osx 10.10.2 / sage 6.5 - how to read jpg/tiff files? - sage -i libjpeg-6b problem

[peter metcalf]

HI All

I'm trying to read jpg files using PIL or matplotlib

any help/suggestions would be most welcome!

the following fails

sage -i libjpeg-6b

the relevant part of the log file may be

==================================================

gcc -fPIC  -I.   -c -o jmemmgr.o jmemmgr.c

gcc -fPIC  -I.   -c -o jmemnobs.o jmemnobs.c

rm -f libjpeg.a

ar rc libjpeg.a  jcapimin.o jcapistd.o jctrans.o jcparam.o jdatadst.o jcinit.o jcmaster.o jcmarker.o jcmainct.o jcprepct.o jccoefct.o jccolor.o jcsample.o jchuff.o jcphuff.o jcdctmgr.o jfdctfst.o jfdctflt.o jfdctint.o jdapimin.o jdapistd.o jdtrans.o jdatasrc.o jdmaster.o jdinput.o jdmarker.o jdhuff.o jdphuff.o jdmainct.o jdcoefct.o jdpostct.o jddctmgr.o jidctfst.o jidctflt.o jidctint.o jidctred.o jdsample.o jdcolor.o jquant1.o jquant2.o jdmerge.o jcomapi.o jutils.o jerror.o jmemmgr.o jmemnobs.o

ranlib libjpeg.a

sh: line 1:  4325 Trace/BPT trap: 5       /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -sdk / -find ranlib 2> /dev/null

ranlib: error: unable to find utility "ranlib", not a developer tool or in PATH

make: *** [libjpeg.a] Error 72

===================================================

I also noted this odd line at the beginning of the log file (I am not Karl Crisman)

===================================================

C compiler: gcc

C compiler version:

Using built-in specs.

COLLECT_GCC=/Applications/sage/local/bin/gcc

COLLECT_LTO_WRAPPER=/Applications/sage/local/bin/../libexec/gcc/x86_64-apple-darwin11.4.2/4.9.2/lto-wrapper

Target: x86_64-apple-darwin11.4.2

Configured with: ../src/configure --prefix=/Users/karl.crisman/Downloads/sage-6.5/local --with-local-prefix=/Users/karl.crisman/Downloads/sage-6.5/local --with-gmp=/Users/karl.crisman/Downloads/sage-6.5/local --with-mpfr=/Users/karl.crisman/Downloads/sage-6.5/local --with-mpc=/Users/karl.crisman/Downloads/sage-6.5/local --with-system-zlib --disable-multilib --disable-nls --enable-languages=c,c++,fortran --disable-libitm --without-isl --without-cloog  

Thread model: posix

[Dima Pasechnik]

On Monday, 23 March 2015 10:22:40 UTC, peter metcalf wrote:

HI All

I'm trying to read jpg files using PIL or matplotlib

any help/suggestions would be most welcome!

the following fails

sage -i libjpeg-6b

the relevant part of the log file may be

==================================================

gcc -fPIC  -I.   -c -o jmemmgr.o jmemmgr.c

gcc -fPIC  -I.   -c -o jmemnobs.o jmemnobs.c

rm -f libjpeg.a

ar rc libjpeg.a  jcapimin.o jcapistd.o jctrans.o jcparam.o jdatadst.o jcinit.o jcmaster.o jcmarker.o jcmainct.o jcprepct.o jccoefct.o jccolor.o jcsample.o jchuff.o jcphuff.o jcdctmgr.o jfdctfst.o jfdctflt.o jfdctint.o jdapimin.o jdapistd.o jdtrans.o jdatasrc.o jdmaster.o jdinput.o jdmarker.o jdhuff.o jdphuff.o jdmainct.o jdcoefct.o jdpostct.o jddctmgr.o jidctfst.o jidctflt.o jidctint.o jidctred.o jdsample.o jdcolor.o jquant1.o jquant2.o jdmerge.o jcomapi.o jutils.o jerror.o jmemmgr.o jmemnobs.o

ranlib libjpeg.a

sh: line 1:  4325 Trace/BPT trap: 5       /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -sdk / -find ranlib 2> /dev/null

ranlib: error: unable to find utility "ranlib", not a developer tool or in PATH

make: *** [libjpeg.a] Error 72

===================================================

I also noted this odd line at the beginning of the log file (I am not Karl Crisman)

it just tells us that you are running a binary distribution of Sage built by Karl.

I suspect that the problem is that the package you're trying to install is a very old (from 2007)
and since then OSX has changed much. And there is no regular testing of experimental packages,
so you're more or less on your own here.

By the way, are you sure you have XCode's command line tools installed?

If yes, it might mean that you need to replace a call to ranlib to an equavalent call to ar:
at least on Linux:
"running ranlib is completely equivalent to executing ar -s"

So you might edit the spkg-install script to fix it, or create a ranlib shell script that will
call ar...

Let us know if this works.

Dmitrii

[peter metcalf]

Thanks Dmitrii

I also get errors with

sage -f python

so there is something more fundamental going on than the problem with libjpeg-6b

I think I do have Xcode command line tools installed 

since 'xcode-select -p'  returns
/Applications/Xcode.app/Contents/Developer

This is the first error in /Applications/sage/logs/pkgs/python.log

=======================

checking for int64_t... yes

checking for ssize_t... yes

checking size of int... 0

checking size of long... 0

checking size of void *... 0

checking size of short... 0

checking size of float... 0

checking size of double... 0

checking size of fpos_t... 0

checking size of size_t... configure: error: in `/Applications/sage/local/var/tmp/sage/build/python-2.7.8/src':

configure: error: cannot compute sizeof (size_t)

See `config.log' for more details

Error configuring Python.

================================================

This is the first error in /Applications/sage/local/var/tmp/sage/build/python-2.7.8/src/config.log

================================================

Target: x86_64-apple-darwin11.4.2

Configured with: ../src/configure --prefix=/Users/karl.crisman/Downloads/sage-6.5/local --with-local-prefix=/Users/karl.crisman/Downloads/sage-6.5/local --with-gmp=/Users/karl.crisman/Downloads/sage-6.5/local --with-mpfr=/Users/karl.crisman/Downloads/sage-6.5/local --with-mpc=/Users/karl.crisman/Downloads/sage-6.5/local --with-system-zlib --disable-multilib --disable-nls --enable-languages=c,c++,fortran --disable-libitm --without-isl --without-cloog  

Thread model: posix

gcc version 4.9.2 (GCC) 

configure:3818: $? = 0

configure:3807: gcc -V >&5

gcc: error: unrecognized command line option '-V'

gcc: fatal error: no input files

compilation terminated.

configure:3818: $? = 1

configure:3807: gcc -qversion >&5

gcc: error: unrecognized command line option '-qversion'

gcc: fatal error: no input files

compilation terminated.

configure:3818: $? = 1

configure:3838: checking whether the C compiler works

===========================================================

[Volker Braun]

Can you try compiling Sage just from source, not inside the mac app...

[peter metcalf]

Thanks

if I type 'make' in SAGE_ROOT this is the first sign of a problem - no installed math library found

===========================================

configure: Excellent, the C, C++ and Fortran compilers are all GCC 4.9.2

configure: Excellent, GCC 4.9.2 is later than the minimum

configure: needed to build Sage, which is GCC version 4.0.1

checking for sqrt in -lm... no

configure: This system has no maths library installed.

configure: error: Exiting, since a maths library was not found.

If you would like to try to build Sage anyway (to help porting),

export the variable 'SAGE_PORT' to something non-empty.

make[2]: *** [/Applications/sage/local/var/lib/sage/installed/prereq] Error 1

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

==============================

Peter

[Volker Braun]

Something is wrong with your xcode command line tools... can you try reinstalling them?

[kcrisman]

it just tells us that you are running a binary distribution of Sage built by Karl.

Which is odd, because I only make the 10.7 binary, which you shouldn't need to run. 

[Peter Metcalf]

Thanks Volker

after 2 hours of searching the web and trying various things there seems to be no obvious way of

reinstalling the xcode command line tools, or of uninstalling xcode and starting fresh

I know this is off topic for sage-devel but if anybody has done this please let me know

Peter

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

Peter Metcalf

http://www.bioscienceresearch.co.nz/staff/peter-metcalf/

Associate Professor in Structural Biology

School of Biological Sciences

University of Auckland

Private Bag 92019 

Auckland 1010

phone +64 9 923 4810

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skype ID pmet007

Courier address:

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[Volker Braun]

"xcode-select --install" usually works.

There is no reasonable way of uninstalling the command line tools.

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[Peter Metcalf]

OK - thanks

I reinstalled the command line tools and then the whole of Xcode from 

https://developer.apple.com/downloads/index.action?=command%20line%20tools#

but still get errors with

sage -f python

I’ve attached the config log file below

Peter

On 24/03/2015, at 8:23 am, Volker Braun <vbrau...@gmail.com> wrote:

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[Francois Bissey]

From config.log

as: error: unable to locate xcodebuild, please make sure the path to the Xcode folder is set correctly!
as: error: You can set the path to the Xcode folder using /usr/bin/xcode-select -switch

I am at eResearchNZ2015 with a NeSI t-shirt are you here as well?

François

> On 24/03/2015, at 11:33, Peter Metcalf <peter....@auckland.ac.nz> wrote:
>
> <config.log>

[Volker Braun]

You are still using the compiler shipped inside the mac app. Download the source tarball (sage-6.5.tar.gz), unpack in your home directory, and run "make".

Configured with: ../src/configure --prefix=/Users/karl.crisman/Downloads/sage-6.5/local --with-local-prefix=/Users/karl.crisman/Downloads/sage-6.5/local --with-gmp=/Users/karl.crisman/Downloads/sage-6.5/local --with-mpfr=/Users/karl.crisman/Downloads/sage-6.5/local --with-mpc=/Users/karl.crisman/Downloads/sage-6.5/local --with-system-zlib --disable-multilib --disable-nls --enable-languages=c,c++,fortran --disable-libitm --without-isl --without-cloog  

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[Peter Metcalf]

All good now - thanks very much for your help

Peter

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