Malloc error brings down site

espenmn · August 23, 2017, 1:07pm

After upgrading one of my Macs, I can not get Plone to run anymore, it always gives me similar errors:

2017-08-23 14:58:34 INFO Zope Ready to handle requests
python(59487,0x70000089a000) malloc: *** error for object 0x7f9475b94920: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug

I have added new users and installed 'in their account',
installed with --build-python (with Universal Installer).

It happens on new sites, without any add-ons installed

Any suggestion ?

hvelarde · August 23, 2017, 1:36pm

please include the versions of your OS system and Python used.

espenmn · August 23, 2017, 2:59pm

OS X 10.11.6
The python was the default, Python 2.7.10
The "Universal installed Python" seems to be: Python 2.7.12

Since it happens to both, I suspect it has something to do with site-packages (or libs ?), I will take a backup and compare them to 'time-machine versions'

dieter · August 23, 2017, 4:22pm

The error tells you that a problem has been detected in the memory management: a released memory block seems to have been overridden. Usually, Python applications (and especially Plone) do not show this kind of problem - unless you are using a buggy external C component.

If you have nothing else changed in your environment (e.g. introduced an additional C extension), this looks like a problem introduced by your (hardware?) upgrade of the Mac -- maybe a bug in the memory modules of your computer. If possible, make a memory check of your computer.

espenmn · August 23, 2017, 4:32pm

I replaced my
/Lib/Python/2.7/site-packages/

with an earlier version and things seems to work now

vedantc98 · March 10, 2018, 4:59am

I'm still getting this error inspite of using a conda virtual environment and switching to a different version of python.
I've also tried migrating macports to my latest OS version, but it doesn't help.
Any idea what I can do?

dieter · March 10, 2018, 6:54am

In order to help, we need precise error information. Do you really get the same error message, i.e. malloc: *** error for object...?

In comment 5, Espen reported that replacing Python's site-packages (that's where Python extensions reside by default) resolved the problem for him -- an indication that his problem was caused by a buggy extension inplemented in C. Have you already tried something similar?

The error mentioned in this discussion indicates a problem related to memory management. There are various potential causes for such a problem and typically, they are non local:

a buggy C extension
hardware problems (quite rare)
a Python bug (very rare)

Problems of this kind are very difficult to analyse. Usually, you make a rough hypothesis (such as Espen hypothesized in comment 5 that some C extension was at fault) and check it (Espen replaced the Python extensions by something older).

You might also try to hire a debugging expert in your neighbourhood to pin down the real problem -- but likely, such an approach could be quite expensive.

gp54321 · March 10, 2018, 7:55am

I remember having seen on this forum one person having problems after upgrading Ubuntu version; problem was that system Python version was upgraded and Plone was using the Python installed with the original Ubuntu version (copied in the Plone directory) AND parts of the system Python library; after upgrade Plone was using a mix of new and old Python to great effect. The isolation from system Python done with Plone install is not perfect, it concerns only the add-ons and the Python libraries installed by Plone, not the Python system libraries. When Python itself is upgraded, things break.

zopyx · March 10, 2018, 8:03am

First ensure that your OS is up-to-date. MacOSX 10.11 is obviously outdated.

tkimnguyen · March 10, 2018, 1:52pm

I'm leery of anything but bugfix OS updates; they seem to require a full rebuilding of Plone, since the compiler and libraries will have changed. For that reason when I do substantial OS upgrades I do them on a new (virtual) machine first.

zopyx · March 10, 2018, 2:09pm

You can upgrade one box at a time when you are running a cluster.
Most hosters provide a snapshot functionalty for easily rolling back.

vedantc98 · March 11, 2018, 4:49am

I'm running MacOS 10.13, so I don't think the OS version is the issue.
Should I try rebuilding Plone within a virtualenv to make sure that all the packages are on the same version?

tkimnguyen · March 11, 2018, 2:45pm

Can you provide more details, like which version of Plone and which installer you're trying to use? Not familiar with conda...

vedantc98 · March 11, 2018, 3:53pm

I'm using Plone 5.1 with the unified installer..MacOS 10.13

gp54321 · March 11, 2018, 4:08pm

conda is an alternative to pip. It brings also the capability to package stuff completely unrelated to Python. It is widely used for scientific applications. Since it uses its own Python and Plone unified installer uses its own Python, I don't quite see how both software will play well together unless someone develops a Plone conda installer (please not yet another 'Gsoc project')
I don't remember if conda can do system-wide install but it's clearly not its primary aim and it seems just such a dumb idea anyway.

tkimnguyen · March 11, 2018, 4:52pm

The unified installer installs its own Python so condo shouldn't be a factor

tkimnguyen · March 11, 2018, 4:54pm

I'll give it a shot. I have macOS 10.13.3 but should be close enough.

