Build error with bzip2 download

[Ted Fujimoto]

Getting the following error using OS X 10.10:

$ make -j8

...

make base

/Users/tcf/Applications/sage/build/pipestatus "sage-spkg -f bzip2-1.0.6.20140317 2>&1" "tee -a /Users/tcf/Applications/sage/logs/pkgs/bzip2-1.0.6.20140317.log"

Found local metadata for bzip2-1.0.6.20140317

Attempting to download package bzip2-1.0.6.20140317

>>> Trying to download http://www.sagemath.org/packages/upstream/bzip2/bzip2-1.0.6.20140317.tar.gz

[Traceback (most recent call last):

  File "<stdin>", line 35, in <module>

  File "/Users/tcf/Applications/sage/local/lib/python/urllib.py", line 240, in retrieve

    fp = self.open(url, data)

  File "/Users/tcf/Applications/sage/local/lib/python/urllib.py", line 208, in open

    return getattr(self, name)(url)

  File "/Users/tcf/Applications/sage/local/lib/python/urllib.py", line 359, in open_http

    return self.http_error(url, fp, errcode, errmsg, headers)

  File "/Users/tcf/Applications/sage/local/lib/python/urllib.py", line 376, in http_error

    return self.http_error_default(url, fp, errcode, errmsg, headers)

  File "<stdin>", line 17, in http_error_default

IOError: [Errno 404] Not Found: '//www.sagemath.org/packages/upstream/bzip2/bzip2-1.0.6.20140317.tar.gz'

Error: failed to download package bzip2-1.0.6.20140317

make[2]: *** [/Users/tcf/Applications/sage/local/var/lib/sage/installed/bzip2-1.0.6.20140317] Error 1

make[1]: *** [all] Error 2

real 0m1.524s

user 0m0.415s

sys 0m0.255s

***************************************************************

Error building Sage.

The following package(s) may have failed to build:

package: bzip2-1.0.6.20140317

log file: /Users/tcf/Applications/sage/logs/pkgs/bzip2-1.0.6.20140317.log

build directory: /Users/tcf/Applications/sage/local/var/tmp/sage/build/bzip2-1.0.6.20140317

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [build] Error 1

[Volker Braun]

There were some changes to how we host the tarballs, get sage-6.7.rc0 instead (which you need anyways to work around bugs in the newest xcode)

[Ted Fujimoto]

Just tried it but now having trouble with NumPy. Is this normal if I already have NumPy installed (using Anaconda distribution)?:

make[1]: *** [all] Error 2

real 91m32.068s

user 259m40.279s

sys 33m41.236s

***************************************************************

Error building Sage.

The following package(s) may have failed to build:

package: numpy-1.8.1.p0

log file: /Users/tcf/Applications/sage-6.7.rc0/logs/pkgs/numpy-1.8.1.p0.log

build directory: /Users/tcf/Applications/sage-6.7.rc0/local/var/tmp/sage/build/numpy-1.8.1.p0

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [build] Error 1

[Dima Pasechnik]

On Saturday, 16 May 2015 02:06:32 UTC+1, Ted Fujimoto wrote:

Just tried it but now having trouble with NumPy. Is this normal if I already have NumPy installed (using Anaconda distribution)?:

The latter is probably OK.
Well, it's hard to say without seeing the log what exactly went wrong.
 

[Ted Fujimoto]

Hope this helps:

Writing /Users/tcf/Applications/sage-6.7.rc0/local/lib/python2.7/site-packages/numpy-1.8.1-py2.7.egg-info

running install_clib

copying build/temp.macosx-10.9-x86_64-2.7/libnpymath.a -> /Users/tcf/Applications/sage-6.7.rc0/local/lib/python2.7/site-packages/numpy/core/lib

Traceback (most recent call last):

  File "<stdin>", line 3, in <module>

  File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 170, in <module>

    from . import add_newdocs

  File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>

    from numpy.lib import add_newdoc

  File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>

    from .type_check import *

  File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>

    import numpy.core.numeric as _nx

  File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 6, in <module>

    from . import multiarray

ImportError: dlopen(/usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so, 2): Symbol not found: _PyUnicodeUCS2_AsASCIIString

  Referenced from: /usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so

  Expected in: flat namespace

 in /usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so

real 2m12.107s

user 1m50.320s

sys 0m8.643s

************************************************************************

Error installing package numpy-1.8.1.p0

************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file

  /Users/tcf/Applications/sage-6.7.rc0/logs/pkgs/numpy-1.8.1.p0.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to

/Users/tcf/Applications/sage-6.7.rc0/local/var/tmp/sage/build/numpy-1.8.1.p0 and type 'make' or whatever is appropriate.

