Re: [Fink-devel] aclocal.m4 error compiling under 10.12

[John Lillibridge]

Hi Fink Developers,

I just wanted to confirm that fink-package-precedence-0.29-1 solves the problem 
with otool-classic under Xcode-8 beta, when building under 10.12 Sierra.

Thanks Daniel,
John

> On Aug 10, 2016, at 01:59 , Daniel Macks <dma...@netspace.org> wrote:
> 
> On Tue, 9 Aug 2016 11:52:39 -0700, Alexander Hansen 
> <alexanderk.han...@gmail.com> wrote:
> 
>>> On Aug 6, 2016, at 20:42, Daniel Macks <dma...@netspace.org> wrote:
>>>> On Sat, 6 Aug 2016 11:56:46 -0700, Alexander Hansen > 
>> <alexanderk.han...@gmail.com> wrote:
>>>>> On Aug 6, 2016, at 11:50, John Lillibridge <isb...@verizon.net> wrote:
>>>>>> I managed to get Fink to build via bootstrap under 10.12 beta >> 
>> (now 3). But certain packages fail to compile with the following >> 
>> types of errors when checking dependencies:
>>>>>> fink-package-precedence --no-headers . >>>> Scanning binaries 
>> for incorrect dyld linking... >>>> >> 
>> /Applications/Xcode-beta.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump:
>>  'aclocal.m4': The file was not recognized as a valid object >> file. >>>> 
>> fatal error: >> 
>> /Applications/Xcode-beta.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool:
>>  internal objdump command >> 
>> failed
>>>>>> Error reading /usr/bin/otool -L: 256
>>>>>> I get the same type of error using the Xcode-8-beta app as well 
>>>> as the Command Line Tools. >>>> Any ideas how to work around this?
>>>>>> Apple decided to change the behavior of otool for Xcode 8 (how 
>> nice >> of them) and it now throws an error instead of silently 
>> ignoring >> non-object files. >> >> As a workaround, change line 263 
>> of /sw/bin/pathsetup.sh to my $otool >> = '/usr/bin/otool-classic’
>>>>>> (I don’t have the Xcode 8 command-line tools deployed, so 
>> I’m not >> 100% sure that otool-classic is accessible there, however.)
>>>> I uploaded a new version of fink-package-precedence (0.19-1) that 
>> uses > "otool-classic" if present (falling back to "otool" if not), 
>> which > should resolve the problem. Please let me know--I don't have 
>> xcode8, so > I'm just implementing what Alexander, and several others 
>> on IRC and > other places, have reported. > > dan
>>>>> --
>>> Daniel Macks
>>> dma...@netspace.org
>>> otool-classic appears to be buried:
>> 
>> 11:35am] howarth: note that otool-clasic is buried in 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>  and 
>> /Library/Developer/CommandLineTools/usr/bin
>> [11:38am] I guess we’d want to check the command-line tools location first. 
> 
> Done in f-p-p 0.20
>  
> dan
>  
> 
> --
> Daniel Macks
> dma...@netspace.org
>  
> 
> 
> --
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Re: [Fink-devel] Got a bunch of .info from a helpful user

[John Lillibridge]

Thanks Alexander,

I'm happy to report that gromacs[-mpi] built without a hitch under 10.12 beta 
4, after updating the finkinfo files:

System Version: macOS 10.12 (16A286a)

Developer Tools:
  Version: 8.0 (8S188o)
  Location: /Applications/Xcode-beta.app

Applications:
  Xcode: 8.0 (11222.4)

> fink list gromacs

Information about 9784 packages read in 1 seconds.
 i   gromacs   5.1.1-100Molecular dynamics package
 i   gromacs-dev   5.1.1-100Molecular dynamics package
 gromacs-mpi   5.1.1-100Molecular dynamics package 
(Parallel version)
 gromacs-mpi-dev   5.1.1-100Molecular dynamics package 
(Parallel version)
 i   gromacs1-mpi-shlibs   5.1.1-100Molecular dynamics package 
(Parallel version)
 i   gromacs1-shlibs   5.1.1-100Molecular dynamics package

Cheers,
John

> On Aug 10, 2016, at 12:17 , Alexander Hansen  
> wrote:
> 
> To my direct email, unfortunately. We really need to get the distribution 
> moved to git so that this kind of thing can be handled via a pull request.
> 
> Anyway, I’ve now got a bunch of .infos which have been test-built on the 
> 10.12 beta, only one of which is for a package for which I am the maintainer 
> of record.  :
> 
> app-defaults.info matplotlib-py.info
> apple-gdb.infomodule-build-pm-10.12.info
> business-isbn-data-pm-10.12.info  module-refresh-pm-10.12.info
> capture-tiny-pm-10.12.infomodule-scandeps-pm-10.12.info
> cpan-changes-pm-10.12.infonetpacket-pm.info
> cwd-guard-pm-10.12.info   ocaml.info
> data-compare-pm-10.12.infopackage-generator-pm-10.12.info
> devel-checkcompiler-pm-10.12.info pegex-pm-10.12.info
> devel-stacktrace-pm-10.12.infoperl5162.info
> dynaloader-functions-pm-10.12.infopo4a-10.12.info
> expect-5.45.info  pod-markdown-pm-10.12.info
> experimental-pm-10.12.infoqt4-base-x11-4.7.3.info
> extutils-makemaker-pm-10.12.info  readonly-pm-10.12.info
> file-finder-pm-10.12.info rec-descent-pm-10.12.info
> fink-10.12.info   #   rstudio-desktop.info
> fixpath-10.12.info *  rstudio-server.info
> ghc-10.12.infosub-infix-pm-10.12.info
> git-remote-mediawiki.info tcltk-8.6.6.info
> git-send-email.info   test-data-pm-10.12.info
> git-svn.info  test-reporter-pm.info
> git.info  test-requires-pm-10.12.info
> gnucash2-10.12.info   test-sharedfork-pm-10.12.info
> gromacs-mpi.info  test-simple-pm-10.12.info
> gromacs.info  test-synopsis-pm-10.12.info
> help2man-perl.infotest-yaml-valid-pm-10.12.info
> icon-naming-utils-10.12.info  tkimg-1.3.info
> intltool40-10.12.info tktreectrl-2.4.1.info
> irssi.infotree-dag-node-pm-10.12.info
> itk-4.0.2.infotree-simple-pm-10.12.info
> iwidgets-4.0.1.info   type-tie-pm-10.12.info
> librasqal3-shlibs-10.12.info  viennarna.info
> llvm-gcc42-10.12.info xinitrc.info @
> log-log4perl-pm-10.12.infoxmkmf.info
> math-matrixreal-pm-10.12.info yaml-tiny-pm-10.12.info
> 
> Notes:
> # Autogenerated from the fink source, so this one will be excluded
> * Mine, so I updated the package.
> @ I just removed the Distribution: 10.8, 10.9, 10.10, 10.11 tag instead
> 
> There’s a a tracker item with an updated gromacs, so I’ll probably merge the 
> changes here onto it and post that onto the tracker for approval.
> 
> I haven’t looked through just yet, but I believe a fair number of these 
> changes are just to add 10.12 to the eligible distributions.  Unless people 
> have strong objections, I’ll just do that. Any packages that have a more 
> extensive update will be posted on the tracker for maintainer evaluation.
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison

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[Fink-devel] aclocal.m4 error compiling under 10.12

[John Lillibridge]

Greetings Fink developers,

I managed to get Fink to build via bootstrap under 10.12 beta (now 3). But 
certain packages fail to compile with the following types of errors when 
checking dependencies:

fink-package-precedence  --no-headers .

Scanning binaries for incorrect dyld linking...

/Applications/Xcode-beta.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump:
 'aclocal.m4': The file was not recognized as a valid object file.

fatal error: 
/Applications/Xcode-beta.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool:
 internal objdump command failed

Error reading /usr/bin/otool -L:  256

I get the same type of error using the Xcode-8-beta app as well as the Command 
Line Tools.

Any ideas how to work around this?

Thanks,
John L.
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Re: [Fink-devel] "Duplicate sources.list entry"

[John Lillibridge - NOAA Federal]

On a more general note: have we lost the ability (temporarily?) to use binary 
distributions
after migrating to 10.9-libcxx?

> From: Daniel Johnson  gmail.com>
> Subject: Re: "Duplicate sources.list entry"
> Newsgroups: gmane.os.apple.fink.devel
> Date: 2015-11-08 10:24:55 GMT (1 week, 4 days, 5 hours and 9 minutes ago)
> > On Nov 7, 2015, at 9:35 PM, Alexander Hansen  
> > gmail.com> wrote:
> > 
> >> 
> >> On Nov 7, 2015, at 16:15, Max Horn  quendi.de> wrote:
> >> 
> >> so, I keep seeing this message at the end of any "fink install" run that 
> >> involves building a package:
> >> 
> >> "
> >> Reading Package Lists... Done
> >> Building Dependency Tree... Done
> >> W: Duplicate sources.list entry 
> http://bindist.finkmirrors.net
>  stable/main Packages 
> (/sw/var/lib/apt/lists/bindist.finkmirrors.net_10.11_dists_stable_main_binary-darwin-x86%5f64_Packages)
> >> W: You may want to run apt-get update to correct these problems
> >> $
> >> "
> >> 
> >> I can fix it by doing what it says and running apt-get update... But the 
> >> problem keeps coming back. Looks as
> if Fink (?) is corrupting sources.list?
> >> 
> >> Here are my system stats (yeah, I finally upgraded my machine from 10.8... 
> >> -- this is a completely fresh
> Fink installation)
> >> 
> >> $ sw_vers
> >> ProductName:   Mac OS X
> >> ProductVersion:10.11.1
> >> BuildVersion:  15B42
> >> $ fink --version
> >> Package manager version: 0.39.2
> >> Distribution version: selfupdate-cvs Wed Oct 21 18:56:26 2015, 10.11, 
> >> x86_64
> >> Trees: local/main stable/main
> >> 
> >> 
> >> Any thoughts as to what might be wrong?
> >> 
> >> 
> >> Cheers,
> >> Max
> > 
> > I’ve never seen this myself, either on an upgraded setup or a clean 
> > bootstrap.  What’s in your
> sources.list ?
> > 
> > —akh
> 
> I was getting this too. I still had the line
> deb http://bindist.finkmirrors.net/10.11 stable main
> in my sources.list even after disabling the bindist in fink.conf. Commenting 
> it out seems to work.
> 
> Because I had the bindist active before updating to 10.11 it seems fink just 
> changed the line from 10.10 to
> 10.11. Could this be because I updated my OS before fink? I did have to 
> manually download and install the
> newer fink version because I didn’t update it first.
> 
> Daniel

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Re: [Fink-devel] El Capitan activities

[John Lillibridge - NOAA Federal]

On Sep 10, 2015, at 17:01, Alexander Hansen  wrote:
> 
> 1)  We should probably put beta install instructions on the website.  Before 
> I do that, I would like to confirm that bootstrapping using the “TheCaptain” 
> branch actually works.  Could someone please confirm that for me?

I can confirm that I was successful with the bootstrap from TheCaptain with an 
earlier version of El Capitan public beta. I’ve now installed the Golden Master 
Candidate, and will do a fresh install just to be sure.

> 2)  At some point soon we’re going to want to switch master and TheCaptain 
> over to use the 10.9-libcxx tree, which is in the process of being populated 
> as I write this.  I’ll prepare pull requests to make it easier for folks to 
> track the changes.

I’m happy to try that again as well. My previous attempt to use that tree were 
unsuccessful.

