag -v <tagname>...

    -l                    list tag names
    -n[<n>]               print <n> lines of each tag message
    -d                    delete tags
    -v                    verify tags

Tag creation options
    -a                    annotated tag, needs a message
    -m <msg>              message for the tag
    -F <FILE>             message in a file
    -s                    annotated and GPG-signed tag
    -u <key-id>           use another key to sign the tag
    -f, --force           replace the tag if exists

Tag listing options
    --contains <commit>   print only tags that contain the commit

Unknown option: -c
usage: git [--version] [--exec-path[=GIT_EXEC_PATH]] [--html-path]
           [-p|--paginate|--no-pager] [--no-replace-objects]
           [--bare] [--git-dir=GIT_DIR] [--work-tree=GIT_WORK_TREE]
           [--help] COMMAND [ARGS]
Error: Could not 'git stash' in /vols/build/snemo/brew!
Please stash/commit manually if you need to keep your changes or, if not, run:
  cd /vols/build/snemo/brew
  git reset --hard origin/master
Warning: binutils 2.31.1_2 is already installed and up-to-date
To reinstall 2.31.1_2, run `brew reinstall binutils`

drbenmorgan · 2019-01-25T15:51:25Z

Ah, sorry, I should have been more explicit in the the settings, as Homebrew now tries harder to install binaries. First make sure you start from a pristine environment (so nothing in PATH except the brew bin dir plus the normal /usr system paths). Then do:

$ export HOMEBREW_NO_AUTO_UPDATE=1
$ export HOMEBREW_BUILD_FROM_SOURCE=1
$ brew rm --force $(brew ls)
$ brew install binutils --build-from-source

If it works correctly, the install step should print something like

Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
==> Installing dependencies for binutils: zlib
==> Installing binutils dependency: zlib
==> Downloading https://zlib.net/zlib-1.2.11.tar.gz
######################################################################## 100.0%
==> ./configure --prefix=/opt/supernemo/Cellar/zlib/1.2.11
==> make install
🍺  /opt/supernemo/Cellar/zlib/1.2.11: 12 files, 445KB, built in 6 seconds
==> Installing binutils
==> Downloading https://ftp.gnu.org/gnu/binutils/binutils-2.31.1.tar.gz
######################################################################## 100.0%
==> ./configure --with-sysroot=/ --enable-deterministic-archives --prefix=/opt/s
==> make
==> make install
==> strip /opt/supernemo/Cellar/binutils/2.31.1_2/bin/elfedit /opt/supernemo/Cel
🍺  /opt/supernemo/Cellar/binutils/2.31.1_2: 4,637 files, 198.3MB, built in 2 minutes 46 seconds

If it doesn't, post the output here.

pfranchini · 2019-01-25T17:26:52Z

Thanks it worked, sorry you for the confusion.

drbenmorgan · 2019-01-25T17:37:07Z

Great! I think with binutils in place, you should be able to build everything. Just to be sure, let's try:

... just to be sure these are set
$ export HOMEBREW_NO_AUTO_UPDATE=1
$ export HOMEBREW_BUILD_FROM_SOURCE=1
$ brew install gcc@7 --without-glibc --build-from-source

... assuming that works ...

$ brew install gdbm --cc=gcc-7 --build-from-source

GDBM was the first package to report an issue, so hopefully this time it goes through...

pfranchini · 2019-01-29T17:23:09Z

Ok this part works. Trying with falaise now...

pfranchini · 2019-02-05T17:57:49Z

Sorry, have been distracted by some other things. Here the last attempt:

[pfranchi@lx00 brew]$ brew install falaise --cc=gcc-7
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: You passed `--cc=gcc-7`.
You will encounter build failures with some formulae.
Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC. You are responsible for resolving any issues you
experience, as you are running this unsupported configuration.

==> Installing falaise from supernemo-dbd/cadfael
==> Installing dependencies for supernemo-dbd/cadfael/falaise: expat, curl, supernemo-dbd/cadfael/xerces-c, supernemo-dbd/cadfael/geant4, supernemo-dbd/cadfael/gsl, libpng, freetype, berkeley-db, perl, autoconf, automake, gperf, libtool, json-c, util-linux, fontconfig, supernemo-dbd/cadfael/qt5-base, supernemo-dbd/cadfael/xrootd, supernemo-dbd/cadfael/root6 and supernemo-dbd/cadfael/bayeux
==> Installing supernemo-dbd/cadfael/falaise dependency: expat
==> Downloading https://github.com/libexpat/libexpat/releases/download/R_2_2_6/expat-2.2.6.tar.bz2
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b70adc747fc7fa4bbd275bc743e73affdccf513188de0c8216aced805f006d36--expat-2.2.6.tar.bz2
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/expat/2.2.6 --mandir=/vols/build/snemo/brew/Cellar/expat/2.2.6/share/man --with-libbsd
Last 15 lines from /home/hep/pfranchi/.cache/Homebrew/Logs/expat/01.configure:
checking for off_t... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for docbook2x-man... no
checking for db2x_docbook2man... no
checking for docbook2man... docbook2man
configure: error: Your local docbook2man was found to work with SGML rather
  than XML. Please install docbook2X and use variable DOCBOOK_TO_MAN to point
  configure to command docbook2x-man of docbook2X.
  Or use DOCBOOK_TO_MAN="xmlto man --skip-validation" if you have xmlto around.
  You can also configure using --without-docbook if you can do without a man
  page for xmlwf.

drbenmorgan · 2019-02-06T12:58:44Z

Hi @pfranchini, could you try

$ brew update
$ brew install expat --cc=gcc-7

please? Pull Request #76 should have fixed this issue, so assuming the expat install now runs, you can try brew install falaise --cc=gcc-7 again after that.

