Re: [Freesurfer] Building from source -- autoconf error

[Yaroslav Halchenko]

On Fri, 19 Feb 2016, Z K wrote:

> Hello Yaroslav,

> Ive built freesurfer on Debian "Jessie" platform. It was just a matter 
> of adding "libtool-bin" and "tcsh" to the list of packages that need to 
> be installed. 

I had tcsh but not libtool-bin installed in that chroot... heh

> Ive update the wiki page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

> I still wasnt quite able to get the freeview GUI to build. But If you 
> change the "--disable-GUI-build" flag to "--without-qt" then you will 
> get all the tktool GUIs except freeview. Im working on getting freeview 
> to build at the moment and will update the wiki page once I figure it out.

sweet! thanks.  I will give it a shot!

in my case I have got stuck still on 14.04 trying to build with GUI but
./configure failed to find xawplus rightfully so since even
centos6-x86_64-packages provides only a static build of it while
configure sensing for a dynamic library.  (and debian/ubuntus do
not provide this antiquity) 

I just wondered how do you guys build against it then? ;) 

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [Freesurfer] Building from source -- autoconf error

[Z K]

Ive discovered that if you add the following line to the 
freeview/Makefile.am file then it will build succcessfully.

  freeview_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS)
  freeview_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS)
-freeview_LDFLAGS   = $(QT_LDFLAGS) $(OS_LDFLAGS)
+freeview_LDFLAGS   = $(QT_LDFLAGS) $(OS_LDFLAGS) \
+   -Wl,--allow-multiple-definition 
  freeview_LDADD= $(QT_LIBS)\
$(addprefix $(top_builddir)/, $(LIBS_MGH)) \
$(top_builddir)/vtkfsio/libvtkfsio.a \

Turns out the issue is with the build of LAPACK provided by Ubuntu, as 
it contains a duplicate function. (https://cmake.org/Bug/view.php?id=12912)

I will be committing the change and pushing to the git repo after some 
testing, probably later this evening.

-Zeke

On 02/19/2016 02:29 PM, Rudolph Pienaar wrote:
> I have been able to build the FS GUI tools succesfully on Ubuntu in the
> past... Admittedly this was a long time ago (pre 14.04 days). I can dig
> through my notes and see if they are still applicable. We no longer have
> any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose
> in a few weeks will be superseded by 16.04's release.
>
>
> On 2/19/16 12:45 , Z K wrote:
>> Hello Yaroslav,
>>
>> Ive built freesurfer on Debian "Jessie" platform. It was just a matter
>> of adding "libtool-bin" and "tcsh" to the list of packages that need to
>> be installed. Ive update the wiki page:
>>
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
>>
>> I still wasnt quite able to get the freeview GUI to build. But If you
>> change the "--disable-GUI-build" flag to "--without-qt" then you will
>> get all the tktool GUIs except freeview. Im working on getting freeview
>> to build at the moment and will update the wiki page once I figure it out.
>>
>> -Zeke
>>
>>
>>
>>
>> On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
>>> Gotcha, thanks!
>>>
>>> On February 18, 2016 3:27:21 PM EST, Z K  
>>> wrote:

> I would be infinitely grateful if freesurfer could build natively on
 Debian
> stable! ;)  Thanks for trying.  In my case I am trying the build
 under jessie
> chroot (using schroot helper), so I could quickly setup/enter such
 environment
> while maintaining user/directory.  I will do the same now for 14.04.
 If you
> would like more -- let me know I could give a bit more detailed
> instructions.
>

 I have a debian jessie system just setup, but I have a high priority
 project due Monday, so I would be able to begin determining the exact
 build procedure on Debian jessie until beginning of next week. It is
 something I have been meaning to do so I plan on getting to it. If you
 dont hear from me by Tuesday/Wedensday feel free to shoot me an email
 for an update. Thanks.

 -Zeke


 The information in this e-mail is intended only for the person to whom
 it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.
>>>
>> ___
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>>
>
>
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Re: [Freesurfer] Building from source -- autoconf error

[Rudolph Pienaar]

I have been able to build the FS GUI tools succesfully on Ubuntu in the 
past... Admittedly this was a long time ago (pre 14.04 days). I can dig 
through my notes and see if they are still applicable. We no longer have 
any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose 
in a few weeks will be superseded by 16.04's release.