> 3)  Regarding 10.9-libcxx:  the current plan is for this to be the 
> distribution tree for 10.9-10.11 for the next fink release. 10.7 and 10.8 
> will still utilize the 10.7 tree.
> 
> 4) Concurrently with releasing a fink with full El Capitan support, we are 
> going to declare 10.7 and 10.8 as EOL. All this requires is ceasing to commit 
> updates to the 10.7 tree—we won’t need to declare special EOL directories 
> (not unlike how we handled 10.6).
> 
> Comments and suggestions are always welcome.
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison

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[Fink-devel] Fink 0.38.99.git (TheCaptain) 10.11 Beta-1

[John Lillibridge - NOAA Federal]

Greetings Fink Developers,

I wanted to share some of my experiences building Fink under El Capitan 10.11 
Public Beta-1. Unlike all the difficulties moving from 10.9 to 10.10 (due to 
the minor version becoming 2-digit) the bootstrap process was painless. Most of 
the packages that I’ve built thus far have gone without a hitch. Here is a list 
of a few specific issues I’ve run into:

0) as mentioned earlier, I got help2man-perl to build by modifying 
finkinfo/devel/help2man-perl.info to include (%type_pkg[custom] = 5182) 10.11”.

1) gcc5 built successfully using the XCode app (vs. CLI tools) with 
/sw/etc/fink.conf MaxBuildJobs: 1”.

2) gcc49 did NOT build successfully; it was initially missing the .info  
.patch files.

3) po4a required a finkinfo/devel/pora-10.11.info file, with Distribution: 
10.11” inside (simply copied po4a-10.10.info  modified)

4) I forced cfitsio to build with gcc5 (since I couldn’t get gcc49 to build) by 
modifying finkinfo/libs/cfitstio.info to have BuildDepends: gcc5”

5) gmt5 built successfully when I chose unixodbc2-nox, because:

6) qt3 did NOT build successfully

7) with those workarounds, I have succeeded to build my nominal set of tools:
   cdo, curl, fftw3, gcc5, gv, gifsicle, gmt5, grib-api, lftp, nco, ncview, wget

All the best,
John


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Re: [Fink-devel] Proposal to create a new distribution for 10.9-10.11

[John Lillibridge - NOAA Federal]

 captain-10.9-libc++ isn’t going to work because we haven’t populated
 the 10.9-libcxx distribution yet.
 The way things are going for me right now, I don’t know if I’m ever going to
 have time to do that before El Capitan is released. 
 Somebody else needs to step up.
 
 —Alexander

I have good news  bad news. First, I switched back to TheCaptain
branch, and answered NO to using binary distributions.

The bad news:
There were 'infinitely recursive' directories in /sw/src/fink.build/tar_1.26-4
(similarly later when I installed coreutils). Those are a bear to remove, but
I finally managed...

The good news:
The bootstrap succeeded without error! I ran into another issue installing
coreutils, regarding a missing dependency on help2man. I had to modify 
/sw/fink/10.11/stable/main/finkinfo/devel/help2man-perl.info to add the
10.11 distribution. It now reads:

Distribution: 
  (%type_pkg[custom] = 5123) 10.7,
  (%type_pkg[custom] = 5124) 10.8,
  (%type_pkg[custom] = 5162) 10.9,
  (%type_pkg[custom] = 5182) 10.10,
  (%type_pkg[custom] = 5182) 10.11

I'm not sure Perl 5182 is correct, but that worked. More to come...

Thanks,
John
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Re: [Fink-devel] Proposal to create a new distribution for 10.9-10.11

[John Lillibridge]

Alexander Hansen alexanderk.hansen at gmail.com writes:

 Oh, and as a side benefit, in principle we could start this new distribution
 on github.
 -

Thanks Alexander. I wanted to relate my initial experiences trying to bootstrap
a 10.11version of Fink on El Capitan Public Beta, using the github trees:

1) I ran into a phase 2 error using TheCaptain github branch, because I had
specified searching for binary packages. Here are the error messages:

Downloading the indexes of available packages in the binary distribution.
/sw/bin/apt-get-lockwait -q update
Err http://bindist.finkmirrors.net stable/main Packages
  404 Not Found
Ign http://bindist.finkmirrors.net stable/main Release
Err http://bindist.finkmirrors.net stable/crypto Packages
  404 Not Found
Ign http://bindist.finkmirrors.net stable/crypto Release
Failed to fetch http://bindist.finkmirrors.net/10.11/dists/stable/main/binary-
darwin-x86_64/Packages  404 Not Found
Failed to fetch http://bindist.finkmirrors.net/10.11/dists/stable/crypto/binary-
darwin-x86_64/Packages  404 Not Found
Reading Package Lists...
Building Dependency Tree...
E: Some index files failed to download, they have been ignored, or old ones
used instead.
### execution of /sw/bin/apt-get-lockwait failed, exit code 100
WARNING: Failure while updating indexes.

ERROR: Bootstrap phase 2 failed!

The solution is to NOT ask to check bindist during the initial fink
configuration. Even after correcting that I ran into problems similar to those
below, so I attempted the other branch.

2) I tried making a bootstrap build with the Captain-10.9-libc++ github 
branch.
This time I got through phase 1  2, but was then unable to build any additional
packages,nor even do a successful 'fink selfupdate'. The error message was:

Scanning package description files
Failed: not a reference at /sw/lib/perl5/Fink/Services.pm line 1887.

So not much success yet. Perhaps the next El Capitan Public Beta release will
behave better, but I wanted you to be aware of these errors in the hope they
can be fixed on the Fink side.