This is the command that is executing for me now:

install.sh standalone \ --target="/Users/kim/PloneBuilds/Plone-5.1-unified" --password="*****..."

Testing /usr/bin/python2.7 for Zope/Plone requirements....
/usr/bin/python2.7 looks OK. We will use it.



Plone installation requires the development versions of libxml2 and libxslt.
libxml2 must be version 2.7.8 or greater\; libxslt must be 1.1.26 or greater.
Ideally, you should install these as dev package libraries before running install.sh.
If -- and only if -- these packages are not available for your platform, you may
try adding --static-lxml=yes to your install.sh command line to force a
local, static build of these libraries. This will require Internet access for the
installer to download the extra source.
Installation aborted.

./install.sh standalone --target="/Users/kim/PloneBuilds/Plone-5.1-unified" --password="admin" --static-lxml=yes

Testing /usr/bin/python2.7 for Zope/Plone requirements....
/usr/bin/python2.7 looks OK. We will use it.

Rootless install method chosen. Will install for use by system user kim


Detailed installation log being written to /Users/kim/Downloads/Plone-5.1.0-UnifiedInstaller-r1/install.log
Installing Plone 5.1.0 at /Users/kim/PloneBuilds/Plone-5.1-unified

Creating Python virtual environment.
New python executable in /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/bin/python
Installing setuptools, pip, wheel...done.
Installing zc.buildout in virtual environment.
Unpacking buildout cache to /Users/kim/PloneBuilds/Plone-5.1-unified/buildout-cache
Copying buildout skeleton
Building lxml with static libxml2/libxslt; this requires Internet access,
and takes a while...
Failed to build working lxml.
lxml built with no errors, but does not have a working etree component.
See log file for details.

Try preinstalling up-to-date libxml2/libxslt development libraries, then run
the installer again.
Buildout returned an error code: 1; Aborting.
Buildout failed. Unable to continue

Installation has failed.
See the detailed installation log at /Users/kim/Downloads/Plone-5.1.0-UnifiedInstaller-r1/install.log
to determine the cause.

brew install libxml2

...same buildout error

brew install libxlst

...same buildout error

When I look at the install.log:

 ./install-sh -c -d '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/bin'
 /usr/bin/install -c xslt-config '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/bin'
 ./install-sh -c -d '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib'
 /usr/bin/install -c -m 644 xsltConf.sh '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib'
 ./install-sh -c -d '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/share/aclocal'
 /usr/bin/install -c -m 644 libxslt.m4 '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/share/aclocal'
 ./install-sh -c -d '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/pkgconfig'
 /usr/bin/install -c -m 644 libxslt.pc libexslt.pc '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/pkgconfig'
lxml: Using xslt-config found in /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/bin/xslt-config.
lxml: Using xml2-config found in /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/bin/xml2-config.
lxml: Removing dynamic libs from path /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt ...
lxml: Removing dynamic libs from path /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2 ...
lxml: Adding ``iconv`` to libs due to a lxml setup bug.
lxml: OS X detected.
lxml: Static build -- adding '-Wl,-search_paths_first'
lxml: Building lxml ...
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'
  warnings.warn(msg)
ld: warning: ld: warning: ld: warning: ignoring file /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libexslt.a, file was built for archive which is not the architecture being linked (i386): /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libexslt.aignoring file /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib/libxml2.a, file was built for archive which is not the architecture being linked (i386): /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib/libxml2.aignoring file /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libxslt.a, file was built for archive which is not the architecture being linked (i386): /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libxslt.a