pfranchini · 2019-02-06T14:13:43Z

[pfranchi@lx00 snemo]$ brew update
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
==> Downloading https://curl.haxx.se/download/curl-7.63.0.tar.bz2
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/4baa673c6a4a5e12cfab6c65dfd3c02ef5fcd8eac1d9ee9aa8aee9aef549be06--curl-7.63.0.tar.bz2
==> ./configure --disable-silent-rules --prefix=/vols/build/snemo/brew/Cellar/curl/7.63.0 --with-ssl=/vols/build/snemo/brew/opt/openssl --with-ca-bund
==> make install
==> make install -C scripts
==> Caveats
zsh completions have been installed to:
  /vols/build/snemo/brew/share/zsh/site-functions
==> Summary
🍺  /vols/build/snemo/brew/Cellar/curl/7.63.0: 447 files, 3.7MB, built in 4 minutes 16 seconds
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
==> Installing dependencies for git: pcre2 and expat
==> Installing git dependency: pcre2
==> Downloading https://ftp.pcre.org/pub/pcre/pcre2-10.32.tar.bz2
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b25f6fb9d2a3483199ce4382905711f6120540947a579e2d7cb5af24507ff1fb--pcre2-10.32.tar.bz2
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/pcre2/10.32 --enable-pcre2-16 --enable-pcre2-32 --enable-pcre2grep-libz --enable-pcre2grep-libb
==> make
==> make install
🍺  /vols/build/snemo/brew/Cellar/pcre2/10.32: 228 files, 6.3MB, built in 49 seconds
==> Installing git dependency: expat
==> Downloading https://github.com/libexpat/libexpat/releases/download/R_2_2_6/expat-2.2.6.tar.bz2
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b70adc747fc7fa4bbd275bc743e73affdccf513188de0c8216aced805f006d36--expat-2.2.6.tar.bz2
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/expat/2.2.6 --mandir=/vols/build/snemo/brew/Cellar/expat/2.2.6/share/man --with-libbsd
Last 15 lines from /home/hep/pfranchi/.cache/Homebrew/Logs/expat/01.configure:
checking for off_t... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for docbook2x-man... no
checking for db2x_docbook2man... no
checking for docbook2man... docbook2man
configure: error: Your local docbook2man was found to work with SGML rather
  than XML. Please install docbook2X and use variable DOCBOOK_TO_MAN to point
  configure to command docbook2x-man of docbook2X.
  Or use DOCBOOK_TO_MAN="xmlto man --skip-validation" if you have xmlto around.
  You can also configure using --without-docbook if you can do without a man
  page for xmlwf.

READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."

drbenmorgan · 2019-02-06T14:53:31Z

Oh @£$$%!ing Homebrew... Can you post the output of

$ brew info expat

If it's truly updated, it'll print something like:

Warning: expat is provided by core, but is now shadowed by supernemo-dbd/cadfael/[email protected].
To refer to the core formula, use Homebrew/core/expat instead.
supernemo-dbd/cadfael/[email protected]: stable 2.2.6, HEAD [keg-only]

I bet it's insisting on installing git before updating (so not actually updating...). So it won't print the above. To rectify that do the following:

$ cd $(brew --repo supernemo-dbd/cadfael)
$ git pull
$ cd backwhereyouwere

Try brew install expat --cc=gcc-7 first, then brew install falaise --cc=gcc-7

pfranchini · 2019-02-06T16:11:47Z

Do not worry we will get there ;)

[pfranchi@lx00 snemo]$ brew info expat
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: expat is provided by core, but is now shadowed by supernemo-dbd/cadfael/[email protected].
To refer to the core formula, use Homebrew/core/expat instead.
supernemo-dbd/cadfael/[email protected]: stable 2.2.6, HEAD
XML 1.0 parser
https://libexpat.github.io/
Not installed
From: https://github.com/supernemo-dbd/homebrew-cadfael/blob/master/Formula/[email protected]
==> Options
--HEAD
        Install HEAD version

So apparently is there, with the proper version, but

[pfranchi@lx00 snemo]$ brew install falaise --cc=gcc-7
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: You passed `--cc=gcc-7`.
You will encounter build failures with some formulae.
Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC. You are responsible for resolving any issues you
experience, as you are running this unsupported configuration.

==> Installing falaise from supernemo-dbd/cadfael
==> Installing dependencies for supernemo-dbd/cadfael/falaise: expat, supernemo-dbd/cadfael/xerces-c, supernemo-dbd/cadfael/geant4, supernemo-dbd/cadfael/gsl, libpng, freetype, berkeley-db, perl, autoconf, automake, gperf, libtool, json-c, util-linux, fontconfig, supernemo-dbd/cadfael/qt5-base, libxml2, supernemo-dbd/cadfael/xrootd, supernemo-dbd/cadfael/root6 and supernemo-dbd/cadfael/bayeux
Error: expat is already installed from supernemo-dbd/cadfael!
Please `brew uninstall expat` first."

I tried doing the uninstall brew uninstall [email protected] but is still there

[pfranchi@lx00 snemo]$ brew uninstall [email protected]
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Uninstalling /vols/build/snemo/brew/Cellar/[email protected]/2.2.6... (18 files, 806.4KB)
[pfranchi@lx00 snemo]$ brew info expat
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: expat is provided by core, but is now shadowed by supernemo-dbd/cadfael/[email protected].
To refer to the core formula, use Homebrew/core/expat instead.
supernemo-dbd/cadfael/[email protected]: stable 2.2.6, HEAD

pfranchini · 2019-02-11T11:37:52Z

Hi Ben, had few more attempts but stuck at that stage...

drbenmorgan · 2019-02-11T11:42:31Z

Hi Paolo, apologies, I missed your previous post... Does

$ brew ls --versions

actually list expat anywhere (and could you also post the exact output of the above please)?

pfranchini · 2019-02-11T12:26:21Z

No worries Ben. Actually I managed to disinstall it.

Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
binutils 2.31.1_2
bison 3.2.4 3.3.1
boost 1.63.0_5
bzip2 1.0.6_1
camp 0.8.0_1
clhep 2.1.3.1_1
cmake 3.13.3 3.13.4
curl 7.63.0
docbook 5.0
docbook2x 0.8.8_1
doxygen 1.8.15
flex 2.6.4
gcc@7 7.4.0
gdbm 1.18.1
gettext 0.19.8.1_1
gmp 6.1.2_2
gpatch 2.7.6
help2man 1.47.8
icu4c 63.1
isl 0.20
libbsd 0.8.3
libffi 3.2.1
libmpc 1.1.0
libxml2 2.9.8_1
libxslt 1.1.33
m4 1.4.18
mpfr 4.0.1
ncurses 6.1
openssl 1.0.2q_1 1.0.2q_2
pcre2 10.32
pkg-config 0.29.2_1
python 3.7.2_1
python@2 2.7.15_2
readline 8.0.0_1
sphinx-doc 1.8.3 1.8.3_1
sqlite 3.26.0_1
xz 5.2.4
zlib 1.2.11

drbenmorgan · 2019-02-11T12:31:27Z

Great! So are you now able to do

$ brew install expat --cc=gcc-7

?

pfranchini · 2019-02-11T12:35:59Z

Done

drbenmorgan · 2019-02-11T12:45:42Z

O.k., so it should (everything crossed...) hopefully be possible to do...

