gfortran transition

p4fftwgel: no rdepends, no binaries, source should be removed following debian.

k6fftwgel should get removed, following unstable (no binaries present, no rdepends)

k7fftwgel should probably get removed as well (and I'm stupid with the last two comments, as I was checking rdepends/binaries on amd64 and these are i386 only).

ok, after going through the wiki list, it looks like my heuristic to determine the number of transitioned/untransitioned packages couldn't have been worse. Looks like the vast majority of hardy packages is *not* yet transitioned.

Currently, I have quite some doubts about starting this big thing so late in the cycle, and I have the slight feeling that it might be better to undo any transitioned packages.

However I'm also too tired now to think straight. What do you think?

With 2/3 people working on this we should be able to finish it in a reasonable time. I can volunteer if we decide to go on with this.

Being more awake now, I also think we're able to finish it, and should do so (and since weekend is coming I might have some time to join in as well).

Furthermore, I guess it would also make sense to stay as close as possible to unstable (there are quite some new upstream versions among the transitioned packages in unstable), so a general FFe for the affected packages might make sense, what do you think?

How many packages are we talking about?

all those listed here need to be transitioned. Hopefully, I didn't forget any.

I think there are few others:

scilab
ratfor
cfortran

They are apparently not in the Debian list even though they show up as rdepends of g77.

From Debichem:

psicode transitioned at 3.3.0-1 (needs FFe)
mpqc transitioned at 2.3.1-3 (no FFe needed)
mopac7 transitioned at 1.13-2 (no FFe needed)
libghemical transitioned at 2.96-2 (no FFe needed)
ghemical transitioned at 2.95-3 (no FFe needed)
not sure about gromacs yet

I'm inclined to go forwared and would accept a blanket FFe if a new feature update is needed for the transition.

Should I assume we are cleared to go? Unless somebody objects I will start working on this asap.

green lights, go go go :)

Needs arpack first (bug #202309) and waiting for the Debian package which is in NEW.

Needs lam first.

This includes a blanked FFe for this transition
(
[21:29:19] <ScottK2> sistpoty: I vote for blanket FFe for version increases needed for the transition.
[21:29:45] <sistpoty> ScottK2: so do I
)

Stefan et al.,

what about all the packages which depends on lam4c2 which we are going to replace with liblam4?

This is the current list of rdepends:

clustalw-mpi (not part of the transition, not yet changed with new lib dependency in Debian)
xmpi (not part of the transition, not yet changed with new lib dependency in Debian)
tree-ppuzzle (not part of the transition, not yet changed with new lib dependency in Debian)
tessa-mpi (not part of the transition, not yet changed with new lib dependency in Debian)
scalapack1-lam (part of the transition)
scalapack-lam-test (part of the transition)
netpipe-lam (not part of the transition, not yet changed with new lib dependency in Debian)
libhdf5-lam-1.6.5-0 (not part of the transition, not yet changed with new lib dependency in Debian)
libalps-mpi1 (not part of the transition, not yet changed with new lib dependency in Debian)
lampython (not part of the transition, not yet changed with new lib dependency in Debian)
lam4-dev (part of the transition)
lam-runtime (part of the transition)
gromacs-openmpi (part of the transition)
gromacs-lam (part of the transition)
blacs1-lam (part of the transition)
blacs-lam-test (part of the transition)

Am I wrong, or those not part of this transition need all to be patched to depend on liblam4 instead of lam4c2?

Cesare, thanks for noting this.

As the build-dependency (liblam4-dev) didn't need to change in the transition, I assume that in most cases a mere rebuild would suffice to pick up the new dependency.
(some are already rebuilt in unstable, e.g. xmpi via binNMUs/binary only uploads).

Stefan, thanks for confirming.
I have opened bug #202337 on this (I assumed they were not properly part of the gfortran transition).
Once lam is in the repo I will check if a rebuild will suffice.

I understand to smooth the transition we will keep refblas3/atlas3/lapack3 and the new refblas/atlas/lapack in hardy.
I assume for intrepid we will remove refblas3/atlas3/lapack3 and therefore we should also check packages which build-depends or depends on refblas3, atlas3 and lapack3?
For instance on atlas3-base there are 5 packages which are not covered by this transition (theseus, shogun, illuminator, apbs and libitpp which we just did) and a couple more build-depends on atlas3-base-dev (hypre, cgal) and lapack3-base-dev (cgal).
I think hypre and cgal should therefore be part of this transition too.

cernlib ftbfs since it requires gfortran >= 4:4.3 (provided by gcc-defaults 1.63) while we only have 4:4.2.3-1ubuntu3 in Ubuntu (provided by gcc-defaults 1.62). Since syncing the new gcc-defaults from unstable I believe is out of the question I have changed build-depends to gfortran >= 4:4.2.3.
The build seems to be sane (build log attached, I'd appreciate it if someone else wants to check it).
Any better solution?

But perhaps more important, since the debian transition is based on gfortran 4.3 (which we don't have in hardy), are we on the right track!?

Cesare, thanks for the additional info!

about gfortran 4.3 vs. 4.2: I'm no gfortran expert. However doko wrote on irc, said "it should build with gfortran" (https://bugs.launchpad.net/ubuntu/+source/libitpp/+bug/199190/comments/9), so I very much guess we're on the right track.

Bug #202817 opened for packages affected by the mpich gfortran transition (not directly part of this list).

This bug was fixed in the package petsc - 2.3.3-6ubuntu1

---------------
petsc (2.3.3-6ubuntu1) hardy; urgency=low

  * Sync from Debian unstable.
    - Now builds with gfortran. (LP: #201962)
  * Drop spooles support, as we don't have it in Hardy.
  * Don't attempt to use -Wno-long-double, as that makes some of configure
    FTBFS for no particularly good reason. (LP: #199256)
  * Mangle Maintainer field.

petsc (2.3.3-6) unstable; urgency=low

  * Rebuild for unstable.

petsc (2.3.3-5) experimental; urgency=low

  * Rebuild against, and depend on, new suitesparse with proper shared
    library versioning.

petsc (2.3.3-4) experimental; urgency=low

  * Build-depends on gfortran-transitioned BLAS, LAPACK and suitesparse
    (closes: #463825).
  * Adds spooles support (closes: #464723).