Thanks,
John


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[Fink-devel] fink-0.37.0 fails to build under Mavericks 10.9 with Xcode-6

[John Lillibridge - NOAA Federal]

Dear Fink Developers,

Last week Apple made Xcode-6 the default Developer environment under Mavericks 
10.9.5. I wanted to alert you that a fresh Fink install via ./bootstrap now 
fails under both the Xcode.app and the CommandLineTools. It breaks when 
building the apt package:

env LANG=C LC_ALL=C /sw2/bin/tar  --no-same-owner --no-same-permissions -xf 
/sw2/src/apt_0.5.4.tar.gz
[ -r /sw2/fink/dists/stable/main/finkinfo/base/apt.patch ]
sed -e 's|@PREFIX@|/sw2|g' -e 's|@DIST@|10.3|g'  
/sw2/fink/dists/stable/main/finkinfo/base/apt.patch | patch -p1
patching file apt-inst/deb/dpkgdb.cc
patching file apt-inst/makefile
patching file apt-pkg/contrib/mmap.cc
patching file apt-pkg/contrib/mmap.h
patching file apt-pkg/deb/debindexfile.cc
patching file apt-pkg/deb/deblistparser.cc
patching file apt-pkg/deb/debsystem.cc
patching file apt-pkg/deb/debsystem.h
patching file apt-pkg/deb/debversion.cc
patching file apt-pkg/init.cc
patching file apt-pkg/pkgcachegen.cc
patching file apt-pkg/pkgcachegen.h
patching file apt-pkg/policy.cc
patching file apt-pkg/tagfile.cc
patching file apt-pkg/tagfile.h
patching file buildlib/environment.mak.in
patching file buildlib/library.mak
patching file buildlib/ostable
patching file cmdline/apt-cache.cc
patching file cmdline/apt-get.cc
patching file cmdline/apt-sortpkgs.cc
patching file configure
patching file configure.in
patching file doc/apt-cache.8
patching file doc/apt-cdrom.8
patching file doc/apt-config.8
patching file doc/apt-get.8
patching file doc/apt_preferences.5
patching file doc/sources.list.5
patching file dselect/install
patching file dselect/setup
patching file dselect/update
patching file methods/connect.cc
patching file methods/ftp.cc
patching file methods/rfc2553emu.h
patching file patch_flush
patching file apt-inst/contrib/extracttar.cc
patching file apt-pkg/contrib/system.h
patching file apt-inst/extract.cc
patching file apt-inst/deb/dpkgdb.cc
patching file apt-pkg/algorithms.cc
patching file apt-pkg/init.cc
patching file apt-pkg/deb/debsystem.cc
patching file apt-pkg/contrib/cdromutl.cc
patching file cmdline/apt-cache.cc
patching file cmdline/apt-config.cc
patching file cmdline/apt-extracttemplates.cc
patching file cmdline/apt-sortpkgs.cc
patching file apt-inst/contrib/extracttar.cc
patching file apt-pkg/deb/debsystem.h
patching file apt-pkg/pkgsystem.h
perl -pi -e 's|vector.h|vector|g' apt-pkg/pkgsystem.h 
include/apt-pkg/pkgsystem.h
Can't open include/apt-pkg/pkgsystem.h: No such file or directory,  line 97.
perl -pi -e 's|iostream.h|iostream|g' apt-inst/contrib/extracttar.cc 
apt-inst/deb/dpkgdb.cc apt-inst/extract.cc apt-pkg/algorithms.cc 
apt-pkg/contrib/error.cc cmdline/apt-cache.cc cmdline/indexcopy.cc 
test/versiontest.cc 
perl -pi -e 's|fstream.h|fstream|g' apt-pkg/sourcelist.cc cmdline/apt-get.cc
sh patch_flush
for i in `grep -rl '#ifdef __GNUG__' .` ; do perl -pi -e 's/#ifdef __GNUG__/#if 
defined(__GNUG__)  !defined(__APPLE_CC__)/' $i; done
echo x86_64\tx86_64  
/sw2/src/fink.build/apt-0.5.4-1061/apt-0.5.4/buildlib/archtable
./configure --prefix=/sw2 --host=x86_64-apple-darwin`uname -r|cut -f1 -d.`
creating cache ./config.cache
checking host system type... x86_64-apple-darwin13
checking target system type... x86_64-apple-darwin13
checking build system type... x86_64-apple-darwin13
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... no
checking for POSIXized ISC... no
checking for c++... c++
checking whether the C++ compiler (c++ -O2 -DEMULATE_MMAP -D__USE_MISC 
-fconstant-cfstrings -DHAVE_SOCKLEN_T=1 ) works... yes
checking whether the C++ compiler (c++ -O2 -DEMULATE_MMAP -D__USE_MISC 
-fconstant-cfstrings -DHAVE_SOCKLEN_T=1 ) is a cross-compiler... no
checking whether we are using GNU C++... yes
checking whether c++ accepts -g... no
checking how to run the C preprocessor... /lib/cpp
checking for ranlib... ranlib
checking for ar... ar
checking for library containing gethostbyname... none required
checking for library containing connect... none required
checking for db2/db.h... no
checking system architecture... x86_64
checking system OS... darwin
checking for C99 integer types... yes
checking for statvfs... yes
checking whether byte ordering is bigendian... no
checking for missing socklen_t... missing.
checking for h_errno... configure: error: not found.
### execution of ./configure failed, exit code 1
phase compiling: apt-0.5.4-1061 failed

Before reporting any errors, please run fink selfupdate and try again.
Also try using fink configure to set your maximum build jobs to 1 and
attempt to build the package again.
If you continue to have issues, please check to see if the FAQ on Fink's 
website solves the problem.  If not, ask on one (not both, please) of
these mailing lists:

The Fink Users List fink-us...@lists.sourceforge.net
The Fink Beginners List 

Re: [Fink-devel] fink-0.37.0 fails to build under Mavericks 10.9 with Xcode-6

[John Lillibridge - NOAA Federal]

Thanks Alexander,

Sorry, I missed the memo! Now I see it's indeed at the top of the News section 
on the front page. However, following the source install instructions - they 
still point to 0.37.0. I guess this page needs to be updated to be consistent 
with the latest version:

http://www.finkproject.org/download/srcdist.php

Thanks,
John

On Sep 22, 2014, at 3:37 PM, Alexander Hansen alexanderk.han...@gmail.com 
wrote:

 On 9/22/14, 11:48 AM, John Lillibridge - NOAA Federal wrote:
 Dear Fink Developers,
 
 Last week Apple made Xcode-6 the default Developer environment under 
 Mavericks 10.9.5. I wanted to alert you that a fresh Fink install via 
 ./bootstrap now fails under both the Xcode.app and the CommandLineTools. 
 It breaks when building the apt package:
 
 env LANG=C LC_ALL=C /sw2/bin/tar  --no-same-owner --no-same-permissions -xf 
 /sw2/src/apt_0.5.4.tar.gz
 [ -r /sw2/fink/dists/stable/main/finkinfo/base/apt.patch ]
 sed -e 's|@PREFIX@|/sw2|g' -e 's|@DIST@|10.3|g'  
 /sw2/fink/dists/stable/main/finkinfo/base/apt.patch | patch -p1
 patching file apt-inst/deb/dpkgdb.cc
 patching file apt-inst/makefile
 patching file apt-pkg/contrib/mmap.cc
 patching file apt-pkg/contrib/mmap.h
 patching file apt-pkg/deb/debindexfile.cc
 patching file apt-pkg/deb/deblistparser.cc
 patching file apt-pkg/deb/debsystem.cc
 patching file apt-pkg/deb/debsystem.h
 patching file apt-pkg/deb/debversion.cc
 patching file apt-pkg/init.cc
 patching file apt-pkg/pkgcachegen.cc
 patching file apt-pkg/pkgcachegen.h
 patching file apt-pkg/policy.cc
 patching file apt-pkg/tagfile.cc
 patching file apt-pkg/tagfile.h
 patching file buildlib/environment.mak.in
 patching file buildlib/library.mak
 patching file buildlib/ostable
 patching file cmdline/apt-cache.cc
 patching file cmdline/apt-get.cc
 patching file cmdline/apt-sortpkgs.cc
 patching file configure
 patching file configure.in
 patching file doc/apt-cache.8
 patching file doc/apt-cdrom.8
 patching file doc/apt-config.8
 patching file doc/apt-get.8
 patching file doc/apt_preferences.5
 patching file doc/sources.list.5
 patching file dselect/install
 patching file dselect/setup
 patching file dselect/update
 patching file methods/connect.cc
 patching file methods/ftp.cc
 patching file methods/rfc2553emu.h
 patching file patch_flush
 patching file apt-inst/contrib/extracttar.cc
 patching file apt-pkg/contrib/system.h
 patching file apt-inst/extract.cc
 patching file apt-inst/deb/dpkgdb.cc
 patching file apt-pkg/algorithms.cc
 patching file apt-pkg/init.cc
 patching file apt-pkg/deb/debsystem.cc
 patching file apt-pkg/contrib/cdromutl.cc
 patching file cmdline/apt-cache.cc
 patching file cmdline/apt-config.cc
 patching file cmdline/apt-extracttemplates.cc
 patching file cmdline/apt-sortpkgs.cc
 patching file apt-inst/contrib/extracttar.cc
 patching file apt-pkg/deb/debsystem.h
 patching file apt-pkg/pkgsystem.h
 perl -pi -e 's|vector.h|vector|g' apt-pkg/pkgsystem.h 
 include/apt-pkg/pkgsystem.h
 Can't open include/apt-pkg/pkgsystem.h: No such file or directory,  line 
 97.
 perl -pi -e 's|iostream.h|iostream|g' apt-inst/contrib/extracttar.cc 
 apt-inst/deb/dpkgdb.cc apt-inst/extract.cc apt-pkg/algorithms.cc 
 apt-pkg/contrib/error.cc cmdline/apt-cache.cc cmdline/indexcopy.cc 
 test/versiontest.cc
 perl -pi -e 's|fstream.h|fstream|g' apt-pkg/sourcelist.cc cmdline/apt-get.cc
 sh patch_flush
 for i in `grep -rl '#ifdef __GNUG__' .` ; do perl -pi -e 's/#ifdef 
 __GNUG__/#if defined(__GNUG__)  !defined(__APPLE_CC__)/' $i; done
 echo x86_64\tx86_64  
 /sw2/src/fink.build/apt-0.5.4-1061/apt-0.5.4/buildlib/archtable
 ./configure --prefix=/sw2 --host=x86_64-apple-darwin`uname -r|cut -f1 -d.`
 creating cache ./config.cache
 checking host system type... x86_64-apple-darwin13
 checking target system type... x86_64-apple-darwin13
 checking build system type... x86_64-apple-darwin13
 checking for gcc... gcc
 checking whether the C compiler (gcc  ) works... yes
 checking whether the C compiler (gcc  ) is a cross-compiler... no
 checking whether we are using GNU C... yes
 checking whether gcc accepts -g... no
 checking for POSIXized ISC... no
 checking for c++... c++
 checking whether the C++ compiler (c++ -O2 -DEMULATE_MMAP -D__USE_MISC 
 -fconstant-cfstrings -DHAVE_SOCKLEN_T=1 ) works... yes
 checking whether the C++ compiler (c++ -O2 -DEMULATE_MMAP -D__USE_MISC 
 -fconstant-cfstrings -DHAVE_SOCKLEN_T=1 ) is a cross-compiler... no
 checking whether we are using GNU C++... yes
 checking whether c++ accepts -g... no
 checking how to run the C preprocessor... /lib/cpp
 checking for ranlib... ranlib
 checking for ar... ar
 checking for library containing gethostbyname... none required
 checking for library containing connect... none required
 checking for db2/db.h... no
 checking system architecture... x86_64
 checking system OS... darwin
 checking for C99 integer types... yes
 checking for statvfs... yes
 checking whether byte ordering is bigendian... no
 checking for missing socklen_t

[Fink-devel] Yosemite - cpan-meta-pm5162

[John Lillibridge - NOAA Federal]

Hi Jacques,

I ran into similar problem with a few .info files when trying to resolve 
dependencies under Yosemite. I was able to workaround this by changing line 4 
of perl5162.info from

Distribution: 10.7, 10.8

to

Distribution: 10.7, 10.8, 10.9, 10.10

Hope that helps,
John
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Re: [Fink-devel] clang34/llvm34 built on Yosemite Beta

[John Lillibridge - NOAA Federal]

Hi David,

I think I've uncovered the source of confusion. If you have the full XCode 
application installed then the headers are buried inside the app under 
lib/c++/v1; if you have only the CommandLineTools installed, then the headers 
are under include/c++/v1. So checking based on $darwin_vers is a BAD idea. It 
should be checking where the headers are coming from, or perhaps best just to 
try both if one fails...

Under 10.9 Mavericks, it compiled fine using lib/c++/v1 ($darwin_vers between 
11 and 14). I then removed XCode.app, so that only the CommandLine tools were 
available. The build failed because the headers were under include 
(specifically /Library/Developer/CommandLineTools/usr/include/c++/v1).

Let me know how you'd like to sort this out in llvm34.info.

Thanks,
John

On Aug 29, 2014, at 2:16 PM, David Fang f...@csl.cornell.edu wrote:

 Hi John,
 
 1) change line 131 of llvm34.info from
 if test $darwin_vers -ge 11
 to
 if test $darwin_vers -ge 11 -a $darwin_vers -lt 14
 
 Does that mean that the libc++ headers are once again in /usr/include?
 Or did you sudo add a symlink to make it work?
 Is there any harm in keeping that section on darwin14/Xcode-future?
 It is intended to work robustly for future Xcodes.
 
 Sorry for the slow reply: apparently in Xcode-6 the c++/v1 directory is once 
 again under include vs. lib,
 so the old behavior from darwin-10 (OS-X 10.6 I guess) works for Yosemite 
 10.10. I checked that this
 modification didn't break anything under darwin-13 Mavericks 10.9, so I 
 believe this will work.
 
 Thanks for the confirmation.  Though I have to ask whether checking for 
 darwin_vers is really the best way to select the behavior of searching for 
 C++ system headers. Are the C++ headers tied more to the version of Xcode or 
 the OS version?
 If indeed the former is true, what's a good way to get the xcode version from 
 the command-line?  Currently the packaging specifies a minimum Xcode version 
 of 4.6, I'd like to keep that as loose as possible.
 
 My packaging concerns:
 And what can one expect if the user switches versions after llvm34 is 
 installed?  I've built llvm34 fairly free-standing in that the system header 
 path should only matter in stage 1 of the bootstrap, but I'm making a huge 
 assumption that the same paths don't wind up somewhere in the C++ driver 
 code.  This just requires investigation on my part.
 
 My hope is that C++ headers are part of the OS, and not the range of versions 
 of Xcode that a given OS version supports.
 Can anyone comment?
 
 David

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[Fink-devel] clang34/llvm34 built on Yosemite Beta

[John Lillibridge - NOAA Federal]

Dear Fink Developers,

I've been working with David Fang to get the clang34/llvm34 compiler suite to 
build under Yosemite Public Beta. Thanks to a recent patch by Jack Howarth 
(languages/llvm34-openmp-cmake.patch; 2014-08-15) these large packages now 
build, once a couple of workarounds are put in place:

1) change line 131 of llvm34.info from

   if test $darwin_vers -ge 11

   to

   if test $darwin_vers -ge 11 -a $darwin_vers -lt 14

2) and similar to the problem that gcc48/49 had (understanding how to parse 
OS-X version 10.10.x) there is a problem in 
cmake-3.0/Modules/Platform/Darwin.cmake;
   for the moment I hardwired a fix so the build would succeed - change lines 
204-216 to:

# Make sure the combination of SDK and Deployment Target are allowed
if(CMAKE_OSX_DEPLOYMENT_TARGET)
 if(${_CMAKE_OSX_SYSROOT_PATH} MATCHES 
^.*/MacOSX([0-9]+\\.[0-9]+)[^/]*\\.sdk)
   set(_sdk_ver ${CMAKE_MATCH_1})
 elseif(${_CMAKE_OSX_SYSROOT_ORIG} MATCHES ^macosx([0-9]+\\.[0-9]+)$)
   set(_sdk_ver ${CMAKE_MATCH_1})
 else()
   set(CMAKE_OSX_SYSROOT /)
   set(_sdk_ver 10.10)
#   message(FATAL_ERROR
# CMAKE_OSX_DEPLOYMENT_TARGET is '${CMAKE_OSX_DEPLOYMENT_TARGET}' 
# but CMAKE_OSX_SYSROOT:\n \${_CMAKE_OSX_SYSROOT_ORIG}\\n
# is not set to a MacOSX SDK with a recognized version.  
# Either set CMAKE_OSX_SYSROOT to a valid SDK or set 
# CMAKE_OSX_DEPLOYMENT_TARGET to empty.)

With Jack/David's patch and these two tweaks clang34 and llvm34 built (after a 
long multi-stage compilation). The change to llvm34.info is backwards 
compatible with Mavericks and earlier; clearly the cmake-3.0 package needs to 
be updated to parse 10.10 properly vs. the hardwired hack I applied...

Cheers,
John
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Re: [Fink-devel] Yosemite (Alexander Hansen) - (some) successbuilding Fink under 10.10 Yosemite

[John Lillibridge - NOAA Federal]

Thanks Daniel,

Hopefully this new version of openSSL works better. However, I have seen 
pod2man issues before, and in the interest of making progress compiling 
packages without being held up by the man pages I worked around the problem by 
linking /usr/bin/pod2man5.16 - pod2man. There is definitely different behavior 
of pod2man in the perl5.18 version that ships with Yosemite 10.10.

After making that change I made a lot of progress compiling packages under 
Yosemite. In a few cases I had to explicitly add a 10.10 Distribution line to 
the .info files to satisfy missing dependencies. Packages that have required 
this so far:

devel/help2man-perl.info
languages/perl5162.info
net/libcurl4.info

I'm sure there will be others...

At this point I've had a lot of success building packages, but I did run into 
compilation failures with two high-profile packages, upon which gmt5 was 
dependent:

gmp5
gcc48

In this case I installed the 10.9 Mavericks version of the .deb file using 
'dpkg -i' in order to continue moving forward. I need to notify these package's 
maintainers with the specifics of the failure...

So there is still work to be done, but a lot of packages are compiling without 
difficulty now.

All the best,
John

On Aug 9, 2014, at 4:48 PM, Daniel Macks dma...@netspace.org wrote:

 On Fri, 8 Aug 2014 16:18:57 -0400, John Lillibridge - NOAA Federal 
 john.lillibri...@noaa.gov wrote:
 
 Hi Alexander,
 
 
 Sorry I wasn't more explicit. The failure occurred in the openssl100-dev 
 package that CVS depends upon. I had seen similar pod2man errors Expected 
 text after =item, not a number and thought it was a more generic problem. 
 Perhaps a newer version of Perl under Yosemite 10.10? In any case, here are 
 the error messages for the OpenSSL package:
 
 
 created directory `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share'
 created directory 
 `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man'
 created directory 
 `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man1'
 created directory 
 `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man3'
 created directory 
 `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man5'
 created directory 
 `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man7'
 
 installing man1/CA.pl.1
 installing man1/asn1parse.1
 installing man1/ca.1
 installing man1/ciphers.1
 installing man1/cms.1
 
 cms.pod around line 457: Expected text after =item, not a number
 cms.pod around line 461: Expected text after =item, not a number
 cms.pod around line 465: Expected text after =item, not a number
 cms.pod around line 470: Expected text after =item, not a number
 cms.pod around line 474: Expected text after =item, not a number
 
 POD document had syntax errors at /usr/bin/pod2man5.18 line 72. 
 make: *** [install_docs] Error 255
 
 ### execution of /tmp/fink.u2mYI failed, exit code 2
 ### execution of /tmp/fink.mdZVk failed, exit code 2
 
 Removing runtime build-lock... Removing build-lock package... 
 /sw/bin/dpkg-lockwait -r fink-buildlock-openssl100-dev-1.0.1e-3
 
 Fink has openssl much newer than 1.0.1e for a while now in the standard 
 package dist, but the bootstrap set is lagging. By eye, the 1.0.1h currently 
 in the dist has changes in those vicinity to fix that sort of problem. I just 
 sync'ed that into the boostrap set in master. Someone please test on 10.10 
 and sync to HalfDome if it's okay. 
 dan
 
 --
 Daniel Macks
 dma...@netspace.org

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Re: [Fink-devel] Yosemite (Alexander Hansen) - (some) success building Fink under 10.10 Yosemite

[John Lillibridge - NOAA Federal]

Dear Alexander  Fink developers,

I wanted to share my experience based on your advice below, to build Fink under 
Yosemite 10.10 (public beta) from https://github.com/fink/fink/tree/HalfDome;.

After installing the XCode 6.0 command line tools, XQuartz, and Java on my 
10.10 test system, I downloaded the HalfDome branch of Fink, and simply ran 
./bootstrap. To my pleasant surprise it completed without error, and I have a 
Yosemite fink distribution based on 0.37.99.git.

I then tried to change the selfupdate method to CVS, which required 'fink 
install cvs'. This failed with a 'pod2man' error that I had seen earlier when 
trying to get Fink to build under 10.10:

cms.pod around line 457: Expected text after =item, not a number
cms.pod around line 461: Expected text after =item, not a number
cms.pod around line 465: Expected text after =item, not a number
cms.pod around line 470: Expected text after =item, not a number
cms.pod around line 474: Expected text after =item, not a number
POD document had syntax errors at /usr/bin/pod2man5.18 line 72.
make: *** [install_docs] Error 255

I wanted to report this problem since it stands in the way of adding additional 
packages to 10.10 when the creation of a man page fails...

Thanks for pointing me to the HalfDome branch, as my attempts to build by 
tweaking the master branch had only been partially successful. I HAD seend this 
pod2man error during that process, but it was avoided in the bootstrap build in 
the HalfDome branch.

All the best,
John Lillibridge

On Aug 8, 2014, at 7:37 AM, fink-devel-requ...@lists.sourceforge.net wrote:

 Date: Fri, 08 Aug 2014 04:37:21 -0700
 From: Alexander Hansen alexanderk.han...@gmail.com
 Subject: Re: [Fink-devel] Yosemite
 To: Jacques Bloch jacques.bl...@ur.de
 Cc: Fink Developers Mailing List fink-devel@lists.sourceforge.net
 Message-ID: 53e4b671.7040...@gmail.com
 Content-Type: text/plain; charset=windows-1252; format=flowed
 
 On 8/8/14, 12:50 AM, Jacques Bloch wrote:
 
 Dear Alexander,
 
 I moved to Yosemite and can no longer use fink, as it does not support
 OSX 10.10. Following something that I found on a fink-forum  I added the
 following lineIn the file /sw/lib/perl5/Fink/Engine.pm:
 $valid_upgrade = 1 if ($osversion eq 10.10 and $distribution eq 10.9);
 
 However, when I now do fink selfupdate I get the error message:
 /could not determine XFree86 version number
 /usr/bin/rsync -az -q
 rsync://distfiles.master.finkmirrors.net/finkinfo//TIMESTAMP
 /sw/fink/TIMESTAMP.tmp
 I will now run the rsync command to retrieve the latest package
 descriptions.
 /usr/bin/rsync -rtz --delete-after --delete -q   --include='10.10/'
 --include='10.10/stable/' --include='10.10/stable/main/'
 --include='10.10/stable/main/finkinfo/'
 --include='10.10/stable/main/finkinfo/*/'
 --include='10.10/stable/main/finkinfo/*'
 --include='10.10/stable/main/finkinfo/**/*' --include='VERSION'
 --include='DISTRIBUTION' --include='README' --exclude='**'
 'rsync://distfiles.master.finkmirrors.net/finkinfo' '/sw/fink/'
 WARNING: Not saving timestamp of selfupdate because could not write
 /sw/fink/10.10/VERSION.selfupdate.tmp: No such file or directory
 Scanning package description files
 Failed: not a reference at /sw/lib/perl5/Fink/Services.pm line 1885./
 
 Moreover when starting the fink command I always get a message that
 Xquartz cannot be opened because X11 us not installed, even though other
 programs can use Xquartz without any problem.
 
 I also tried ?fink reinstall fink? and get the error message:
 /Scanning package description files/
 /not a reference at /sw/lib/perl5/Fink/Services.pm line 1885./
 
 Do you have any idea how to resolve the problem?
 
 Thanks,
 Jacques
 
 cc-ing the fink-devel mailing list since Yosemite is in public beta.
 
 Please don't contact me personally about things like this.  That is why 
 the Fink project has mailing lists.  I'm not personal unpaid technical 
 support.
 
 The X11 issues are possibly due to your not having the /usr/X11R6 - 
 /usr/X11 and /usr/X11/ - /opt/X11 convenience symlinks.   Do you have 
 those?
 
 Your rsync command isn't working because we have not created a 10.10 
 directory.  And we may well not do that.
 
 You _might_ be able to fix fink in place if you download the Yosemite 
 development branch:
 
 https://github.com/fink/fink/tree/HalfDome
 
 Download the source zip archive, unpack it, then apply the change change 
 to perlmods/Fink/Engine.pm in that source directory, and then use 
 ./inject.pl to upgrade.  I honestly don't know how well that will work, 
 since I haven't had time to work with Fink on Yosemite.
 -- 
 Alexander Hansen, Ph.D.

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Re: [Fink-devel] Yosemite (Alexander Hansen) - (some) success building Fink under 10.10 Yosemite

[John Lillibridge - NOAA Federal]

Hi Alexander,

Sorry I wasn't more explicit. The failure occurred in the openssl100-dev 
package that CVS depends upon. I had seen similar pod2man errors Expected text 
after =item, not a number and thought it was a more generic problem. Perhaps a 
newer version of Perl under Yosemite 10.10? In any case, here are the error 
messages for the OpenSSL package:


created directory `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share'
created directory `/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man'
created directory 
`/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man1'
created directory 
`/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man3'
created directory 
`/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man5'
created directory 
`/sw/src/fink.build/root-openssl100-dev-1.0.1e-3/sw/share/man/man7'

installing man1/CA.pl.1
installing man1/asn1parse.1
installing man1/ca.1
installing man1/ciphers.1
installing man1/cms.1

cms.pod around line 457: Expected text after =item, not a number
cms.pod around line 461: Expected text after =item, not a number
cms.pod around line 465: Expected text after =item, not a number
cms.pod around line 470: Expected text after =item, not a number
cms.pod around line 474: Expected text after =item, not a number

POD document had syntax errors at /usr/bin/pod2man5.18 line 72.

make: *** [install_docs] Error 255

### execution of /tmp/fink.u2mYI failed, exit code 2
### execution of /tmp/fink.mdZVk failed, exit code 2

Removing runtime build-lock...
Removing build-lock package...

/sw/bin/dpkg-lockwait -r fink-buildlock-openssl100-dev-1.0.1e-3

(Reading database ... 4576 files and directories currently installed.)

Removing fink-buildlock-openssl100-dev-1.0.1e-3 ...
Failed: phase installing: openssl100-dev-1.0.1e-3 failed


Hope that helps,
John

On Aug 8, 2014, at 3:57 PM, Alexander Hansen alexanderk.han...@gmail.com 
wrote:

 On 8/8/14, 9:50 AM, John Lillibridge - NOAA Federal wrote:
 
 Dear Alexander  Fink developers,
 
 I wanted to share my experience based on your advice below, to build Fink 
 under Yosemite 10.10 (public beta) from 
 https://github.com/fink/fink/tree/HalfDome;.
 
 After installing the XCode 6.0 command line tools, XQuartz, and Java on my 
 10.10 test system, I downloaded the HalfDome branch of Fink, and simply ran 
 ./bootstrap. To my pleasant surprise it completed without error, and I 
 have a Yosemite fink distribution based on 0.37.99.git.
 
 I then tried to change the selfupdate method to CVS, which required 'fink 
 install cvs'. This failed with a 'pod2man' error that I had seen earlier 
 when trying to get Fink to build under 10.10:
 
 cms.pod around line 457: Expected text after =item, not a number
 cms.pod around line 461: Expected text after =item, not a number
 cms.pod around line 465: Expected text after =item, not a number
 cms.pod around line 470: Expected text after =item, not a number
 cms.pod around line 474: Expected text after =item, not a number
 POD document had syntax errors at /usr/bin/pod2man5.18 line 72.
 make: *** [install_docs] Error 255
 
 I wanted to report this problem since it stands in the way of adding 
 additional packages to 10.10 when the creation of a man page fails...
 
 Thanks for pointing me to the HalfDome branch, as my attempts to build by 
 tweaking the master branch had only been partially successful. I HAD seend 
 this pod2man error during that process, but it was avoided in the bootstrap 
 build in the HalfDome branch.
 
 All the best,
 John Lillibridge
 
 
 I'm not showing anything about cms.pod in the cvs build.  What package 
 actually failed?  We'll want to apply the fix in the right place.
 
 -- 
 Alexander Hansen, Ph.D.
 Fink User Liaison
 My package updates: http://finkakh.wordpress.com/

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