$ brew install falaise --cc=gcc-7

pfranchini · 2019-02-11T12:50:33Z

Yeah I am keeping crossing stuff, but back where we were before

[pfranchi@lx00 snemo]$ brew install expat --cc=gcc-7                                                                                                  
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: expat is provided by core, but is now shadowed by supernemo-dbd/cadfael/[email protected].
To refer to the core formula, use Homebrew/core/expat instead.
Warning: You passed `--cc=gcc-7`.
You will encounter build failures with some formulae.
Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC. You are responsible for resolving any issues you
experience, as you are running this unsupported configuration.

==> Installing [email protected] from supernemo-dbd/cadfael
==> Downloading https://github.com/libexpat/libexpat/releases/download/R_2_2_6/expat-2.2.6.tar.bz2
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b70adc747fc7fa4bbd275bc743e73affdccf513188de0c8216aced805f006d36--expat-2.2.6.tar.bz2
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/[email protected]/2.2.6 --mandir=/vols/build/snemo/brew/Cellar/[email protected]/2.2.6/share/man --without-
==> make install
🍺  /vols/build/snemo/brew/Cellar/[email protected]/2.2.6: 18 files, 806.4KB, built in 35 seconds
[pfranchi@lx00 snemo]$ brew install falaise --cc=gcc-7
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: You passed `--cc=gcc-7`.
You will encounter build failures with some formulae.
Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC. You are responsible for resolving any issues you
experience, as you are running this unsupported configuration.

==> Installing falaise from supernemo-dbd/cadfael
==> Installing dependencies for supernemo-dbd/cadfael/falaise: bison, expat, curl, supernemo-dbd/cadfael/xerces-c, supernemo-dbd/cadfael/geant4, supernemo-dbd/cadfael/gsl, libpng, freetype, berkeley-db, perl, autoconf, automake, gperf, libtool, json-c, util-linux, fontconfig, supernemo-dbd/cadfael/qt5-base, libxml2, supernemo-dbd/cadfael/xrootd, supernemo-dbd/cadfael/root6 and supernemo-dbd/cadfael/bayeux
==> Installing supernemo-dbd/cadfael/falaise dependency: bison
==> Downloading https://ftp.gnu.org/gnu/bison/bison-3.3.2.tar.xz
######################################################################## 100.0%
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/bison/3.3.2
==> make install
🍺  /vols/build/snemo/brew/Cellar/bison/3.3.2: 145 files, 3.2MB, built in 2 minutes 30 seconds
Error: expat is already installed from supernemo-dbd/cadfael!
Please `brew uninstall expat` first."


[pfranchi@lx00 snemo]$ brew ls --versions | grep expat
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
[email protected] 2.2.6

drbenmorgan · 2019-02-11T13:12:40Z

Ugh, I bet this is related to "you can use a tap, but" issues. Bear with me, I'll try and fire up a container to reproduce this.

pfranchini · 2019-02-11T13:28:34Z

Sure thanks for that. BTW what is the problem? would have been more straightforward in CentOS7?

drbenmorgan · 2019-02-11T13:45:56Z

You can try CentOS7 if you have it available. That'll solve the binutils issue, but the error above looks like it's down to Homebrew complaining that you haven't installed its expat rather than the one we want. It's possible that this is simply due to the previous update issues, so trying on a clean machine/install would help.

pfranchini · 2019-02-12T12:12:16Z

Still in CentOS6 I have redone the installation from scratch but got at the very same point Error: expat is already installed from supernemo-dbd/cadfael!

[pfranchi@lx00 snemo]$ brew install falaise --cc=gcc-7
Warning: Calling HOMEBREW_BUILD_FROM_SOURCE is deprecated! Use --build-from-source instead.
Warning: You passed `--cc=gcc-7`.
You will encounter build failures with some formulae.
Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC. You are responsible for resolving any issues you
experience, as you are running this unsupported configuration.

==> Installing falaise from supernemo-dbd/cadfael
==> Installing dependencies for supernemo-dbd/cadfael/falaise: pkg-config, gdbm, openssl, gpatch, ncurses, readline, sqlite, xz, bzip2, libffi, python, sphinx-doc, cmake, bison, help2man, gettext, flex, doxygen, icu4c, supernemo-dbd/cadfael/boost, supernemo-dbd/cadfael/camp, supernemo-dbd/cadfael/clhep, libbsd, expat, curl, supernemo-dbd/cadfael/xerces-c, supernemo-dbd/cadfael/geant4, supernemo-dbd/cadfael/gsl, libpng, freetype, berkeley-db, perl, autoconf, automake, gperf, libtool, json-c, python@2, util-linux, fontconfig, supernemo-dbd/cadfael/qt5-base, libxml2, supernemo-dbd/cadfael/xrootd, supernemo-dbd/cadfael/root6 and supernemo-dbd/cadfael/bayeux
==> Installing supernemo-dbd/cadfael/falaise dependency: pkg-config
==> Downloading https://pkgconfig.freedesktop.org/releases/pkg-config-0.29.2.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/5bdbf3b3fdadaf72744884b98b74a2ff887bd63a20b246f811a222a146ad7b64--pkg-config-0.29.2.tar.gz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/pkg-config/0.29.2_1 --disable-host-tool --with-internal-glib --with-pc-path=/vols/build/snemo/b
==> make
==> make check
==> make install
🍺  /vols/build/snemo/brew/Cellar/pkg-config/0.29.2_1: 11 files, 699.5KB, built in 2 minutes 31 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: gdbm
==> Downloading https://ftp.gnu.org/gnu/gdbm/gdbm-1.18.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/c6e5196e3cea2a139cb849d508032f117c6351da5fe84323dc13ad2a0600264a--gdbm-1.18.1.tar.gz
==> ./configure --disable-silent-rules --without-readline --prefix=/vols/build/snemo/brew/Cellar/gdbm/1.18.1 --enable-libgdbm-compat CPPFLAGS=-D_GNU_S
==> make install
🍺  /vols/build/snemo/brew/Cellar/gdbm/1.18.1: 40 files, 940.8KB, built in 42 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: openssl
==> Downloading https://www.openssl.org/source/openssl-1.0.2q.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/bfd5d14e97371eed56ab875871c8e05eb1db5bc099a6353e46bae830f9bcc8ff--openssl-1.0.2q.tar.gz
==> perl ./Configure --prefix=/vols/build/snemo/brew/Cellar/openssl/1.0.2q_2 --openssldir=/vols/build/snemo/brew/etc/openssl no-ssl2 no-ssl3 no-zlib s
==> make depend
==> make
==> make test
==> make install MANDIR=/vols/build/snemo/brew/Cellar/openssl/1.0.2q_2/share/man MANSUFFIX=ssl
==> Downloading https://curl.haxx.se/ca/cacert-2019-01-23.pem
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/71a7eb8318a4935314ce9c1d9594fecfd8cc8a186f32ac4e3869400b445c48b2--cacert-2019-01-23.pem
==> Caveats
A CA file has been bootstrapped using certificates from the SystemRoots
keychain. To add additional certificates (e.g. the certificates added in
the System keychain), place .pem files in
  /vols/build/snemo/brew/etc/openssl/certs