 -- William Grant <email address hidden> Thu, 13 Mar 2008 08:13:23 +1100

Dear Friends,

I appreciate that you guys are doing a superb job with the transition. I have been involved with the transition on Debian side, and would love to hear from you guys if you foresee a problem or find a more elegant solution adopted for a package.

Thanks.

Heya Kumar,

thanks for popping up and for all your work on this.

Please sync from Debian. This is fixed in 4.1.2-4

Hello,

Le mercredi 19 mars 2008 à 13:35 +0000, William Grant a écrit :
> ** Changed in: scilab (Ubuntu)
> Status: In Progress => New
Why did you switched it to new ? :)

S

Sylvestre Ledru wrote:
> [snip]
> Why did you switched it to new ? :)

Because nobody is working on it at this moment.

--
William Grant

This bug was fixed in the package wsjt - 5.9.7.r383-1.1ubuntu1

---------------
wsjt (5.9.7.r383-1.1ubuntu1) hardy; urgency=low

  * Sync from Debian unstable (LP: #201962).
    - Remaining Ubuntu changes have been implemented in Debian.
  * debian/rules: unexport LDFLAGS to avoid FTBFS with new dpkg-buildpackage.
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

wsjt (5.9.7.r383-1.1) unstable; urgency=low

  * Non-maintainer upload.
  * transition to gfortran, closes: 469658
    - Thanks Kumar Appaiah

 -- Cesare Tirabassi <email address hidden> Thu, 20 Mar 2008 23:50:00 +0100

In principle the version in hardy is already transitioned. However, since there is a new version in unstable which has only bug fixes, I will look into merging that.

This bug was fixed in the package pfstools - 1.6.4-1ubuntu1

---------------
pfstools (1.6.4-1ubuntu1) hardy; urgency=low

  * Merge from Debian unstable (LP: #201962). Remaining Ubuntu changes:
    - octave2.{1,9} -> octave3.0 transition
      + debian/control:
        removed build-dep-conflicts against octave2.9-headers
        changed build-dep from octave2.1 to octave3.0
        changed dep for octave-pfstools binary package to octave3.0
        changed dep for pfstools binary package to octave3.0
      + src/octave/pfsopen.cpp:
        Applied patch from upstream
        Patch taken from:
        http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=458131
    - debian/rules:
      + change chmod 644 debian/tmp/usr/share/octave/site/api-v13/m/pfstools/*
        to chmod 644 debian/tmp/$(MDIR)/pfstools/* to avoid FTBFS
    - Set maintainer to MOTU.
  * octave2.{1,9} -> octave3.0 transition
    - src/octave/pfsoctavelum & src/octave/pfsoctavergb:
      + Applied patch from upstream
        Patch taken from:
        http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=458131

pfstools (1.6.4-1) unstable; urgency=low

  * New upstream release.
    - Added missing includes required by gcc-4.3 (Closes: #455648).
  * Downgraded pfstool's requirement on octave{,pfstools} to a recommendation
    (Closes: #445909).
  * Added new binary packages for pfsglview and pfsview to prevent users from
    having to install OpenGL/GLUT and Qt.
  * Removed a bashism from debian/rules (Closes: #456508).
  * Renamed "XS-Vcs-*" fields to Vcs-* and moved "Homepage" field from the
    package description to the source stanza:
    - Added versioned build dependency on dpkg-dev (>= 1.14.6).
  * Updated to standards version 3.7.3 (no changes).
  * Changed maintainer to pkg-phototools team:
    - Moved myself to uploaders.
  * Added a watch file, thanks to Cyril Brulebois.

 -- Cesare Tirabassi <email address hidden> Fri, 21 Mar 2008 11:52:39 +0100

This bug was fixed in the package pdl - 1:2.4.3-6ubuntu1

---------------
pdl (1:2.4.3-6ubuntu1) hardy; urgency=low

  * Merge from Debian unstable (LP: #201962). Remaining Ubuntu changes:
    - Enabled NAN support.
    - Munge Maintainer field as per spec.

pdl (1:2.4.3-6) unstable; urgency=low

  [ Rafael Laboissiere ]
  * Switch from g77 to gfortran

  [ Henning Glawe ]
  * apply Rafael's patch (closes: #468637)

 -- Cesare Tirabassi <email address hidden> Fri, 21 Mar 2008 12:48:31 +0100

This bug was fixed in the package cernlib - 2006.dfsg.2-11ubuntu1

---------------
cernlib (2006.dfsg.2-11ubuntu1) hardy; urgency=low

  * Sync from Debian unstable (LP: #201962):
    - Desktop file dropped in agreement with Debian (see #471039)
  * debian/control and debian/control.d/0base.control:
    - Change Build-Depends on gfortran to (>= 4:4.2.3) to avoid ftbfs
      Once gfortran (>= 4:4.3) is available in Ubuntu this can be dropped.
  * Modify Maintainer value to match Debian-Maintainer-Field Spec

cernlib (2006.dfsg.2-11) unstable; urgency=low

  * Patch 102: Add kernlib/kerngen/tcgen/tlsc.F to the list of files not
    to compile optimized, due to mis-compiled code at -O2 on ia64 (bug filed
    against gfortran-4.3 as #466948). Should fix FTBFS on ia64.
  * New patch 217: Force mathlib/gen test program "gent" to exit non-zero
    if any individual test fails, so I don't have to inspect test suite
    output manually for test failures in buildd logs.

cernlib (2006.dfsg.2-10) unstable; urgency=low

  * Patch 304: Adjustments to compiler flags to solve various problems:
    - Do not build with -funroll-loops, in order to work around compiler
      bugs: ICE on arm at kernlib/kerngen/tcgen/ranecu.F (filed as #466791)
      and bad code on ia64 at mathlib/gen/tests/c201s.F (filed as #466911).
    - Build with -fno-range-check option to gfortran to ignore arithmetic
      overflow compiler errors, as g77 does by default (closes: #466834),
      and therefore...
  * Patch 321: Revert work-around for that purpose from release -8.

cernlib (2006.dfsg.2-9) unstable; urgency=low

  * Upload gfortran-transitioned CERNLIB to unstable.