ld: warning: ignoring file /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libxslt.a, file was built for archive which is not the architecture being linked (i386): /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libxslt.a
ld: warning: ignoring file /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libexslt.a, file was built for archive which is not the architecture being linked (i386): /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib/libexslt.a
ld: warning: ignoring file /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib/libxml2.a, file was built for archive which is not the architecture being linked (i386): /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib/libxml2.a
Building lxml version 3.4.4.
Building without Cython.
Using build configuration of libxslt 1.1.29
Building against libxml2/libxslt in one of the following directories:
  /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxslt/lib
  /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib
  /usr/local/Cellar/xz/5.2.3/lib
Installing lxmlpy.
Generated interpreter '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/bin/lxmlpy'.
Traceback (most recent call last):
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/bin/lxmlpy", line 18, in <module>
    exec(_val)
  File "<string>", line 1, in <module>
ImportError: dlopen(/Users/kim/PloneBuilds/Plone-5.1-unified/buildout-cache/eggs/lxml-3.4.4-py2.7-macosx-10.13-intel.egg/lxml/etree.so, 2): Symbol not found: _lzma_auto_decoder
  Referenced from: /Users/kim/PloneBuilds/Plone-5.1-unified/buildout-cache/eggs/lxml-3.4.4-py2.7-macosx-10.13-intel.egg/lxml/etree.so
  Expected in: flat namespace
 in /Users/kim/PloneBuilds/Plone-5.1-unified/buildout-cache/eggs/lxml-3.4.4-py2.7-macosx-10.13-intel.egg/lxml/etree.so

I then tried

STATIC_DEPS=true ./install.sh standalone --target="/Users/kim/PloneBuilds/Plone-5.1-unified" --password="admin" --static-lxml=yes