and run
  /vols/build/snemo/brew/opt/openssl/bin/c_rehash
==> Summary
🍺  /vols/build/snemo/brew/Cellar/openssl/1.0.2q_2: 1,794 files, 14.2MB, built in 8 minutes 13 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: gpatch
==> Downloading https://ftp.gnu.org/gnu/patch/patch-2.7.6.tar.xz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/2f0091adb183b747ac383680614e2094894c4420e49316df3b03a0473b57615c--patch-2.7.6.tar.xz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/gpatch/2.7.6
==> make install
🍺  /vols/build/snemo/brew/Cellar/gpatch/2.7.6: 10 files, 354.2KB, built in 2 minutes 11 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: ncurses
==> Downloading https://ftp.gnu.org/gnu/ncurses/ncurses-6.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b57cba28b3f3a973519acc164cdc15cd23c8ad7c614ce0e8df3da033e70f0ed1--ncurses-6.1.tar.gz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/ncurses/6.1 --enable-pc-files --with-pkg-config-libdir=/vols/build/snemo/brew/Cellar/ncurses/6.
==> make install
🍺  /vols/build/snemo/brew/Cellar/ncurses/6.1: 3,878 files, 8.9MB, built in 2 minutes 40 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: readline
==> Downloading https://ftp.gnu.org/gnu/readline/readline-8.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/2dd06cc6b778b6977a66d7986a2c0e71e557ff460a093af91f0f77a60d4e6d14--readline-8.0.tar.gz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/readline/8.0.0_1 --with-curses
==> make install SHLIB_LIBS=-lcurses
🍺  /vols/build/snemo/brew/Cellar/readline/8.0.0_1: 48 files, 1.9MB, built in 42 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: sqlite
==> Downloading https://sqlite.org/2018/sqlite-autoconf-3260000.tar.gz
######################################################################## 100.0%
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/sqlite/3.26.0_1 --enable-dynamic-extensions --enable-readline --disable-editline
==> make install
🍺  /vols/build/snemo/brew/Cellar/sqlite/3.26.0_1: 12 files, 4.3MB, built in 1 minute 44 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: xz
==> Downloading https://downloads.sourceforge.net/project/lzmautils/xz-5.2.4.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/60057e32fccba99ff98a423a0d5bbb3299325346de36997e4e59bb96a3c2da2e--xz-5.2.4.tar.gz
==> ./configure --disable-silent-rules --prefix=/vols/build/snemo/brew/Cellar/xz/5.2.4
==> make check
==> make install
🍺  /vols/build/snemo/brew/Cellar/xz/5.2.4: 99 files, 1.4MB, built in 1 minute 16 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: bzip2
==> Downloading https://ftp.osuosl.org/pub/clfs/conglomeration/bzip2/bzip2-1.0.6.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/e61d839a95ea1c150c5c07bdc457a1d666c40e1af090e0e57dd48b3a655e0dc3--bzip2-1.0.6.tar.gz
==> make install PREFIX=/vols/build/snemo/brew/Cellar/bzip2/1.0.6_1
==> make -f Makefile-libbz2_so clean
==> make -f Makefile-libbz2_so
🍺  /vols/build/snemo/brew/Cellar/bzip2/1.0.6_1: 30 files, 536KB, built in 7 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: libffi
==> Downloading https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/7f73f553e1ca54d2b6118a9c2232e54ff4abdb6f962eb50219efc62994220b76--libffi-3.2.1.tar.gz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/libffi/3.2.1
==> make install
🍺  /vols/build/snemo/brew/Cellar/libffi/3.2.1: 17 files, 333.5KB, built in 40 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: python
==> Downloading https://www.python.org/ftp/python/3.7.2/Python-3.7.2.tgz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/c0a14628b5078ca696f1e18227df67d9c5fbe04462c041d9252709c120ea3e1a--Python-3.7.2.tgz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/python/3.7.2_1 --enable-ipv6 --datarootdir=/vols/build/snemo/brew/Cellar/python/3.7.2_1/share -
==> make
==> make install PYTHONAPPSDIR=/vols/build/snemo/brew/Cellar/python/3.7.2_1
==> Downloading https://files.pythonhosted.org/packages/37/1b/b25507861991beeade31473868463dad0e58b1978c209de27384ae541b0b/setuptools-40.6.3.zip
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/db35d64db50c77fd8d1c71a34dea53793212ff10926cce3996211152a2be6077--setuptools-40.6.3.zip
==> Downloading https://files.pythonhosted.org/packages/45/ae/8a0ad77defb7cc903f09e551d88b443304a9bd6e6f124e75c0fbbf6de8f7/pip-18.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/49675dad98271e4b941f60d10b32b309d3d0a8133fc6f779c65eb050e19f4f84--pip-18.1.tar.gz
==> Downloading https://files.pythonhosted.org/packages/d8/55/221a530d66bf78e72996453d1e2dedef526063546e131d70bed548d80588/wheel-0.32.3.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/67e874601fa70fac6ed5e2bd91f7a9d719609be2b09874b79b0b2a11b90028dc--wheel-0.32.3.tar.gz
==> /vols/build/snemo/brew/Cellar/python/3.7.2_1/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/vols/build/snemo/b
==> /vols/build/snemo/brew/Cellar/python/3.7.2_1/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/vols/build/snemo/b
==> /vols/build/snemo/brew/Cellar/python/3.7.2_1/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/vols/build/snemo/b
==> Caveats
Python has been installed as
  /vols/build/snemo/brew/bin/python3

Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
  /vols/build/snemo/brew/opt/python/libexec/bin

If you need Homebrew's Python 2.7 run
  brew install python@2

You can install Python packages with
  pip3 install <package>
They will install into the site-package directory
  /vols/build/snemo/brew/lib/python3.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python
==> Summary
🍺  /vols/build/snemo/brew/Cellar/python/3.7.2_1: 8,089 files, 123.5MB, built in 9 minutes 31 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: sphinx-doc
==> Downloading https://files.pythonhosted.org/packages/dd/f8/df628d41f42793d446285767164c6a8da71d82892f2c98c43e0523836d39/Sphinx-1.8.4.tar.gz
######################################################################## 100.0%
==> Downloading https://github.com/pypa/virtualenv/archive/16.2.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/bfb26e5e9fbf90082f14312f9f0af39c489fc665de9adcc2c003f3e4c533bfd6--virtualenv-16.2.0.tar.gz
==> python3 -c import setuptools... --no-user-cfg install --prefix=/vols/build/snemo/tmp/sphinx-doc--homebrew-virtualenv-20190212-107339-1bkcayt/targe
==> python3 -s /vols/build/snemo/tmp/sphinx-doc--homebrew-virtualenv-20190212-107339-1bkcayt/target/bin/virtualenv -p python3 /vols/build/snemo/brew/C
==> Downloading https://files.pythonhosted.org/packages/cc/b4/ed8dcb0d67d5cfb7f83c4d5463a7614cb1d078ad7ae890c9143edebbf072/alabaster-0.7.12.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/6fe7e7241e703f9e3f03f1600efd5a1f03bb466b8bc79871d35be3da87239d71--alabaster-0.7.12.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/be/cc/9c981b249a455fa0c76338966325fc70b7265521bad641bf2932f77712f4/Babel-2.6.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/8a881c6f33f4772863d5aff1625f2c32759af1702c8875574d74fd1e4b478997--Babel-2.6.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed/certifi-2018.11.29.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/ede4159ed11d21e4394c4f87494740a01978922d37cef11f621c593c644938da--certifi-2018.11.29.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d/chardet-3.0.4.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/de28644dd0ba2aaf30228e9b28ba90366e333e7a34e1b1f97cf85d0edd0cb278--chardet-3.0.4.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/84/f4/5771e41fdf52aabebbadecc9381d11dea0fa34e4759b4071244fa094804c/docutils-0.14.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/082747f2931278a960879f30afd38989c894b92d04eda36ead03e57dfb6703fc--docutils-0.14.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7/idna-2.8.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b3673db65852656b6c4f3e1dbb5c5528f2a4e12a92dba9ca1950f133a076ff63--idna-2.8.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/41/f5/3cf63735d54aa9974e544aa25858d8f9670ac5b4da51020bbfc6aaade741/imagesize-1.1.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/947cc8c7ba94af5bc75dd494e3e3282b56d7e80031b05e9cd3572c2ef837a186--imagesize-1.1.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/56/e6/332789f295cf22308386cf5bbd1f4e00ed11484299c5d7383378cf48ba47/Jinja2-2.10.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/9c1a9f477c7fcc5026a536febac3cb5774febecd6fde81311142f0d682749f6f--Jinja2-2.10.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/ac/7e/1b4c2e05809a4414ebce0892fe1e32c14ace86ca7d50c70f00979ca9b3a3/MarkupSafe-1.1.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/311d62bdf4f4a176670774758a0cb966479df4f7b18140e5b8ef83559b992c3f--MarkupSafe-1.1.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/95/a8/b4706a6270f0475541c5c1ee3373c7a3b793936ec1f517f1a1dab4f896c0/numpydoc-0.8.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/1ff11690c8e114e67b3981f111c07581270502fcb5ff52097d922b7cbe5f491e--numpydoc-0.8.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/16/51/d72654dbbaa4a4ffbf7cb0ecd7d12222979e0a660bf3f42acc47550bf098/packaging-19.0.tar.gz
######################################################################## 100.0%
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/64/69/413708eaf3a64a6abb8972644e0f20891a55e621c6759e2c3f3891e05d63/Pygments-2.3.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/44ce5a95408411fc473666c85026facdc752eeecccdfe2dd80c3d3a044df4f17--Pygments-2.3.1.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/b9/b8/6b32b3e84014148dcd60dd05795e35c2e7f4b72f918616c61fdce83d27fc/pyparsing-2.3.1.tar.gz
######################################################################## 100.0%
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/77/f9/8c63766fe271549db3a578b652dea6678b90b593300315507b9c922f7173/python-docs-theme-2018.7.ta
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/a0acdee5785d44da7e1d40bab52eb0499aa126b0383fc2bc0383ffde9a951664--python-docs-theme-2018.7.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/af/be/6c59e30e208a5f28da85751b93ec7b97e4612268bb054d0dff396e758a90/pytz-2018.9.tar.gz
######################################################################## 100.0%
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/52/2c/514e4ac25da2b08ca5a464c50463682126385c4272c18193876e91f4bc38/requests-2.21.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/2e72e9245cb0b6828e4efd59b77aed0867131eb09b69434cb0c2cf58155dd612--requests-2.21.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/dd/bf/4138e7bfb757de47d1f4b6994648ec67a51efe58fa907c1e11e350cddfca/six-1.12.0.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/67394630b155f56230b742a843fa06c075326535c4341969d7a513d591ddbe2b--six-1.12.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/20/6b/d2a7cb176d4d664d94a6debf52cd8dbae1f7203c8e42426daa077051d59c/snowballstemmer-1.2.1.tar.g
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/dd968e2929df3be2459ad1e62b881a9752fab4541e62711318eafc7892756d5a--snowballstemmer-1.2.1.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/07/7a/e74b06dce85555ffee33e1d6b7381314169ebf7e31b62c18fcb2815626b7/sphinxcontrib-websupport-1.
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/31541de88dd8a859543b479e8baec83c1fc7a905d3b319017c894acfc7da60c6--sphinxcontrib-websupport-1.1.0.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/bf/9b/2bf84e841575b633d8d91ad923e198a415e3901f228715524689495b4317/typing-3.6.6.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/3f3cc6492e2dbcf8a0fb5ea5ac1637e17f0afb3483a5b8309638286f3a638974--typing-3.6.6.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Downloading https://files.pythonhosted.org/packages/b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1/urllib3-1.24.1.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/173fa09533cdd3445d6b72b7ed12c9400b4d171d947fac860c7140fb9b247152--urllib3-1.24.1.tar.gz
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /vols/build/snemo/tmp/sph
==> Caveats
sphinx-doc is keg-only, which means it was not symlinked into /vols/build/snemo/brew,
because this formula is mainly used internally by other formulae.
Users are advised to use `pip` to install sphinx-doc.