cernlib (2006.dfsg.2-8) experimental; urgency=low

  * Patch 321: In kernlib/kerngen/tcgens/lnxppcgs/{ubunch.F,ublow.F}, work
    around gfortran overflow error in initializing 4-byte integer with
    "data mask1/x'ff000000'/" statement. N.B. these files are only compiled
    by big-endian architectures, so this change is irrelevant to i386, etc.
  * debian/debhelper/cernlib-base.README.debian: Update to mention the new
    montecarlo-data binary package and the soversion bump for libisajet.
  * debian/control.d/libmathlib2-dev.control: Revert back to depending on
    libblas-dev and liblapack-dev by default, as the libatlas-base-dev
    package (and friends) does not ship liblapack.so and libblas.so symlinks
    where the compiler and linker will see them automatically.
  * debian/control.d/libmathlib2-dev.control: Also Conflict against
    g77-based libdevel packages refblas3-dev and lapack3-dev.
  * debian/NEWS: s/unstable/experimental/ in 2006.dfsg.2-7 NEWS entry to fix
    newly introduced lintian warning.

cernlib (2006.dfsg.2-7) experimental; urgency=low

  * Tweak dependencies and build-deps to use new libblas-dev and
    liblapack-dev packages; also gfortran 4.3. No longer force installation
    of BLAS and LAPACK reference implementations instead of ATLAS at
    install time, only at build time.

  * Patch updates to fix new issues that arose with gfortran 4.3:
    - Patch 216: Fix compiler error "Result of LGAMMA overflows its kind" on
      mathlib GEN test 310 by using the CERNLIB log-gamma funct...

unasssigning myself from atlas3, I actually am working on atlas right now, which FTBFS on i386 (and hence is missing the arch:all package I'm looking for... damn *g*).

This bug was fixed in the package pysparse - 1.0.1-4ubuntu1

---------------
pysparse (1.0.1-4ubuntu1) hardy; urgency=low

  * Sync from Debian unstable (LP: #201962).
  * debian/rules:
    - change rmdir to rm -rf to fix FTBFS.
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

pysparse (1.0.1-4) unstable; urgency=low

  * New upload for unstable.
  * Removed a few unnecessary library linkages.

pysparse (1.0.1-3) experimental; urgency=low

  * Rebuild against, and depend on, suitesparse with proper shared libs.

pysparse (1.0.1-2) experimental; urgency=low

  * Changed build-depends to gfortran and its BLAS and LAPACK libs
    (closes: #464973).
  * Added build-depends on suitesparse and superlu, and changed build system to
    use installed umfpack and superlu instead of included source.
  * Doing this required forward-porting to superlu 3.0.

 -- Cesare Tirabassi <email address hidden> Sat, 22 Mar 2008 15:34:17 +0100

Anyhow, I think atlas3 is fixed already.

This bug was fixed in the package saods9 - 4.0b7-1.5ubuntu2

---------------
saods9 (4.0b7-1.5ubuntu2) hardy; urgency=low

  * Transition to gfortran (LP: #201962):
    - debian/control:
      + change Build-Depends from g77 to gfortran
    - debian/patches/02_fix_gfortran.dpatch:
      + fix Makefile(s) to work with gfortran
      + fix the f77.h header file name mangling to work with gfortran
  * Add icon to .desktop file

 -- Cesare Tirabassi <email address hidden> Sat, 22 Mar 2008 15:56:03 +0100

sivp may need rebuilding once scilab is available.

Hm... I have no clue at all what the real problem is with the atlas build failure on i386: https://launchpad.net/ubuntu/+source/atlas/3.6.0-21.1ubuntu2/+build/510163

I'll upload a package now (once I've test-build on i386 and amd64), which will simply not bail out, if this very test fails. Of course that's a bad move, and I'm very welcome for anyone to look for the real reason of the failure (heck, I couldn't even find out, what of atlas is getting tested in this very test).

Side note: if s.th. FTBFS on i386 build-depending on atlas binaries, I'll try to hide :P

I believe lapack3 is also already fixed.

Package synced from Debian :)

It builds and runs fine.

abinit (5.3.4.dfsg-3) unstable; urgency=low

  * Add XS-DM-Upload-Allowed: yes
   * shifted Build-Depends to use the new gfortran based Lapack and Blas
     packages in order to phase out packages dependent on the old g2c/g77
     (Closes: #463942)
   * Homepage field converted to the new style
   * Standards version updated to 3.7.3
   * Old FSF address fixed in debian/copyright
   * abinit-doc moved to the section doc.
   * doc/Makefile.in patch moved to debian/patches managed by quilt

 -- Ondrej Certik <email address hidden> Tue, 05 Feb 2008 14:09:20 +0100

arpack (2.1+parpack96-5) unstable; urgency=low

  [ Daniel Leidert ]
   * debian/arpack2-dev.doc-base (Section): Fixed accordingly to latest
     doc-base policy.
   * debian/libarpack2-dev.doc-base (Section): Ditto.
   * debian/control (Build-Depends): Use libopenmpi-dev on kfreebsd-i386,
     kfreebsd-amd64 and hurd-i386 too.
   * debian/rules (build/libarpack2): Build and link files in UTIL/ to avoid
     missing symbols (closes: #470415). Add -lgfortran to resolve gfortran
     symbols. Link with -lmpi_f77 on libopenmpi enabled architectures. Link
     with -larpack for svout and other functions used in libparapack.
   * debian/patches/no_external_etime.patch: Added.
     - ARPACK/UTIL/second.f, UTIL/second.f: EXTERNAL for etime() is wrong here.
   * debian/patches/series: Adjusted.

  [ Rafael Laboissiere ]
   * Add Daniel Leidert to the list of Uploaders
   * Allow upload by Debian Maintainers

 -- Daniel Leidert (dale) <email address hidden> Tue, 11 Mar 2008 02:49:46 +0100

arpack (2.1+parpack96-4) unstable; urgency=low

  * debian/libarpack2-dev.install: Install doc files in proper directory,
     avoiding conflicts with the libarpack2 package (closes: #469286)

 -- Rafael Laboissiere <email address hidden> Tue, 04 Mar 2008 14:22:55 +0100

arpack (2.1+parpack96-3) unstable; urgency=low

  * debian/rules: Set variables PSRCdir and PUTILdir for the invocation of
     "make clean". We cannot rely on parpack-clean-dirs.patch for doing
     this and the previous version was still causing problems with the
     buildds.