Instead, the following commands setup all environment variables

correctly and load a subshell for you to debug the error:

  (cd '/Users/tcf/Applications/sage-6.7.rc0/local/var/tmp/sage/build/numpy-1.8.1.p0' && '/Users/tcf/Applications/sage-6.7.rc0/sage' --sh)

When you are done debugging, you can type "exit" to leave the subshell.

************************************************************************

[Dima Pasechnik]

indeed, this is the interference from another installation of numpy.
Before running make, remove everything that starts from /usr/local from
PATH in the shell you start make from.
Hopefully it will work then.
(if not, post the new log...)

OK, we should put Anaconda on our blacklist :-)


 

[Ted Fujimoto]

I removed all starting with /usr/local on my PATH but getting the same error on my Homebrew version of Python:

Writing /Users/tcf/Applications/sage-6.7.rc0/local/lib/python2.7/site-packages/numpy-1.8.1-py2.7.egg-info

running install_clib

copying build/temp.macosx-10.9-x86_64-2.7/libnpymath.a -> /Users/tcf/Applications/sage-6.7.rc0/local/lib/python2.7/site-packages/numpy/core/lib

Traceback (most recent call last):

  File "<stdin>", line 3, in <module>

  File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 170, in <module>

    from . import add_newdocs

  File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>

    from numpy.lib import add_newdoc

  File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>

    from .type_check import *

  File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>

    import numpy.core.numeric as _nx

  File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 6, in <module>

    from . import multiarray

ImportError: dlopen(/usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so, 2): Symbol not found: _PyUnicodeUCS2_AsASCIIString

  Referenced from: /usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so

  Expected in: flat namespace

 in /usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so

real 2m15.443s

user 1m49.642s

sys 0m8.702s

************************************************************************

Error installing package numpy-1.8.1.p0

************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file

  /Users/tcf/Applications/sage-6.7.rc0/logs/pkgs/numpy-1.8.1.p0.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to

/Users/tcf/Applications/sage-6.7.rc0/local/var/tmp/sage/build/numpy-1.8.1.p0 and type 'make' or whatever is appropriate.

Instead, the following commands setup all environment variables

correctly and load a subshell for you to debug the error:

  (cd '/Users/tcf/Applications/sage-6.7.rc0/local/var/tmp/sage/build/numpy-1.8.1.p0' && '/Users/tcf/Applications/sage-6.7.rc0/sage' --sh)

When you are done debugging, you can type "exit" to leave the subshell.

************************************************************************

make[2]: *** [/Users/tcf/Applications/sage-6.7.rc0/local/var/lib/sage/installed/numpy-1.8.1.p0] Error 1

make[1]: *** [all] Error 2

real 2m19.942s

user 1m50.269s

sys 0m9.297s

***************************************************************

Error building Sage.

The following package(s) may have failed to build:

package: numpy-1.8.1.p0

log file: /Users/tcf/Applications/sage-6.7.rc0/logs/pkgs/numpy-1.8.1.p0.log

build directory: /Users/tcf/Applications/sage-6.7.rc0/local/var/tmp/sage/build/numpy-1.8.1.p0

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [build] Error 1

[Dima Pasechnik]

On Saturday, 16 May 2015 20:18:26 UTC+1, Ted Fujimoto wrote:

I removed all starting with /usr/local on my PATH but getting the same error on my Homebrew version of Python:t

right, Homebrew/Fink/MacPorts are known to create problems with building on OSX.

In SAGEROOT/configure there is a comment:
###########################################################################
# (OS X only)
# Sage will probably not build at all if either Fink or MacPorts can be
# found, and the error messages can be extremely confusing.  Even if it does
# build, the product will probably be wrong.  This runs a basic check to
# find them. Once the Sage build process is perfected, this won't be necessary.

and in fact Fink/MacPorts are detected, but probably not HomeBrew...

anyhow, this what is to be done in case of the former:
"Either:
(1) rename /opt/local and /sw, or
(2) change PATH and DYLD_LIBRARY_PATH
(Once Sage is built, you can restore them.)"

I don't know what exactly needs to be removed from the above PATH to have this fixed in Homebrew case...

[ksk...@gmail.com]

I've run into similar issues building development branches on other platforms. Is there a generic workaround I should know about?

Kiran

On Friday, May 15, 2015 at 12:28:28 AM UTC-7, Volker Braun wrote: