Unix software for Apple Macintosh general discussion

Alexander Hansen | 1 Oct 2011 01:14

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re-alpine build issue was Re: ccp4 and re-alpine installation fails on Mac OS X.7 (Lion)


On 9/30/11 11:37 AM, Helge Dorfmueller wrote:
> Dear Users,
> 
> trying to install via fink the program 're-alpine' and 'ccp4',
> however, despite the
> 
>> fink selfupdate fink update-all
> 
> I cannot install 'ccp4' via
>> fink install ccp4
> 
> Failed: phase compiling: ccp4-6.2.0-102 failed
> 
> 
> 
> and the same for 're-alpine'.
> 
> 
> Could you please have a look at the attached file to help me? This
> would be very much appreciated to install these important
> programs!
> 
> 
> Thanks a lot in advance for your help!!!!
> 
> 
> Best wishes,
> 
>

(Continue reading)

Dmitry Rodionov, Mr | 1 Oct 2011 01:06

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ccp4 fails to build on 10.7

Hi everyone,
ccp4 fails to build on a fresh fink install on 10.7:

test -z "/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin" || ./install-sh -c -d "/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin"
gfortran -m64 -O2  -fno-second-underscore -c chegv.f
  /bin/sh ./libtool   --mode=install cp -p 'automask' '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/automask'
gfortran -m64 -O2  -fno-second-underscore -c chegvd.f
gfortran -m64 -O2  -fno-second-underscore -c chegvx.f
gfortran -m64 -O2  -fno-second-underscore -c cherfs.f
cp -p automask /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/automask
gfortran -m64 -O2  -fno-second-underscore -c chesv.f
  /bin/sh ./libtool   --mode=install cp -p 'diffdump' '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diffdump'
gfortran -m64 -O2  -fno-second-underscore -c chesvx.f
gfortran -m64 -O2  -fno-second-underscore -c chetd2.f
gfortran -m64 -O2  -fno-second-underscore -c chetf2.f
cp -p diffdump /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diffdump
  /bin/sh ./libtool   --mode=install cp -p 'printpeaks' '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/printpeaks'
gfortran -m64 -O2  -fno-second-underscore -c chetrd.f
gfortran -m64 -O2  -fno-second-underscore -c chetrf.f
cp -p printpeaks /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/printpeaks
gfortran -m64 -O2  -fno-second-underscore -c chetri.f
gfortran -m64 -O2  -fno-second-underscore -c chetrs.f
  /bin/sh ./libtool   --mode=install cp -p 'diff2jpeg' '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diff2jpeg'
gfortran -m64 -O2  -fno-second-underscore -c chgeqz.f
gfortran -m64 -O2  -fno-second-underscore -c chpcon.f
cp -p diff2jpeg /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diff2jpeg
gfortran -m64 -O2  -fno-second-underscore -c chpev.f
……
gfortran -m64 -O2  -fno-second-underscore -c izmax1.f
gfortran -m64 -O2  -fno-second-underscore -c dzsum1.f

(Continue reading)

Hisashi T Fujinaka | 1 Oct 2011 02:39

Re: re-alpine build issue was Re: ccp4 and re-alpine installation fails on Mac OS X.7 (Lion)

On Fri, 30 Sep 2011, Alexander Hansen wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> On 9/30/11 11:37 AM, Helge Dorfmueller wrote:
>> Dear Users,
>>
>> trying to install via fink the program 're-alpine' and 'ccp4',
>> however, despite the
>>
>>> fink selfupdate fink update-all
>>
>> I cannot install 'ccp4' via
>>> fink install ccp4
>>
>> Failed: phase compiling: ccp4-6.2.0-102 failed
>>
>>
>>
>> and the same for 're-alpine'.
>>
>>
>> Could you please have a look at the attached file to help me? This
>> would be very much appreciated to install these important
>> programs!
>>
>>
>> Thanks a lot in advance for your help!!!!
>>

(Continue reading)

Alexander Hansen | 1 Oct 2011 03:02

Picon

Re: re-alpine build issue was Re: ccp4 and re-alpine installation fails on Mac OS X.7 (Lion)