 -- Rafael Laboissiere <email address hidden> Sat, 01 Mar 2008 18:58:19 +0100

arpack (2.1+parpack96-2) unstable; urgency=low

  [ Christophe Prud'homme ]
   * debian/control: fixed liblapack3gf dep (closes: #467576)

  [ Rafael Laboissiere ]
   * debian/dirs: Delete this unnecessary file, avoiding some Lintian warnings
   * debian/control:
     + Add my name to the list of Uploaders
     + Build-depends on libopenmpi-dev only on some selected architectures
       (closes: #468795)
   * debian/rules: Reactivate CDBS' quilt support
   * debian/patches/use-gfortran.patch: New patch for using gfortran
     instead of g77. This patch was integrated in the .diff.gz file of the
     previous release, so that Bug#463926 was effectively closed.
   * debian/patches/parpack-clean-dirs.patch: New patch to avoid doing cd
     commands on non-existent directories. This was causing problems with
     the autobuilders (closes: #467327)

 -- Rafael Laboissiere <email address hidden> Sat, 01 Mar 2008 12:22:32 +0100

arpack (2.1+parpack96-1) unstable; urgency=low

  [ Rafael Laboissiere ]

   * debian/control: Added XS-Vcs-Svn and XS-Vcs-Browser fields to the Source
     section

  [Christophe Prud'homme]

   * RiceBSD.*: added license clarification
   * Bug fix: "Wishlist: parpack", thanks to Viral Shah (Closes: #195579).
   * debian/control: use gfortran
   * Bug fix: "arpack -- please Build-Depend on gfortran based lapack and
     blas.", thanks to Kumar Appaiah (Closes: #463926).
   * Bug fix: "libarpack2: symbol duplication with LAPACK", thanks to
     Andreas Kloeckner ...

blacs-pvm (1.1-18) unstable; urgency=low

  * Bumped standards version to 3.7.3
   * debian/compat file was created.
   * Webpage was moved from blacs-pvm's description to control tag.
   * The package is now built using gfortran instead of g77. Thanks to Colin
     Tuckley for proving patches and helping.(Closes: #459589)
   * Depend on the gfortran version of pvm i.e. > 3.4.5-9.

 -- Muammar El Khatib <email address hidden> Wed, 09 Jan 2008 00:00:30 -0430

lush (1.2.1-6+cvs20080204) unstable; urgency=low

  * Fresh CVS snapshot.
   * g77 -> gfortran, lapack3-dev -> liblapack-dev transition (Closes: #463966).
     Thanks Kumar Appaiah.
   * Homepage migrated into header field.
   * Changing versioing scheme to include CVS snapshot date into debian
     revision after + (instead of . which is used for NMUs)
   * Boosted standards to 3.7.3:
    - ${source:Version} instead of ${Source-Version}

 -- Yaroslav Halchenko <email address hidden> Mon, 04 Feb 2008 23:27:34 -0500

blitz++ (1:0.9-7) unstable; urgency=low

  * Added patch to fix FTBFS with GCC 4.3: missing #includes
     (Thanks to "brian m. carlson" <email address hidden>)
     Closes: #455661
   * Added quilt to Build-Depends
   * Standards-Version: 3.7.3 (No changes needed)
   * Homepage tag instead of putting it into long description
   * debian/rules: F77=gfortran; Adjusting Build-Depends to
     accomplish g77 to gfortran transition (Thanks to
     Kumar Appaiah <email address hidden>)
     Closes: #463935
   * libblitz0-dev to section libdevel
   * debian/libblitz-doc.doc-base removed useless whitespace
   * debian/rules: Removed bashism

 -- Andreas Tille <email address hidden> Sun, 17 Feb 2008 21:31:47 +0100

dsdp (5.8-4) unstable; urgency=low

  [ Soeren Sonnenburg ]
   * Adjust Build-Depends for gfortran transition (Closes: #463947)
   * Fix typo in package description (Closes: Bug#464213)
  [ Torsten Werner ]
   * Rename package libdsdp-5.8 to libdsdp-5.8gf.
   * Change Build-Depends: libg2c0-dev to gfortran.
   * Add LAPACKBLAS="-llapack" to make arguments.
   * Add suffix 'gf' to soname.
   * Link shared library with all needed libraries.

 -- Torsten Werner <email address hidden> Fri, 08 Feb 2008 22:14:59 +0100

dsdp (5.8-3) unstable; urgency=low

   * Bump Standards-Version to 3.7.3

 -- Soeren Sonnenburg <email address hidden> Wed, 02 Jan 2008 19:23:31 +0100

fftw (2.1.3-20.1) unstable; urgency=low

  * Non-maintainer Upload.
   * Use/depend on gfortran based Lapack and Blas packages (Closes: #466366).
   * Build with gfortran instead of g77.

 -- Colin Tuckley <email address hidden> Mon, 25 Feb 2008 09:37:07 +0000

mpb (1.4.2-11.1) unstable; urgency=low

  * Non-maintainer upload.
   * Use gfortran, Closes: #468879, #467351
     Thanks Rafael Laboissiere, Kumar Appaiah
   * use binNMU compatigle binary:Version substvar.