If you need to have sphinx-doc first in your PATH run:
  echo 'export PATH="/vols/build/snemo/brew/opt/sphinx-doc/bin:$PATH"' >> ~/.bash_profile

==> Summary
🍺  /vols/build/snemo/brew/Cellar/sphinx-doc/1.8.4: 4,288 files, 63.6MB, built in 8 minutes 29 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: cmake
==> Downloading https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/ad50fa5d55785a2649cbffe335acd739009962224f435b9bb4e09d9f35416a97--cmake-3.13.4.tar.gz
==> ./bootstrap --prefix=/vols/build/snemo/brew/Cellar/cmake/3.13.4 --no-system-libs --parallel=40 --datadir=/share/cmake --docdir=/share/doc/cmake --
==> make
==> make install
==> Caveats
Emacs Lisp files have been installed to:
  /vols/build/snemo/brew/share/emacs/site-lisp/cmake
==> Summary
🍺  /vols/build/snemo/brew/Cellar/cmake/3.13.4: 5,544 files, 55.7MB, built in 17 minutes 52 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: bison
==> Downloading https://ftp.gnu.org/gnu/bison/bison-3.3.2.tar.xz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/0583d005562aa50924abf4b2faab1071160df96898fd8a6a41f7080e57bc10cf--bison-3.3.2.tar.xz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/bison/3.3.2
==> make install
🍺  /vols/build/snemo/brew/Cellar/bison/3.3.2: 145 files, 3.2MB, built in 2 minutes 10 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: help2man
==> Downloading https://ftp.gnu.org/gnu/help2man/help2man-1.47.8.tar.xz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b559f106ee2aa595b9b463fdab9cbd4265ea38b8a080ac80fcba19f102fc51f3--help2man-1.47.8.tar.xz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/help2man/1.47.8
==> make install
🍺  /vols/build/snemo/brew/Cellar/help2man/1.47.8: 9 files, 115.9KB, built in 11 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: gettext
==> Downloading https://ftp.gnu.org/gnu/gettext/gettext-0.19.8.1.tar.xz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/9d18bbc4036e7ebcce01a57f3b21c17bd5e67618e25231698c8e8ec9ead922f9--gettext-0.19.8.1.tar.xz
==> Downloading http://xmlsoft.org/sources/libxml2-2.9.7.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/32f8e17935c44a004fe0c1db6777e3e0829abd419eebe79e1b06b6c158690015--libxml2-2.9.7.tar.gz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/gettext/0.19.8.1_1/libexec --without-python --without-lzma
==> make install
==> ./configure --disable-silent-rules --prefix=/vols/build/snemo/brew/Cellar/gettext/0.19.8.1_1  --with-included-glib --with-included-libcroco --with
==> make
==> make install
==> Caveats
Emacs Lisp files have been installed to:
  /vols/build/snemo/brew/share/emacs/site-lisp/gettext
==> Summary
🍺  /vols/build/snemo/brew/Cellar/gettext/0.19.8.1_1: 2,204 files, 27.8MB, built in 13 minutes 31 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: flex
==> Downloading https://github.com/westes/flex/releases/download/v2.6.4/flex-2.6.4.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/4c923b0def66967b27bb97fc512c040d33b8c116a7a7bf01ffc4170e2a7aef41--flex-2.6.4.tar.gz
==> ./configure --disable-silent-rules --enable-shared --prefix=/vols/build/snemo/brew/Cellar/flex/2.6.4
==> make install
🍺  /vols/build/snemo/brew/Cellar/flex/2.6.4: 47 files, 1.5MB, built in 48 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: doxygen
==> Downloading http://doxygen.nl/files/doxygen-1.8.15.src.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/26299af90764399a4f41a4cd011a73b668c27ef31c7c070f4d3bd65a1869080a--doxygen-1.8.15.src.tar.gz
==> Downloading https://github.com/doxygen/doxygen/commit/889eab308b564c4deba4ef58a3f134a309e3e9d1.diff?full_index=1
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/15e26635c2afad4b2715d684f536dfb9e6f3f3bd1088229669894f7852a47e0f--889eab308b564c4deba4ef58a3f134a309e3e9d1.diff
==> Patching
==> Applying 889eab308b564c4deba4ef58a3f134a309e3e9d1.diff
patching file src/config.xml
==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/vols/build/snemo/brew/Cellar/doxygen/1.8.15 -
==> make
🍺  /vols/build/snemo/brew/Cellar/doxygen/1.8.15: 9 files, 15.3MB, built in 1 minute 30 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: icu4c
==> Downloading https://ssl.icu-project.org/files/icu4c/63.1/icu4c-63_1-src.tgz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/ec2c7ac7e6eac337ad9faa0cbb84d28a36d54132b3c810cc248d304a05e15bbd--icu4c-63_1-src.tgz
==> ./configure --prefix=/vols/build/snemo/brew/Cellar/icu4c/63.1 --disable-samples --disable-tests --enable-static
==> make
==> make install
🍺  /vols/build/snemo/brew/Cellar/icu4c/63.1: 254 files, 72.8MB, built in 3 minutes 50 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: supernemo-dbd/cadfael/boost
==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.63.0/boost_1_63_0.tar.bz2
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/1e246222098679c68a93d0676bd5bf12c7aeeca738a1a336582b6c84c2a05f86--boost_1_63_0.tar.bz2
==> ./bootstrap.sh --prefix=/vols/build/snemo/brew/Cellar/boost/1.63.0_5 --libdir=/vols/build/snemo/brew/Cellar/boost/1.63.0_5/lib --with-icu=/vols/bu
==> ./b2 headers
==> ./b2 --prefix=/vols/build/snemo/brew/Cellar/boost/1.63.0_5 --libdir=/vols/build/snemo/brew/Cellar/boost/1.63.0_5/lib -d2 -j40 --layout=tagged --us
🍺  /vols/build/snemo/brew/Cellar/boost/1.63.0_5: 12,443 files, 123.7MB, built in 37 minutes 28 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: supernemo-dbd/cadfael/camp
==> Cloning https://github.com/drbenmorgan/camp.git
Updating /home/hep/pfranchi/.cache/Homebrew/camp--git
==> Checking out revision 7564e57f7b406d1021290cf2260334d57d8df255
HEAD is now at 7564e57... Merge pull request #2 from drbenmorgan/cmake-support
HEAD is now at 7564e57 Merge pull request #2 from drbenmorgan/cmake-support
==> cmake . -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/vols/build/snemo/brew/Cellar/camp/0.8.0_1 -DCM
==> make
==> make install
🍺  /vols/build/snemo/brew/Cellar/camp/0.8.0_1: 111 files, 954.4KB, built in 52 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: supernemo-dbd/cadfael/clhep
==> Downloading http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/clhep-2.1.3.1.tgz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/b080c4ff200ce3bd49fa34566442684463fc071c5d0614dbb0e8c8300bc59465--clhep-2.1.3.1.tgz
==> Patching
patching file CLHEP/Matrix/src/Vector.cc
==> cmake ../CLHEP -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/vols/build/snemo/brew/Cellar/clhep/2.1.
==> make install
🍺  /vols/build/snemo/brew/Cellar/clhep/2.1.3.1_1: 331 files, 11.3MB, built in 2 minutes 4 seconds
==> Installing supernemo-dbd/cadfael/falaise dependency: libbsd
==> Downloading https://libbsd.freedesktop.org/releases/libbsd-0.8.3.tar.xz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/7ff840e9065dd98eb6495e7eecaa7fb03fb2cfb00ccf47aca1d1a88107f9da13--libbsd-0.8.3.tar.xz
==> ./configure --disable-silent-rules --prefix=/vols/build/snemo/brew/Cellar/libbsd/0.8.3
==> make install
🍺  /vols/build/snemo/brew/Cellar/libbsd/0.8.3: 83 files, 725.0KB, built in 39 seconds
Error: expat is already installed from supernemo-dbd/cadfael!
Please `brew uninstall expat` first."

