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Christian Schaffner | 1 Apr 2007 18:27
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Re: Failed compiling of m4-1.4.8-1


On 29.03.2007, at 17:55, Christian Schaffner wrote:

>
> On 28.03.2007, at 10:01, Christian Schaffner wrote:
>
>>
>> On 27.03.2007, at 17:56, Christian Schaffner wrote:
>>
>>> Hi Chris
>>>
>>> I tested some more, and it appears to only fail if compiled using
>>> the buildfink script (the script to build our binary dists in the
>>> future). It seems to fail on both 10.3 and 10.4 in that case.
>>>
>>> I found a patch to solve that problem here:
>>> http://www.mail-archive.com/m4-patches <at> gnu.org/msg00500.html
>>> (see attached .patch file)
>>>
>>> Do you think it would be ok to commit? If you don't mind I will add
>>> the patch to the 10.3 and 10.4 unstable versions in the coming
>>> days. Ok?
>>
>> I committed this fix to the 10.3 and 10.4 unstable trees (no need to
>> up revision, since only self test changes). Version 1.4.9 does indeed
>> include this fix, so it probably would be a good idea to update m4 to
>> that version.
>
> I just found out that m4 doesn't seem to build on 10.3 if texinfo is
> not installed. Any objections to add that build dependency? I will
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William Scott | 3 Apr 2007 20:03
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emboss-4.1.0-1 on a (new) intel iMac


Hi Koen:

Thanks for maintaining EMBOSS.  I just tried installing on a new  
intel iMac and got the following error:

ajjava.c:93:19: error: crypt.h: No such file or directory

I've got   i   system-openssl-dev       0.9.7-6             
Placeholder to force the use of the system SSL

Thanks.

Bill

gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"  
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" - 
DVERSION=\"4.1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 - 
DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 - 
DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 - 
DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1  
-DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1  
-DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1  
-DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  
-DPLD_png=1 -I. -I. -DAJAX_FIXED_ROOT=\"/sw/src/fink.build/ 
emboss-4.1.0-1/EMBOSS-4.1.0/emboss\" -DPREFIX=\"/sw\" -I../plplot - 
DPOSIX_MALLOC_THRESHOLD=10 -DAJ_MACOSXLF -Dstat64=stat -I/sw/include - 
DLENDIAN -I/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/ 
Home -DHAVE_JAVA -I/System/Library/Frameworks/JavaVM.framework/ 
Versions/1.4.2/Home/include -DNO_AUTH -O1 -c ajjava.c  -fno-common -
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Alexander K. Hansen | 4 Apr 2007 02:44
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Finally have some time to catch up on the tracker

What with moving, no Mac at work, delays in getting my home internet and 
home office set up, and other life events, I haven't had much time to 
work on the package submissions tracker.  Things have calmed down a bit, 
so I should have more available time.  Don't despair if you have an item 
sitting there!

By the way, if people without commits access want to test out packages 
in which they are interested, that would be great!  Email me or post the 
results on the tracker item.  That way if a package seems otherwise good 
I just have to do a clean-system build to verify that the  dependencies 
are right.

--

-- 
Alexander K. Hansen
(akh)
Fink User Liason and Documenter

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Koen van der Drift | 4 Apr 2007 03:11
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Re: emboss-4.1.0-1 on a (new) intel iMac

Hi Bill,

Thanks for the report. I am very busy, but may have some time later  
this week or next week to look into this. If anyone else on the list  
has a clue in the meantime, please let me know, Iand I can update the  
package accordingly.

- Koen.

On Apr 3, 2007, at 2:03 PM, William Scott wrote:

>
> Hi Koen:
>
> Thanks for maintaining EMBOSS.  I just tried installing on a new  
> intel iMac and got the following error:
>
> ajjava.c:93:19: error: crypt.h: No such file or directory
>
> I've got   i   system-openssl-dev       0.9.7-6             
> Placeholder to force the use of the system SSL
>
> Thanks.
>
> Bill
>
>
>
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION= 
> \"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=
(Continue reading)

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William Scott | 4 Apr 2007 03:18
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Re: emboss-4.1.0-1 on a (new) intel iMac


Hi Koen:

I just found that making a symbolic link to 

/sw/include/gcrypt.h

which is provided by

libgcrypt: /sw/include/gcrypt.h

allowed it to compile.  So it's probably just a case of replacing crypt.h 
with gcrypt.h somewhere (or changing libgcrypt).

Bill

On Tue, 3 Apr 2007, Koen van der Drift wrote:

     Hi Bill,

     Thanks for the report. I am very busy, but may have some time later this
     week or next week to look into this. If anyone else on the list has a clue
     in the meantime, please let me know, Iand I can update the package
     accordingly.