On 9/30/11 8:39 PM, Hisashi T Fujinaka wrote:
> On Fri, 30 Sep 2011, Alexander Hansen wrote:
> 
>> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
>> 
>> On 9/30/11 11:37 AM, Helge Dorfmueller wrote:
>>> Dear Users,
>>> 
>>> trying to install via fink the program 're-alpine' and 'ccp4', 
>>> however, despite the
>>> 
>>>> fink selfupdate fink update-all
>>> 
>>> I cannot install 'ccp4' via
>>>> fink install ccp4
>>> 
>>> Failed: phase compiling: ccp4-6.2.0-102 failed
>>> 
>>> 
>>> 
>>> and the same for 're-alpine'.
>>> 
>>> 
>>> Could you please have a look at the attached file to help me?
>>> This would be very much appreciated to install these important 
>>> programs!
>>> 
>>> 
>>> Thanks a lot in advance for your help!!!!

(Continue reading)

Alexander Hansen | 1 Oct 2011 03:47

Picon

Re: ccp4 fails to build on 10.7


On 9/30/11 7:06 PM, Dmitry Rodionov, Mr wrote:
> Hi everyone, ccp4 fails to build on a fresh fink install on 10.7:
> 
> test -z "/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin" ||
> ./install-sh -c -d
> "/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin" gfortran -m64
> -O2  -fno-second-underscore -c chegv.f /bin/sh ./libtool
> --mode=install cp -p 'automask'
> '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/automask' 
> gfortran -m64 -O2  -fno-second-underscore -c chegvd.f gfortran -m64
> -O2  -fno-second-underscore -c chegvx.f gfortran -m64 -O2
> -fno-second-underscore -c cherfs.f cp -p automask
> /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/automask gfortran
> -m64 -O2  -fno-second-underscore -c chesv.f /bin/sh ./libtool
> --mode=install cp -p 'diffdump'
> '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diffdump' 
> gfortran -m64 -O2  -fno-second-underscore -c chesvx.f gfortran -m64
> -O2  -fno-second-underscore -c chetd2.f gfortran -m64 -O2
> -fno-second-underscore -c chetf2.f cp -p diffdump
> /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diffdump /bin/sh
> ./libtool   --mode=install cp -p 'printpeaks'
> '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/printpeaks' 
> gfortran -m64 -O2  -fno-second-underscore -c chetrd.f gfortran -m64
> -O2  -fno-second-underscore -c chetrf.f cp -p printpeaks
> /sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/printpeaks 
> gfortran -m64 -O2  -fno-second-underscore -c chetri.f gfortran -m64
> -O2  -fno-second-underscore -c chetrs.f /bin/sh ./libtool
> --mode=install cp -p 'diff2jpeg'
> '/sw/src/fink.build/ccp4-6.2.0-102/ccp4-6.2.0/bin/diff2jpeg'

(Continue reading)

Alexander Hansen | 1 Oct 2011 12:31

Picon

Re: ccp4 fails to build on 10.7


On 10/1/11 12:25 AM, William G. Scott wrote:
> 
> On Sep 30, 2011, at 6:47 PM, Alexander Hansen wrote:
> 
>> Yes.  fink-0.31.2 has introduced using multiple threads to build 
>> packages by default.  Some packages aren't compatible with this,
>> and it appears that ccp4 is one of them.
> 
> OK, this seems to have fixed it (at least on my computer), so I
> have committed the fix to fink stable cvs for 10.7 and 10.4.
> 
> Alexander, many thanks for that bit of advice.  I would have wasted
> hours pulling my hair out.
> 
> Bill
> 
> 

You're welcome.  The core developers were testing this feature out in
pre-release fink for a while, so I knew what the signatures are
(missing files is the most common one).

--

-- 
Alexander Hansen, Ph.D.
Fink User Liaison
http://finkakh.wordpress.com/

William G. Scott | 1 Oct 2011 05:06

Re: ccp4 fails to build on 10.7

Thanks.  I am testing this now, and will commit the fix as soon as I verify it indeed 
solves the problem (the tar ball also got changed upstream, so I don't have a proper 
experimental control).

> 
> Yes.  fink-0.31.2 has introduced using multiple threads to build
> packages by default.  Some packages aren't compatible with this, and
> it appears that ccp4 is one of them.
> 
> Dmitry, Helge, and Tim, you can work around this issue, which is
> OS-version independent, by running "fink configure" and choosing to
> use one processor for builds temporarily.
> 
> Bill, you can mark the .info file with
> 
> UseMaxBuildJobs: false
> 
> to force the package to build in only one thread.  This shouldn't
> require a new revision.
> - -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> http://finkakh.wordpress.com/
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.11 (Darwin)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iEYEARECAAYFAk6GcRgACgkQB8UpO3rKjQ9wswCgo3jVcqw13jVFUlhERBmRCByS
> tYkAnjyKJ0A5Q1Yfl0SLZihmrVLTTCUl
> =lOLf

(Continue reading)

William G. Scott | 1 Oct 2011 06:25

Re: ccp4 fails to build on 10.7


On Sep 30, 2011, at 6:47 PM, Alexander Hansen wrote:

> Yes.  fink-0.31.2 has introduced using multiple threads to build
> packages by default.  Some packages aren't compatible with this, and
> it appears that ccp4 is one of them.

OK, this seems to have fixed it (at least on my computer), so I have committed the fix to fink stable cvs for
10.7 and 10.4.

Alexander, many thanks for that bit of advice.  I would have wasted hours pulling my hair out.

Bill

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Dmitry Rodionov, Mr | 2 Oct 2011 04:52

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Re: ccp4 fails to build on 10.7

Thanks a million, Alexander!
I confirm, reducing the number of parallel build jobs to 1 does the trick.

Best regards,
	Dmitry

On 2011-09-30, at 9:47 PM, Alexander Hansen wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On 9/30/11 7:06 PM, Dmitry Rodionov, Mr wrote:
>> Hi everyone, ccp4 fails to build on a fresh fink install on 10.7:
>> 
> Failed: phase compiling: ccp4-6.2.0-102 failed
>> -------- Package manager version: 0.31.2 Distribution version:
>> selfupdate-rsync Fri Sep 30 14:34:45 2011, 10.7, x86_64 Trees:
>> local/main stable/main Xcode: 4.1
>> 
>> 
>> Any ideas?
>> 
>> Best regards, Dmitry
> 
> 
> Yes.  fink-0.31.2 has introduced using multiple threads to build
> packages by default.  Some packages aren't compatible with this, and
> it appears that ccp4 is one of them.
> 
> Dmitry, Helge, and Tim, you can work around this issue, which is

(Continue reading)

Bill Waggoner | 2 Oct 2011 17:49

Picon

fontconfig-config compile/link error

I'm having trouble updating after the recent update to fink to 0.31.2

My system is:
Package manager version: 0.31.2
Distribution version: selfupdate-rsync Sun Oct  2 10:43:46 2011, 10.7, i386
Trees: local/main stable/main stable/crypto local/injected

When updating fontconfig-config I get the following error:

/bin/sh ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.
-I.. -I.. -I../src -I/sw/include/freetype2 -I/sw/include
-I/sw/include/libxml2 -I/sw/include  -Wall -Wpointer-arith
-Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations
-Wnested-externs -fno-strict-aliasing
-DFC_CACHEDIR='"/sw/var/cache/fontconfig-2.4"'
-DFONTCONFIG_PATH='"/sw/etc/fonts"'  -I/sw/include  -fno-common -g -Os
-MT ftglue.lo -MD -MP -MF .deps/ftglue.Tpo -c -o ftglue.lo ftglue.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../src
-I/sw/include/freetype2 -I/sw/include -I/sw/include/libxml2
-I/sw/include -Wall -Wpointer-arith -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wnested-externs
-fno-strict-aliasing -DFC_CACHEDIR=\"/sw/var/cache/fontconfig-2.4\"
-DFONTCONFIG_PATH=\"/sw/etc/fonts\" -I/sw/include -fno-common -g -Os
-MT ftglue.lo -MD -MP -MF .deps/ftglue.Tpo -c ftglue.c  -fno-common
-DPIC -o .libs/ftglue.o
mv -f .deps/ftglue.Tpo .deps/ftglue.Plo
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -fno-common -g -Os
-version-info 5:4:4 -no-undefined  -L/sw/lib -o libfontconfig.la
-rpath /sw/lib/fontconfig2/lib fcatomic.lo fcblanks.lo fccache.lo
fccfg.lo fccharset.lo fcdbg.lo fcdefault.lo fcdir.lo fcformat.lo

(Continue reading)

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