drbenmorgan · 2019-02-12T14:22:33Z

Bear with me, sort of able to reproduce this on CentOS7, so I'll need to fix those issues and push the changes to #71. Will also need that merged to guarantee everything working...

pfranchini · 2019-02-25T10:32:55Z

Hi Ben, any news on that? cheers, Paolo

…

On 12/02/2019 14:22, Ben Morgan wrote: Bear with me, sort of able to reproduce this on CentOS7, so I'll need to fix those issues and push the changes to #71 <SuperNEMO-DBD/homebrew-cadfael#71>. Will also need that merged to guarantee everything working... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/SuperNEMO-DBD/homebrew-cadfael/issues/69#issuecomment-462777824>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AinxTAM9N5fi7ToeQrh2gcFw7kSLAsu1ks5vMs4pgaJpZM4aF2xw>.

drbenmorgan · 2019-02-27T16:17:01Z

Hi @pfranchini, could you please delete any existing brew setup you have and attempt a fresh installation following the instructions in the README for a Native install please? Basically, these two sections:

It should work on CentOS7, CentOS6 may still have issues, but let's see what happens by following the above first before attempting any fixes.

pfranchini · 2019-02-27T16:38:54Z

Hi Ben. Will do, both on CentOS6 and 7. I do not really need to stay on CentOS6 so will be my last attempt before moving to 7.

Thanks.

pfranchini · 2019-03-01T12:51:35Z

Since Singularity is not installed on our CentOS6 machines, I moved to CentOS7.
I have got this error:

[pfranchi@lx02 snemo]$ brew snemo-bootstrap
[...]
==> Installing dependencies for falaise: root6 and bayeux
==> Installing falaise dependency: root6
==> Downloading https://root.cern.ch/download/root_v6.16.00.source.tar.gz
Already downloaded: /home/hep/pfranchi/.cache/Homebrew/downloads/23d7322cce57f6f5f7aedf40598eccc32ad6f024620307f869f9bfe2a4d69365--root_v6.16.00.source.tar.gz
==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/vols/build/snemo/snemo-sdk/Cellar/root6/6.16.
==> make install
Last 15 lines from /home/hep/pfranchi/.cache/Homebrew/Logs/root6/02.make:
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/usr/bin/ranlib ../libLLVMCodeGen.a
make[2]: Leaving directory `/vols/build/snemo/tmp/root6-20190301-38534-1kr2owx/root-6.16.00/cmake-build'
[ 71%] Built target LLVMCodeGen
make[1]: Leaving directory `/vols/build/snemo/tmp/root6-20190301-38534-1kr2owx/root-6.16.00/cmake-build'
make: *** [all] Error 2

READ THIS: https://github.com/SuperNEMO-DBD/brew/issues
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."

Installing falaise has failed!
Homebrew Bundle failed! 1 Brewfile dependency failed to install.

drbenmorgan · 2019-03-01T13:28:25Z

O.k., could you run and post the output of:

brew snemo-doctor
brew config

and also run brew gist-logs root6 and post the link here please?

pfranchini · 2019-03-01T13:34:32Z

[pfranchi@lx02 snemo]$ brew snemo-doctor
Please note that these warnings are just used to help the SuperNEMO maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: An outdated version (1.8.3.1) of Git was detected in your PATH.
Git 2.7.0 or newer is required for Homebrew.
Please upgrade:
  brew install git

Warning: Your Homebrew's prefix is not /home/linuxbrew/.linuxbrew.
Some of Homebrew's bottles (binary packages) can only be used with the default
prefix (/home/linuxbrew/.linuxbrew).
You may encounter build failures with some formulae as
brew is being run in an unsupported configuration
In these cases, please raise an issue at https://github.com/SuperNEMO-DBD/homebrew-core/issues


Warning: Your Linux system is missing several system packages required 
to bootstrap or install SuperNEMO software. You, or a user with sufficient 
adminstrator privileges, will need to run:

  yum install

to install them.