     - Koen.
(Continue reading)

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William Scott | 4 Apr 2007 03:21
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Re: emboss-4.1.0-1 on a (new) intel iMac


... and with the miracle of recursive globbing in zsh, I found two 
instances:

% grep crypt.h **/*
ajax/ajjava.c:#include <crypt.h>
emboss/jembossctl.c:#include <crypt.h>

shall I fix the package?

Bill

On Tue, 3 Apr 2007, Koen van der Drift wrote:

     Hi Bill,

     Thanks for the report. I am very busy, but may have some time later this
     week or next week to look into this. If anyone else on the list has a clue
     in the meantime, please let me know, Iand I can update the package
     accordingly.

     - Koen.

     

     
     On Apr 3, 2007, at 2:03 PM, William Scott wrote:

     > 
     > Hi Koen:
(Continue reading)

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Koen van der Drift | 4 Apr 2007 03:49
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Re: emboss-4.1.0-1 on a (new) intel iMac

Hi Bill,

Thanks for finding that. If it works, please go ahead and commit the  
change. Is the fix for Intel only, or also for PPCs?

- Koen.

On Apr 3, 2007, at 9:21 PM, William Scott wrote:

> ... and with the miracle of recursive globbing in zsh, I found two
> instances:
>
> % grep crypt.h **/*
> ajax/ajjava.c:#include <crypt.h>
> emboss/jembossctl.c:#include <crypt.h>
>
> shall I fix the package?

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William Scott | 4 Apr 2007 06:16
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Re: emboss-4.1.0-1 on a (new) intel iMac


I just tested on my ppc G5 and it compiles on that, too. I don't know how 
to test whatever encryption thing this is used for.

Anyway, it compiles now so it presumably is an improvement.

On Tue, 3 Apr 2007, Koen van der Drift wrote:

     Hi Bill,

     Thanks for finding that. If it works, please go ahead and commit the
     change. Is the fix for Intel only, or also for PPCs?

     - Koen.

     

     On Apr 3, 2007, at 9:21 PM, William Scott wrote:

     > ... and with the miracle of recursive globbing in zsh, I found two
     > instances:
     > 
     > % grep crypt.h **/*
     > ajax/ajjava.c:#include <crypt.h>
     > emboss/jembossctl.c:#include <crypt.h>
     > 
     > shall I fix the package?

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Daniel Macks | 4 Apr 2007 07:22

Can't install latest mysql

10.3/unstable, trying to install latest mysql (5.0.38-1) with the
previous version of that package (5.0.34-6) installed, I got:

Setting up mysql (5.0.38-1) ...
Installing MySQL system tables...
070403 12:42:22 [Warning] Setting lower_case_table_names=2 because file system for /sw/var/mysql/ is
case insensitive
ERROR: 1136  Column count doesn't match value count at row 1
070403 12:42:23 [ERROR] Aborting

070403 12:42:23 [Note] /sw/sbin/mysqld: Shutdown complete

Installation of system tables failed!

Looking at the PostInst, I see it's doing:

 # create initial database
 # it is safe to call mysql_install_db even if a db is already present
 /sw/bin/mysql_install_db --user=mysql

Digging into that script, apparently it doesn't realize I already have
a mysql database installed, so it tries to set up a new one, which is
different from the old. Got a lot of errors from the mysql_upgrade
script that mysql_install_db, so gave up and started over:

  rm -rf /sw/var/mysql
  dpkg --r mysql
  fink install mysql

That worked. For fun, I tried 'fink reinstall mysql', which gives:
(Continue reading)

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Daniel E. Macks | 4 Apr 2007 07:36

Re: emboss-4.1.0-1 on a (new) intel iMac

Many of the function prototypes in /usr/include/crypt.h on my RedHat
box are in /usr/include/unistd.h on my OS X machine. Maybe that would
suffice for this package? In cases like this, I usually first just
comment-out an unsatisfied #include. That way the compiler will issue
warnings about what symbols it wants, and then try find the header to
supply them, instead of assuming a header with a "reasonably-close"
filename has the same symbols in it.

dan

Koen van der Drift <kvddrift <at> earthlink.net> said:
>
> Thanks for the report. I am very busy, but may have some time later  
> this week or next week to look into this. If anyone else on the list  
> has a clue in the meantime, please let me know, Iand I can update the  
> package accordingly.
>
> On Apr 3, 2007, at 2:03 PM, William Scott wrote:
>>
>> Thanks for maintaining EMBOSS.  I just tried installing on a new  
>> intel iMac and got the following error:
>>
>> ajjava.c:93:19: error: crypt.h: No such file or directory
>>
>> I've got   i   system-openssl-dev       0.9.7-6             
>> Placeholder to force the use of the system SSL
>>
>> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION= 
>> \"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE= 
>> \"EMBOSS\" -DVERSION=\"4.1.0\" -DSTDC_HEADERS=1 -
(Continue reading)

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Gmane