On 2/19/16 12:45 , Z K wrote:
> Hello Yaroslav,
>
> Ive built freesurfer on Debian "Jessie" platform. It was just a matter
> of adding "libtool-bin" and "tcsh" to the list of packages that need to
> be installed. Ive update the wiki page:
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
>
> I still wasnt quite able to get the freeview GUI to build. But If you
> change the "--disable-GUI-build" flag to "--without-qt" then you will
> get all the tktool GUIs except freeview. Im working on getting freeview
> to build at the moment and will update the wiki page once I figure it out.
>
> -Zeke
>
>
>
>
> On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
>> Gotcha, thanks!
>>
>> On February 18, 2016 3:27:21 PM EST, Z K  
>> wrote:
>>>
 I would be infinitely grateful if freesurfer could build natively on
>>> Debian
 stable! ;)  Thanks for trying.  In my case I am trying the build
>>> under jessie
 chroot (using schroot helper), so I could quickly setup/enter such
>>> environment
 while maintaining user/directory.  I will do the same now for 14.04.
>>> If you
 would like more -- let me know I could give a bit more detailed
 instructions.

>>>
>>> I have a debian jessie system just setup, but I have a high priority
>>> project due Monday, so I would be able to begin determining the exact
>>> build procedure on Debian jessie until beginning of next week. It is
>>> something I have been meaning to do so I plan on getting to it. If you
>>> dont hear from me by Tuesday/Wedensday feel free to shoot me an email
>>> for an update. Thanks.
>>>
>>> -Zeke
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>
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>


-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] Building from source -- autoconf error

[Z K]

Hello Yaroslav,

Ive built freesurfer on Debian "Jessie" platform. It was just a matter 
of adding "libtool-bin" and "tcsh" to the list of packages that need to 
be installed. Ive update the wiki page:

 
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

I still wasnt quite able to get the freeview GUI to build. But If you 
change the "--disable-GUI-build" flag to "--without-qt" then you will 
get all the tktool GUIs except freeview. Im working on getting freeview 
to build at the moment and will update the wiki page once I figure it out.

-Zeke




On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote:
> Gotcha, thanks!
>
> On February 18, 2016 3:27:21 PM EST, Z K  wrote:
>>
>>> I would be infinitely grateful if freesurfer could build natively on
>> Debian
>>> stable! ;)  Thanks for trying.  In my case I am trying the build
>> under jessie
>>> chroot (using schroot helper), so I could quickly setup/enter such
>> environment
>>> while maintaining user/directory.  I will do the same now for 14.04.
>> If you
>>> would like more -- let me know I could give a bit more detailed
>>> instructions.
>>>
>>
>> I have a debian jessie system just setup, but I have a high priority
>> project due Monday, so I would be able to begin determining the exact
>> build procedure on Debian jessie until beginning of next week. It is
>> something I have been meaning to do so I plan on getting to it. If you
>> dont hear from me by Tuesday/Wedensday feel free to shoot me an email
>> for an update. Thanks.
>>
>> -Zeke
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>
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Re: [Freesurfer] Building from source -- autoconf error

[Yaroslav Halchenko]

On Thu, 18 Feb 2016, Z K wrote:
> > is there a public clone of freesurfer on github?

> Sorry, their is no public freesurfer on github. But at the current 
> moment (and forseeable future) the public repo is an exact mirro of the 
> private repo.


> > --disable-GUI-build  -- wouldn't it disable then building all so necessary 
> > GUI
> > tools?  is there  a way to overcome the shortcoming?


> I was never able to get the GUI tools to build on Ubuntu. It is 
> something I may revisit in the near future, but as of now, in order to 
> build on an Ubuntu platform you will need to disable GUI building.

just confirming that I have managed to build it under 14.04 -- hip hip
hoorray! ;)  next one will be to try with GUI ;)

the only concern is that currently some subdirs makefiles do not care about
DESTDIR, which is generally respected by autotools... attached patch should
help (if only there was a public github... ;)) to make it 'installable' e.g. via

make install DESTDIR=$PWD/INSTALL-DIR/

it would be a nice "test" to add to .travis.yml upon successful build, without
system wide installation with sudo ;)

> We simply dont have the resources to ensure build capability on all 
> linux (and mac) based OSes. For now simply we make the claim that 
> freesurfer will build on centos, and will run on nearly all the major 
> linux distros.