but ran into other errors like

/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in libxslt
  CC       attrvt.lo
  CC       xslt.lo
  CC       xsltlocale.lo
  CC       xsltutils.lo
  CC       pattern.lo
pattern.c:2592:7: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
                    xsltFreeCompMatchListEntry);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
  CC       templates.lo
  CC       variables.lo
variables.c:1345:35: warning: incompatible pointer types passing 'void (void *, void *, const xmlChar *)' (aka 'void (void *, void *, const unsigned char *)') to parameter of type 'xmlHashScanner' (aka 'void (*)(void *, void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashScan(ctxt->globalVars, xsltEvalGlobalVariableWrapper, ctxt);
                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:210:22: note: passing argument to parameter 'f' here
                                         xmlHashScanner f,
                                                        ^
variables.c:2249:35: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(ctxt->globalVars, xsltFreeStackElemEntry);
                                  ^~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
  CC       keys.lo
  CC       numbers.lo
2 warnings generated.
  CC       extensions.lo
keys.c:167:26: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
        xmlHashFree(keyt->keys, xsltFreeNodeSetEntry);
                                ^~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
1 warning generated.
  CC       extra.lo
extensions.c:1050:42: warning: incompatible pointer types passing 'void (void *, void *, const xmlChar *)' (aka 'void (void *, void *, const unsigned char *)') to parameter of type 'xmlHashScanner' (aka 'void (*)(void *, void *, unsigned char *)') [-Wincompatible-pointer-types]
            xmlHashScan(style->extInfos, xsltInitCtxtExt, &ctx);
                                         ^~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:210:22: note: passing argument to parameter 'f' here
                                         xmlHashScanner f,
                                                        ^
extensions.c:1104:33: warning: incompatible pointer types passing 'void (void *, void *, const xmlChar *)' (aka 'void (void *, void *, const unsigned char *)') to parameter of type 'xmlHashScanner' (aka 'void (*)(void *, void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashScan(ctxt->extInfos, xsltShutdownCtxtExt, ctxt);
                                ^~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:210:22: note: passing argument to parameter 'f' here
                                         xmlHashScanner f,
                                                        ^
extensions.c:1105:33: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(ctxt->extInfos, xsltFreeExtDataEntry);
                                ^~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
extensions.c:1156:34: warning: incompatible pointer types passing 'void (void *, void *, const xmlChar *)' (aka 'void (void *, void *, const unsigned char *)') to parameter of type 'xmlHashScanner' (aka 'void (*)(void *, void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashScan(style->extInfos, xsltShutdownExt, style);
                                 ^~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:210:22: note: passing argument to parameter 'f' here
                                         xmlHashScanner f,
                                                        ^
extensions.c:1157:34: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(style->extInfos, xsltFreeExtDataEntry);
                                 ^~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
extensions.c:1345:55: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    ret = xmlHashRemoveEntry(xsltExtensionsHash, URI, xsltFreeExtModuleEntry);
                                                      ^~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:157:47: note: passing argument to parameter 'f' here
                           xmlHashDeallocator f);
                                              ^
extensions.c:1365:37: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(xsltExtensionsHash, xsltFreeExtModuleEntry);
                                    ^~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
extensions.c:1665:25: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
                        xsltFreeExtElementEntry);
                        ^~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:137:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
extensions.c:1808:31: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
                              xsltFreeExtElementEntry);
                              ^~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:160:70: note: passing argument to parameter 'f' here
                            const xmlChar *name2, xmlHashDeallocator f);
                                                                     ^
extensions.c:1825:35: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(xsltElementsHash, xsltFreeExtElementEntry);
                                  ^~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
extensions.c:2303:37: warning: incompatible pointer types passing 'void (void *, void *, const xmlChar *)' (aka 'void (void *, void *, const unsigned char *)') to parameter of type 'xmlHashScanner' (aka 'void (*)(void *, void *, unsigned char *)') [-Wincompatible-pointer-types]
        xmlHashScan(xsltModuleHash, xsltHashScannerModuleFree, 0);
                                    ^~~~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:210:22: note: passing argument to parameter 'f' here
                                         xmlHashScanner f,
                                                        ^
1 warning generated.
  CC       functions.lo
  CC       namespaces.lo
11 warnings generated.
  CC       imports.lo
  CC       attributes.lo
  CC       documents.lo
  CC       preproc.lo
  CC       transform.lo
imports.c:68:39: warning: incompatible pointer types passing 'void (void *, void *, const xmlChar *)' (aka 'void (void *, void *, const unsigned char *)') to parameter of type 'xmlHashScanner' (aka 'void (*)(void *, void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashScan(style->templatesHash, xsltNormalizeCompSteps, master);
                                      ^~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:210:22: note: passing argument to parameter 'f' here
                                         xmlHashScanner f,
                                                        ^
attributes.c:1246:7: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
                    xsltFreeAttributeSetsEntry);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
1 warning generated.
  CC       security.lo
1 warning generated.
  CCLD     libxslt.la
Making all in libexslt
  CC       exslt.lo
  CC       common.lo
  CC       crypto.lo
  CC       math.lo
  CC       sets.lo
  CC       functions.lo
  CC       strings.lo
  CC       date.lo
  CC       saxon.lo
functions.c:233:23: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(data, exsltFuncFreeDataEntry);
                      ^~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
1 warning generated.
  CC       dynamic.lo
saxon.c:57:23: warning: incompatible pointer types passing 'void (void *, const xmlChar *)' (aka 'void (void *, const unsigned char *)') to parameter of type 'xmlHashDeallocator' (aka 'void (*)(void *, unsigned char *)') [-Wincompatible-pointer-types]
    xmlHashFree(data, exsltSaxonFreeCompExprEntry);
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/include/libxml2/libxml/hash.h:113:26: note: passing argument to parameter 'f' here
                                         xmlHashDeallocator f);
                                                            ^
1 warning generated.
  CCLD     libexslt.la
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libexslt.a(crypto.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libexslt.a(crypto.o) has no symbols
Making all in xsltproc
  CC       xsltproc.o
  CC       testThreads.o
  CCLD     testThreads
  CCLD     xsltproc
clang: error: no such file or directory: '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib/libxml2.dylib'
make[2]: *** [testThreads] Error 1
make[2]: *** Waiting for unfinished jobs....
clang: error: no such file or directory: '/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/parts/lxml/libxml2/lib/libxml2.dylib'
make[2]: *** [xsltproc] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Building lxml version 3.4.4.
Latest version of libiconv is 1.15
Downloading libiconv into libs/libiconv-1.15.tar.gz
Unpacking libiconv-1.15.tar.gz into build/tmp
Latest version of libxml2 is 2.9.8
Downloading libxml2 into libs/libxml2-2.9.8.tar.gz
Unpacking libxml2-2.9.8.tar.gz into build/tmp
Latest version of libxslt is 1.1.33-rc1
Downloading libxslt into libs/libxslt-1.1.33-rc1.tar.gz
Unpacking libxslt-1.1.33-rc1.tar.gz into build/tmp
Starting build in build/tmp/libiconv-1.15
Starting build in build/tmp/libxml2-2.9.8
Starting build in build/tmp/libxslt-1.1.33
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 2312, in main
    **kw
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/__init__.py", line 129, in setup
    return distutils.core.setup(**attrs)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 412, in run
    self.easy_install(spec, not self.no_deps)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 654, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 699, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 884, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1152, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1138, in run_setup
    run_setup(setup_script, args)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
    raise
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
    _execfile(setup_script, ns)
  File "/Users/kim/PloneBuilds/Plone-5.1-unified/zinstance/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
    exec(code, globals, locals)
  File "/var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4/setup.py", line 230, in <module>
    **setup_extra_options()
  File "/var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4/setup.py", line 144, in setup_extra_options
    STATIC_CFLAGS, STATIC_BINARIES)
  File "/var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4/setupinfo.py", line 57, in ext_modules
    multicore=OPTION_MULTICORE)
  File "/var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4/buildlibxml.py", line 370, in build_libxml2xslt
    cmmi(libxslt_configure_cmd, libxslt_dir, multicore, **call_setup)
  File "/var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4/buildlibxml.py", line 285, in cmmi
    cwd=build_dir, **call_setup)
  File "/var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4/buildlibxml.py", line 268, in call_subprocess
    raise Exception('Command "%s" returned code %s' % (cmd_desc, returncode))
Exception: Command "make -j5" returned code 512
An error occurred when trying to install /var/folders/nz/x0t781tx0674r3h71hg19jk80000gn/T/tmpJWHHDQbuild/lxml-3.4.4. Look above this message for any errors that were output by easy_install.
While:
  Installing lxml.
Error: Couldn't install: lxml 3.4.4