 -- Riku Voipio <email address hidden> Sun, 09 Mar 2008 13:21:16 +0200

octaviz (0.4.6+cvs20080113-2) unstable; urgency=low

  * debian/control: Removed Cyril Brulebois from the list of Uploaders, at
     his request
   * debian/control: Force the build-dependency on octave3.0 >= 3.0.0-2,
     ensuring the transition from g77 to gfortran

 -- Rafael Laboissiere <email address hidden> Sun, 24 Feb 2008 10:50:36 +0100

octplot (0.4.0-6) unstable; urgency=low

  * Rebuilt against octave3.0, forcing the build-dependency to be >=
     3.0.0-2, ensuring the transition from g77 to gfortran

 -- Rafael Laboissiere <email address hidden> Sun, 24 Feb 2008 10:36:00 +0100

openmx (3.2.4.dfsg-3) unstable; urgency=low

  * Add XS-DM-Upload-Allowed: yes
   * Use gfortran based Lapack (Closes: #466061)
   * /usr/sbin empty directory removed
   * Homepage moved to the homepage field
   * Standards-Version bumped to 3.7.3
   * Use quilt for patches
   * Vcs-Svn and Vcs-Browser fields added

 -- Ondrej Certik <email address hidden> Sat, 16 Feb 2008 12:30:31 +0100

r-base (2.6.2-2) unstable; urgency=low

  * debian/{rules,control}: Reverting the use of Debian's lapack as we got
     a SVD-related bug report with a day -- thanks, Ben! (Closes: #464833)
      - remove 'liblapack-dev' from Build-Depends
      - call configure with

 -- Dirk Eddelbuettel <email address hidden> Sat, 09 Feb 2008 10:05:24 -0600

r-base (2.6.2-1) unstable; urgency=low

  * New upstream version released this morning
  * debian/control: Added 'liblapack-dev' to Build-Depends: to switch back
     to using Debian's Lapack rather than the version supplied by R.
   * debian/rules: Dito, call configure with '--with-lapack'

 -- Dirk Eddelbuettel <email address hidden> Fri, 08 Feb 2008 09:40:02 -0600

r-base (2.6.1-2) unstable; urgency=low

  * debian/control: Replace Build-Depends: on 'refblas3-dev | atlas3-base-dev'
     with 'libblas-dev' to use the new gfortran-built BLAS libraries. Thanks
     to Riku Voipio for the heads-up and patch. (Closes: #461767)
  * debian/control: Likewise set the Depends: for the quasi-virtual
     r-base-dev on 'libblas-dev' to enfore use of the new BLAS.
  * debian/control: Update Standards-Version: to current value.
  * debian/{r-base-core,r-recommended}.lintian: Add a few silencers for
     the 'package-contains-empty-directory' warnings.

 -- Dirk Eddelbuettel <email address hidden> Sun, 20 Jan 2008 20:24:52 -0600

scilab (4.1.2-4) unstable; urgency=low

    * Replace g77 by gfortran.
    * Improve dependencies on wish and scilab-doc.
    * Drop compatibility with versions prior the Etch release.

 -- Torsten Werner <email address hidden> Sun, 09 Mar 2008 19:37:55 +0100

scilab (4.1.2-3) unstable; urgency=low

    * Add debian/watch.
    * Update Homepage and Vcs headers in debian/control.
    * Change Standards-Version: 3.7.3.
    * Switch to debhelper 5.

 -- Torsten Werner <email address hidden> Sun, 16 Dec 2007 23:03:17 +0100

semidef-oct (1:2003-6) unstable; urgency=low

    [ Thomas Weber ]
    * Switch to Octave 3.0 instead of 2.9
    * Compat level 6 and depend on debhelper >= 6
    * Bumped Standards-Version to 3.7.3 (no changes needed)
    * Added myself to Uploaders
    * Removed Emacs code in debian/changelog

   [ Rafael Laboissiere ]
    * debian/control:
      + Removed Cyril Brulebois from the list of Uploaders at his request
      + Use the Vcs-* headers instead of the deprecated XS-Vcs-* ones
    * debian/copyright: Add more comments about the licensing terms of the
      different parts of the package
    * debian/rules:
      + Add test suite
      + Do not install the sp.m, prompt.m, and run_cmd.m files. The first
        conflicts with sp.oct, while the two others are already in the main
        octave3.0 package (in m/control/util)
    * debian/patches/50_strstream-namespace-std.dpatch: Make the package
      build with GCC 4.3 (closes: #461719)

 -- Rafael Laboissiere <email address hidden> Sat, 23 Feb 2008 15:26:07 +0100

harminv (1.3.1-1.1) unstable; urgency=low

  * Non-maintainer upload.
   * Use gfortran based Lapack and Blas packages (Closes: #463953).

 -- Colin Tuckley <email address hidden> Fri, 22 Feb 2008 15:12:09 +0000

mpich (1.2.7-7.1) unstable; urgency=low

  * Non-maintainer upload.
   * New patch 23 to fix configure's g++ tests to include iostream instead of
     iostream.h. Fixes FTBFS with gcc-4.3. (Closes: #468068)

 -- James Vega <email address hidden> Sun, 09 Mar 2008 00:10:37 -0500

mpich (1.2.7-7) unstable; urgency=low

  * Fixed shared library packages (thanks to Kumar Appaiah) (closes: #465285).

 -- Adam C. Powell, IV <email address hidden> Mon, 11 Feb 2008 18:41:43 -0500

mpich (1.2.7-6) unstable; urgency=low

  * Working gfortran support (thanks to Kumar Appaiah <email address hidden>).
   * This release also includes mpif90 (closes: #195509).
   * Changed shlib package names to gf reflecting the interface change due to
     the g77-gfortran transition.

 -- Adam C. Powell, IV <email address hidden> Fri, 01 Feb 2008 16:06:59 -0500

lam (7.1.2-1.3) unstable; urgency=low

  * Non-maintainer upload.
   * Fix the second argument to main() in the test programs used by configure.
     Fixes FTBFS with gcc-4.3. (Closes: #468065)

 -- James Vega <email address hidden> Sun, 09 Mar 2008 00:13:40 -0500

lam (7.1.2-1.2) unstable; urgency=low

  * Non-maintainer upload.
   * Upload to unstable

 -- Riku Voipio <email address hidden> Sat, 09 Feb 2008 23:04:48 +0200

lam (7.1.2-1.1) experimental; urgency=low

  * Non-maintainer upload.
   * transition to gfortran, closes: #456418
   * rename package for long double transition, closes: #430241
   * remove pre-depends on stone-age dpkg version
   * remove versioned depends on essential package findutils and debianutils
   * Depend on ssh-client instead of ssh, closes: #418988
   * Edit changelog to get rid of lintian warning on long changelog

 -- Riku Voipio <email address hidden> Tue, 29 Jan 2008 22:24:19 +0200

Seems good but I'm waiting for cernlib to be out of the new queue before proceeding:

https://launchpad.net/ubuntu/hardy/+queue?queue_state=0&queue_text=cernlib-base-dev

Since paw is part of the main knot and the shared library package has been renamed, please make also sure that packages that build-depends/depends on it are rebuilt and /or patched once this is in the repo.

Thanks!

Ah of course. sry.
Just saw that you uploaded cernlib on 2008-03-21 so I thought I can post paw debdiff alreaday here.

This bug was fixed in the package paw - 1:2.14.04.dfsg.2-3ubuntu1

---------------
paw (1:2.14.04.dfsg.2-3ubuntu1) hardy; urgency=low

  * Sync from Debian unstable (LP: #201962)
  * debian/control and debian/control.d/0base.control
    - Change Build-Depends on gfortran to (>= 4:4.2.3) to avoid ftbfs
      Once gfortran (>= 4:4.3) is available in Ubuntu this can be dropped.
  * Modify Maintainer value to match Debian-Maintainer-Field Spec

paw (1:2.14.04.dfsg.2-3) unstable; urgency=low

  * Fix unescaped hyphens in paw.1 man page.
  * Remove deprecated Encoding field from Paw++ desktop entry.
  * Upload to unstable.

paw (1:2.14.04.dfsg.2-2) experimental; urgency=low

  * Transition to gfortran:
    - Re-do build dependencies (require minimum of 2006.dfsg.2-7 for CERNLIB
      dependencies and 4.4-10 for cfortran) and append "-gfortran" suffix to
      runtime library package names. Explicitly Build-Depend on new
      libblas-dev and liblapack-dev packages and gfortran (>= 4:4.3).
    - Patch 320: Add -DgFortran to the build flags in a few additional places.
    - Depend on gfortran rather than g77 as FORTRAN compiler (closes: #440755).
    - Update README.64-bit and other files to mention gfortran in place of g77.

  * Bump Standards-Version to 3.7.3:
    - Menu policy update: Apps/Science -> Applications/Science/Data Analysis.

  * Miscellaneous small changes:
    - Remove mention of no-longer-used "keepbuild" $DEB_BUILD_OPTION in
      README.source.
    - Make sure all patches have a "## DP:" comment header.
    - Add Homepage field in control file.
    - Mention the (somewhat ambiguous) switch to GPL v3 in copyright file.
    - Uniformly capitalize CERNLIB, COMIS, PAW and Paw++ properly in Debian
      packaging files (except old changelog entries).
    - Minor updates / improvements to README.64-bit and paw{,++}.README.debian.
    - Reference kuesvr man page now in section 7 instead of 1.
    - Do not assume that $LD_LIBRARY_PATH is empty in debian/rules (fixes
      error messages from fakeroot).
    - Increase left bar of Paw++ GUI from 80 to 100 pixels width in Paw++
      app-defaults file, to make the appearance of an annoying horizontal
      scroll-bar less likely.

 -- Stefan Ebner <email address hidden> Sat, 23 Mar 2008 13:44:29 +0100

gfortran transition has been carried out for illuminator_0.11.0-1 in Debian unstable. However, this version fails to build for me in hardy. Will investigate further.

This bug was fixed in the package mclibs - 2006.dfsg.2-5ubuntu1

---------------
mclibs (2006.dfsg.2-5ubuntu1) hardy; urgency=low

  * debian/control: weaken build-dep on gfortran, to match what we
    have in hardy for the gfortran transition (LP: #201962).
    This change can be safely dropped, once we have a newer gfortran in
    the archives.
  * Same change for debian/control.d/0base.control (which is checked against
    control during build time).
  * debian/control, debian/control.d/0base.control: update Maintainer field
    as per spec.

mclibs (2006.dfsg.2-5) unstable; urgency=low

  * "Apps/Science" --> "Science/Physics" in doc-base files, following
    section update in doc-base 0.8.10.
  * Upload to unstable.

mclibs (2006.dfsg.2-4) experimental; urgency=low

  * Gfortran transition:
    - Add -gfortran suffix to runtime library package names.
    - Change build-depends and -dev package depends appropriately.
    - s/g77/gfortran/g in various files.
  * Take this opportunity to insert the soversion into the libphotos202
    package name, fixing lintian warning.
  * Make libisajet arch: any, since perhaps gfortran will be able to compile
    it on m68k more successfully than g77 was (crossing fingers).
  * New patch 220: Build libisajet with isaset() compiled in.
  * New patch 221: Patch hepevt.inc before compiling rather than after.
  * Patch 806, debian/debhelper/*isajet*, debian/control.d/*isajet*: Hence,
    bump isajet soversion to 3 due to ABI change.
  * Remove obsolete tetex-bin alternative from build-depends.
  * Resurrect montecarlo-data arch: all package, and move data files to
    /usr/share/montecarlo-data/ (in order to be installable in parallel with
    old g77-based runtime library packages). Have the cojets, isajet and
    eurodec runtime and libdevel packages Recommend montecarlo-data.
  * Install example files for libisajet and libcojets into their libdevel
    packages. Add a couple of files explaining how to build and run the
    example programs.
  * debian/copyright*: Mention the (optional) switch to GPL v3.

  * Trivial changes:
    - Bump Standards-Version to 3.7.3.
    - Fix extra leading whitespace in doc-base abstracts.
    - Add dpatch comment to dummy patch 000.
    - Remove mention of no-longer-used "keepbuild" $DEB_BUILD_OPTIONS flag in
      README.source.
    - debian/*: Uniformly capitalize CERNLIB, CERN and GEANT (except in old
      changelog and NEWS entries).

mclibs (2006.dfsg.2-3) unstable; urgency=low

  * New patch 807: Compile libeurodec test program statically linked
    against CERN libs on 64-bit machines.

mclibs (2006.dfsg.2-2) unstable; urgency=low

  * Build-Depend on a cernlib-base-dev new enough to include the test
    suite rules for make, and to have a fix for a bug that occurs if there
    are no *.dpatch.in files in debian/patches.
  * Get rid of alternative tetex-bin Build-Dependency.
  * Ensure that upstream's test suite is run by adding TEST_PACKAGES variable
    in debian/add-ons/Makefile.
  * New patch 213, many thanks to Patrice Dumas: Fix Imakefiles for building
    test programs.
  * Revise patch 321 to sync with change in patch 213 to the file
    mclibs/isajet/tes...

Ops, sorry about that. Had an old page open and didn't see you had assigned yourself to this. Luckily enough there is bugmail!

r-noncran-lindsey (1.0.20071024-1) unstable; urgency=low

  * New upstream release.
  * Rebuild for gfortran transition.

fftw needs to be rebuilt following the libmpich transition.

This bug was fixed in the package fftw - 2.1.3-20.1build1

---------------
fftw (2.1.3-20.1build1) hardy; urgency=low

  * Rebuild for libmpich1.0ldbl -> libmpich1.0gf
    transition (LP: #201962).

 -- Cesare Tirabassi <email address hidden> Wed, 26 Mar 2008 17:48:14 +0100

This bug was fixed in the package cgal - 3.3.1-2ubuntu1

---------------
cgal (3.3.1-2ubuntu1) hardy; urgency=low

  * Update build-depends in debian/control for gfortran transition
    (patch from Kumar Appaiah, see Debian #470359), LP: #201962.
  * Add debian/patches/gfortran_transition.dpatch (other hunks from above
    patch) for g77 to gfortran transition. Add it to debian/patches/00list.
  * debian/control: update maintainer field as per spec.

cgal (3.3.1-2) unstable; urgency=low

  * debian/control: Really really drop support for atlas and lapack on arm
    and m68k, fix atlas and lapack support on other architectures.
  * debian/control: Extend exclusions for arm to variants armeb and armel
    (Closes: #460141).
  * debian/control: Remove virtual dependency liblapack-3.so which is
    provided by atlas3-base-dev (which does *not* provide
    /usr/lib/liblapack.so, just /usr/lib/atlas/liblapack.so).
  * debian/control: Replace virtual dependency libblas-3.so by
    libatlas-3.so.
  * Add patch qt-compatibility-headers.dpatch (Closes: #464251).
  * debian/control: Add Homepage: field, adjust Description: accordingly.
  * Update Standards-Version to 3.7.3 (no changes needed).

 -- Stefan Potyra <email address hidden> Wed, 26 Mar 2008 21:56:15 +0100

This bug was fixed in the package geant321 - 1:3.21.14.dfsg-8ubuntu1

---------------
geant321 (1:3.21.14.dfsg-8ubuntu1) hardy; urgency=low

  * Sync from Debian unstable (LP: #201962).
  * debian/control and debian/control.d/0base.control:
    - Change Build-Depends on gfortran to (>= 4:4.2.3) to avoid ftbfs
      Once gfortran (>= 4:4.3) is available in Ubuntu this can be dropped.
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

geant321 (1:3.21.14.dfsg-8) unstable; urgency=low

  * Change Apps/Science to Science/Physics in doc-base file.
  * Upload to unstable, completing the g77 -> gfortran transition of CERNLIB.
    - Fixes FTBFS in unstable (closes: #467572).

geant321 (1:3.21.14.dfsg-7) experimental; urgency=low

  * Gfortran transition (closes: #429439).
    - Change build-depends and -dev package depends appropriately.
    - Add -gfortran suffix to runtime library package name.
    - s/g77/gfortran/g in various files.
    - Call gfortran rather than f77 from gxint script (update to patch 321).

  * Lintian clean-up:
    - Bump Standards-Version to 3.7.3.
    - Use ${binary:Version} instead of deprecated ${Source-Version} in
      debian/control.
    - Add dpatch descriptions to patches 000, 002.
    - Remove extra leading spaces from doc-base abstract.

  * Other minor improvements:
    - Tweak dependencies and descriptions in debian/control file.
    - Add Homepage field in control file.
    - Update reference to GEANT-FLUKA FAQ in README.debian files.
    - Remove mention of no-longer-used "keepbuild" $DEB_BUILD_OPTION in
      README.source.
    - Mention the (somewhat ambiguous) switch to GPL v3 in copyright file.
    - Uniformly capitalize CERNLIB, GEANT and FLUKA properly in Debian
      packaging files (except old Debian changelog and NEWS entries).
    - Increase left bar of GEANT 3.21 Lesstif GUI from 80 to 100 pixels
      width in app-defaults file, to make the appearance of an annoying
      horizontal scroll-bar less likely.

geant321 (1:3.21.14.dfsg-6) unstable; urgency=low

  * Build-Depend on a cernlib-base-dev new enough to include the test suite
    rules for make.
  * Ensure that upstream's test suite is run by adding TEST_PACKAGES variable
    in debian/add-ons/Makefile.
  * Revised patch 001: Do not build test 4; it requires non-free FLUKA.
  * New patch 213, many thanks to Patrice Dumas: Fix Imakefiles for building
    test programs.
  * New patch 807: Compile test programs statically linked to CERN libraries
    on 64-bit systems.

 -- Cesare Tirabassi <email address hidden> Tue, 25 Mar 2008 17:02:41 +0100

sync request filed (bug #207705)

sync request filed (bug #207683)

This bug was fixed in the package hypre - 1.6.0-4ubuntu1

---------------
hypre (1.6.0-4ubuntu1) hardy; urgency=low

  * debian/control:
    Adjust Build-Depends and Depends to the gfortran transition (LP: #201962)
    - change atlas3-base-dev to libatlas-base-dev
    - change libblas-3.so to libblas-3gf.so
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

 -- Cesare Tirabassi <email address hidden> Thu, 27 Mar 2008 18:24:25 +0100

arpack++ (2.3-1) unstable; urgency=low

  [ Christophe Prud'homme ]
  * New upstream release
  * debian/control: update Standards-Version to 3.7.3, no changes
  * debian/control: removed XS- prefix
  * upstream is now hosted on gforge.imag.fr
  * Fixed "please update to use gfortran based lapack, blas", thanks to
    Kumar Appaiah (Closes: #463931).

blacs-mpi (1.1-28) unstable; urgency=low

  * The package now Build-Depends on Gfortran.
  * Homepage was moved from blacs-mpi's description to control tag.
  * Bump Standards-Version to 3.7.3
  * Bug 'FTBFS: btprim_MPI.f:(.text+0x56): undefined reference to
    `mpi_type_size__' has been fixed in this revision. (Closes: #465638)
  * Bug 'blacs-mpi -- Please rebuild with gfortran and new lam, mpich' has
    been fixed in this revision. Thanks to Kumar Appaiah for providing a
    patch. (Closes: #465366)

cvxopt (0.9.3-1) unstable; urgency=low

  * new upstream release (Closes: #471368)
  * Remove the former +nogs1 suffix.
  * Update patch doc.diff.

cvxopt (0.9.2+nogs1-1) unstable; urgency=low

 * Do not generate .pdf images on the fly but on obtaining source package to
   workaround failing epstopdf on some architectures

cvxopt (0.9.2-2) unstable; urgency=low

  [ Soeren Sonnenburg ]
  * Change Build-Depends of atlas, blas and lapack to match gfortran
    transition (Closes: #463938)
  * Tighten Build-Depends on dsdp >= 5.8-3

  [ Torsten Werner ]
  * Remove atlas support temporarily.

cvxopt (0.9.2-1) unstable; urgency=low

  [ Soeren Sonnenburg ]
  * New upstream version
  * Generate indexed pdf

  [ Torsten Werner ]
  * Add Build-Depends: texlive-latex-extra.
  * Change Build-Depends: gs-gpl to ghostscript.
  * Fix white space in doc-base file.

libextutils-f77-perl (1.16-2) unstable; urgency=low

  [ Damyan Ivanov ]
  * debian/control: Added: Vcs-Svn field (source stanza); Vcs-Browser
    field (source stanza); Homepage field (source stanza).

  [ gregor herrmann ]
  * debian/rules:
    - delete /usr/lib/perl5 only if it exists
    - specify correct package in install target
    - remove MacOS resource file ._F77.pm
  * debian/control:
    - changed: Maintainer set to Debian Perl Group <pkg-
      <email address hidden>> (was: Jose Luis Rivas
      <email address hidden>); Jose Luis Rivas <email address hidden> moved
      to Uploaders
    - build depend on gfortran instead of g77 (closes: #470254)
    - moved: gfortran to Build-Depends-Indep
  * Set Standards-Version to 3.7.3 (no changes).
  * debian/watch: use dist-based URL.
  * debian/copyright: use author-independent upstream URL.

mn-fit (5.13-6) unstable; urgency=low

  * Require libgfortran libraries (instead of -lg2c) in gfortran dpatch #40.
    (Has no effect at the moment since ROOT is not yet in Sid to link against)
  * New dpatch 45-fix-bashisms to work around the fact that dash's built-in
    echo interprets backslashes as escape sequences (and has no way to turn
    this off) in scripts/mn_tutorial_tex.  (closes: #459092)
  * Do not ignore failure of "make clean" or "make cleantut" in debian/rules,
    in order to fix Lintian warning.  (Therefore, work around command in
    "make clean" rule that fails if manual/mn_fit_html directory doesn't
    already exist.)
  * Change "Apps/Science" -> "Science/Data Analysis" in doc-base files.
  * s/Root/ROOT/g in man page and README.Debian.
  * Upload to unstable for g77 -> gfortran transition.

mn-fit (5.13-5) experimental; urgency=low

  * Change Build-Depends for gfortran and TeX Live transitions.
  * New dpatch 40-gfortran-transition to change g77 to gfortran in Makefiles.
  * Bump Standards-Version to 3.7.3.
  * Menu policy transition: Apps/Science -> Applications/Science/Data Analysis.
  * Add Homepage field to control file.
  * Mention in debian/copyright where GPL v2 can be found as well as the
    current GPL version (Mn_Fit is licensed with the "version 2 or later,
    at your option" phrasing).
  * Set $(TEXMFVAR) to $(CURDIR)/.texmf-var in debian/rules as requested by
    Debian TeX maintainers.  Take care of creating and removing this
    directory in the appropriate targets.

meep (0.10-2.1) unstable; urgency=low

  * Non-maintainer upload.
  * Add include to fix FTBFS on gcc4.3, closes: 455289
  * Transition to gortran, closes: 468877
  * make package binNMUable.

 -- Morten Kjeldgaard < <email address hidden>> Fri, 28 Mar 2008 10:00:28 +0000

illuminator (0.11.0-1) unstable; urgency=low

  * New upstream: bug fixes.
  * Update to new PETSc 2.3.3 and rebuild with new gfortran (closes: #472411).
  * Included math-blaslapack.m4 dropped by petsc package (closes: #443033).
  * Dropped Alpha dependency on orphaned libffm-dev (closes: #452571).
  * Changed tetex dependencies to texlive (closes: #419564).
  * Regenerates debian/rules in clean target (closes: #424418).

 -- Morten Kjeldgaard < <email address hidden>> Fri, 28 Mar 2008 09:49:33 +0000

scalapack (1.8.0-2) unstable; urgency=low

  * Bumped standards version to 3.7.3.
  * Scalpack is now building with Gfortran instead of G77. Thanks to Kumar
    Appaiah for providing a patch. (Closes: #465392)
  * Bug:' FTBFS: psblas1tst.f:(.text+0x156): undefined reference to
    `blacs_pinfo__'' has been fixed in this revision. (Closes: #462510)

 -- Cesare Tirabassi < <email address hidden>> Tue, 01 Apr 2008 00:58:25 +0100

Re-opening blacs-pvm:

The blacs-pvm-test package still Depends on blacs-test-common, while the transitioned blacs-mpi package provides now the blacsgf-test-common.

Re-opening since this needs to be build with gfortran 4.2.3 to avoid ftbfs.

This bug was fixed in the package mn-fit - 5.13-6ubuntu1

---------------
mn-fit (5.13-6ubuntu1) hardy; urgency=low

  * Change Build-Depends on gfortran to (>= 4:4.2.3) to fix FTBFS (LP: #201962)
    Once gfortran (>= 4:4.3) is available in Ubuntu this can be dropped.
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

 -- Cesare Tirabassi <email address hidden> Tue, 01 Apr 2008 12:43:11 +0200

blacs-pvm (1.1-18ubuntu1) hardy; urgency=low

  * For the blacs-pvm-test binary package, change Depends: from
    blacs-test-common to blacsgf-test-common which is now provided
    by the gfortran transitioned blacs-mpi package.
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

 -- Cesare Tirabassi < <email address hidden>> Tue, 01 Apr 2008 12:55:03 +0200

python-numarray, together with python-numpy, python-scipy and python-numeric, have been done by doko already.