[pfranchi@lx02 snemo]$ brew config
HOMEBREW_VERSION: >=1.7.1 (shallow or no git repository)
ORIGIN: https://github.com/SuperNEMO-DBD/brew.git
HEAD: d7267eba56e7ed12f7de0baab6dad761e98a8def
Last commit: 2 days ago
Core tap ORIGIN: https://github.com/supernemo-dbd/homebrew-core
Core tap HEAD: 15b2f6fc8fdc24fdb353ad770297a4bbea60fe71
Core tap last commit: 2 days ago
HOMEBREW_PREFIX: /vols/build/snemo/snemo-sdk
HOMEBREW_REPOSITORY: /vols/build/snemo/snemo-sdk
HOMEBREW_CELLAR: /vols/build/snemo/snemo-sdk/Cellar
HOMEBREW_CACHE: /home/hep/pfranchi/.cache/Homebrew
HOMEBREW_TEMP: /vols/build/snemo/tmp
HOMEBREW_BUILD_FROM_SOURCE: 1
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_LOGS: /home/hep/pfranchi/.cache/Homebrew/Logs
HOMEBREW_NO_ANALYTICS: 1
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_SYSTEM_CURL_TOO_OLD: 1
CPU: 32-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /vols/build/snemo/snemo-sdk/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: N/A
Git: 1.8.3.1 => /bin/git
Curl: 7.64.0 => /vols/build/snemo/snemo-sdk/opt/curl/bin/curl
Kernel: Linux 3.10.0-862.14.4.el7.x86_64 x86_64 GNU/Linux
OS: CentOS Linux release 7.6.1810 (Core)  (Core)
Host glibc: 2.17
/usr/bin/gcc: 4.8.5
glibc: N/A
gcc: N/A
xorg: N/A

[pfranchi@lx02 snemo]$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)
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.

drbenmorgan · 2019-03-01T13:51:07Z

... and the gist logs for root6 as well please!

pfranchini · 2019-03-01T14:04:58Z

02_make.log

drbenmorgan · 2019-03-01T14:24:14Z

Thanks! Two possibilities:

How much RAM does this system have? There are a lot of cores!
More likely is the unknown symbol. I'll try and reproduce on a Skylake system. May need a binutils bump, but let me try first as I have seen other issues with doing this.

pfranchini · 2019-03-01T14:32:06Z

There are 10Gb free at the moment. I might even try to wipe and retry.
126G in total and 8(?) used

drbenmorgan · 2019-03-01T14:42:09Z

O.k., so about 4GB per core, which should be fine unless anything is hogging this system whilst you were doing the build. It might be worth trying again and setting the HOMEBREW_MAKE_JOBS environment variable to something lower, for example

$ export HOMEBREW_MAKE_JOBS=8
$ brew snemo-bootstrap

It'll be a little slow to compile ROOT, but could help check for any issues due to RAM etc...

drbenmorgan · 2019-03-01T16:07:14Z

Hi @pfranchini, I've tested on the following system:

$ brew doctor
HOMEBREW_VERSION: >=1.7.1 (shallow or no git repository)
ORIGIN: https://github.com/supernemo-dbd/brew
HEAD: 35b2daf735f29764f612b99f07c3afb72ce0ad4f
Last commit: 3 hours ago
Core tap ORIGIN: https://github.com/supernemo-dbd/homebrew-core
Core tap HEAD: 15b2f6fc8fdc24fdb353ad770297a4bbea60fe71
Core tap last commit: 2 days ago
HOMEBREW_PREFIX: /tmp/brew
HOMEBREW_REPOSITORY: /tmp/brew
HOMEBREW_CELLAR: /tmp/brew/Cellar
HOMEBREW_CACHE: /home/physics/phsdbc/.cache/Homebrew
HOMEBREW_BUILD_FROM_SOURCE: 1
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_LOGS: /home/physics/phsdbc/.cache/Homebrew/Logs
HOMEBREW_NO_ANALYTICS: 1
HOMEBREW_NO_AUTO_UPDATE: 1
HOMEBREW_SYSTEM_CURL_TOO_OLD: 1
CPU: octa-core 64-bit skylake
Homebrew Ruby: 2.3.7 => /tmp/brew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: N/A
Git: 1.8.3.1 => /bin/git
Curl: 7.64.0 => /tmp/brew/opt/curl/bin/curl
Kernel: Linux 3.10.0-957.5.1.el7.x86_64 x86_64 GNU/Linux
OS: CentOS Linux release 7.6.1810 (Core)  (Core)
Host glibc: 2.17
/usr/bin/gcc: 4.8.5
glibc: N/A
gcc: N/A
xorg: N/A

Everything installed fine, so I'd suspect that your build went over some resource limit for gcc, so please try the suggestion above on limiting the number of make jobs. Let's see what happens with that, and I think 8 should be enough for a reasonable build time with enough resource.

pfranchini · 2019-03-01T16:30:21Z

Great! I have got at the end of the Falaise installation, thanks for that.
I can run Falaise simulation, reconstruction and visualisation commands so everything seems to be fine.

drbenmorgan · 2019-03-01T16:42:37Z

👍 ! I'll leave the issue open for now just in case anything else pops up in the near term, so please close once you're happy with things!

pfranchini · 2019-03-01T16:47:17Z

Thanks for your help.
A question: what would be the advantage of using an image instead of the standalone installation?

drbenmorgan self-assigned this Jan 17, 2019

drbenmorgan transferred this issue from SuperNEMO-DBD/homebrew-cadfael Feb 27, 2019

drbenmorgan added bug Something isn't working CentOS CentOS 6 or 7 system Formula Relating to Formulae labels Mar 1, 2019

Document HOMEBREW_ARCH issues #1

Document HOMEBREW_ARCH issues #1

Comments

drbenmorgan commented Jan 17, 2019

Bug reports:

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