I remembered how I've been getting around this problem...

cd /Users/kim/PloneBuilds/Plone-5.1-unified/zinstance
bin/pip install lxml
bin/buildout

got a bit farther...

svx · March 11, 2018, 5:16pm

AFAIK the Unified Installer does not use its own python per default.

The installer first checks if a 'valid python2.7' is already installed and if so per default it will use that one.
You can see that in the main install script.

Only if you run the installer with --build-python the UI will build and use its own python from the beginning.

Moving on to condor aka anaconda, I strongly advise against the use of that, use it only if you are well experienced with conda and Plone.

conda install its own versions of python, ssl, ssl python libs, readline, setuptools, etc, etc.

AFAIK we do not test the UI with/against conda.

I suggest to follow our docs to install Plone

gp54321 · March 11, 2018, 5:25pm

maybe but it does not matter as much as you think, since the system python is copied

gp@plonestd:~/Plone/zinstance/bin$ ls python* -lart
-rwxr-xr-x 1 gp gp 3546104 May 22  2017 python2.7
lrwxrwxrwx 1 gp gp       9 May 22  2017 python2 -> python2.7
lrwxrwxrwx 1 gp gp       9 May 22  2017 python -> python2.7
-rwxr-xr-x 1 gp gp    2342 May 22  2017 python-config
gp@plonestd:~/Plone/zinstance/bin$ whereis python
python: /usr/bin/python3.5 /usr/bin/python3.5m /usr/bin/python2.7 /usr/bin/python2.7-config /usr/bin/python /usr/lib/python3.5 /usr/lib/python2.7 /etc/python2.7 /etc/python /etc/python3.5 /usr/local/lib/python2.7 /usr/local/lib/python3.5 /usr/include/python2.7 /usr/share/python /usr/share/man/man1/python.1.gz
gp@plonestd:~/Plone/zinstance/bin$ ls -lart /usr/bin/python2.7
-rwxr-xr-x 1 root root 3492656 Dec  4 18:14 /usr/bin/python2.7
gp@plonestd:~/Plone/zinstance/bin

so if system python is upgraded, Plone python is not. As long as these system upgrades are backward compatible, all is well. However,

Python 2.7.12 (default, Nov 19 2016, 06:48:10) 
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/home/gp/Plone/zinstance/lib/python2.7', '/home/gp/Plone/zinstance/lib/python2.7/plat-x86_64-linux-gnu', '/home/gp/Plone/zinstance/lib/python2.7/lib-tk', '/home/gp/Plone/zinstance/lib/python2.7/lib-old', '/home/gp/Plone/zinstance/lib/python2.7/lib-dynload', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/home/gp/Plone/zinstance/local/lib/python2.7/site-packages', '/home/gp/Plone/zinstance/lib/python2.7/site-packages']

the Plone python depends on system libraries (/usr/lib above).