Fair enough.  but may be together we could push it forward step by step
;)

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
From 1983364a101d9543f6d80c45b968aa194e023288 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko 
Date: Fri, 19 Feb 2016 05:06:24 +
Subject: [PATCH] BF: adjusted use of $(DESTDIR) so installs fine under DESTDIR

---
 BrainstemSS/Makefile.am | 4 ++--
 BrainstemSS/linux_x86_64/Makefile.am| 4 ++--
 GEMS/data/Makefile.am   | 4 ++--
 HippoSF/Makefile.am | 4 ++--
 HippoSF/linux_x86_64/Makefile.am| 4 ++--
 distribution/average/Buckner_JNeurophysiol11_MNI152/Makefile.am | 4 ++--
 distribution/average/Choi_JNeurophysiol12_MNI152/Makefile.am| 4 ++--
 distribution/average/Makefile.am| 4 ++--
 distribution/average/Yeo_JNeurophysiol11_MNI152/Makefile.am | 4 ++--
 distribution/average/surf/Makefile.am   | 4 ++--
 distribution/fsafd/Makefile.am  | 4 ++--
 distribution/fsl-extra/Makefile.am  | 2 +-
 distribution/lib/bem/Makefile.am| 4 ++--
 distribution/subjects/Makefile.am   | 4 ++--
 fsfast/docs/Makefile.am | 4 ++--
 images/Makefile.am  | 4 ++--
 matlab/Makefile.am  | 8 
 mri_cvs_register/Makefile.am| 2 +-
 qdec/Makefile.am| 8 
 talairach_avi/Makefile.am   | 4 ++--
 20 files changed, 42 insertions(+), 42 deletions(-)

diff --git a/BrainstemSS/Makefile.am b/BrainstemSS/Makefile.am
index d0d505e..3bcf40e 100644
--- a/BrainstemSS/Makefile.am
+++ b/BrainstemSS/Makefile.am
@@ -21,8 +21,8 @@ segmentBS.sh \
 quantifyBrainstemStructures.sh
 
 install-data-local:
-	test -z $(foodir) || $(mkdir_p) $(foodir)
-	$(INSTALL_DATA) $(foo_datafiles) $(foodir)
+	test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir)
+	$(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir)
 
 # Our release target. Include files to be excluded here. They will be
 # found and removed after 'make install' is run during the 'make
diff --git a/BrainstemSS/linux_x86_64/Makefile.am b/BrainstemSS/linux_x86_64/Makefile.am
index 3543581..0f47fd7 100644
--- a/BrainstemSS/linux_x86_64/Makefile.am
+++ b/BrainstemSS/linux_x86_64/Makefile.am
@@ -17,8 +17,8 @@ foo_binaryfiles = \
 	SegmentSubject.bin
 
 install-data-local:
-	test -z $(foodir) || $(mkdir_p) $(foodir)
-	$(INSTALL) -m 755 $(foo_binaryfiles) $(foodir)
+	test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir)
+	$(INSTALL) -m 755 $(foo_binaryfiles) $(DESTDIR)$(foodir)
 
 # Our release target. Include files to be excluded here. They will be
 # found and removed after 'make install' is run during the 'make
diff --git a/GEMS/data/Makefile.am b/GEMS/data/Makefile.am
index 97a7eb1..cf29198 100644
--- a/GEMS/data/Makefile.am
+++ b/GEMS/data/Makefile.am
@@ -15,8 +15,8 @@ kvlQuantifyHippocampalSubfieldSegmentations.sh.help.xml \
 kvlSegmentHippocampalSubfields.sh.help.xml
 
 

Re: [Freesurfer] Building from source -- autoconf error

[Z K]

>
> is there a public clone of freesurfer on github?

Sorry, their is no public freesurfer on github. But at the current 
moment (and forseeable future) the public repo is an exact mirro of the 
private repo.

>
> --disable-GUI-build  -- wouldn't it disable then building all so necessary GUI
> tools?  is there  a way to overcome the shortcoming?
>

I was never able to get the GUI tools to build on Ubuntu. It is 
something I may revisit in the near future, but as of now, in order to 
build on an Ubuntu platform you will need to disable GUI building.

We simply dont have the resources to ensure build capability on all 
linux (and mac) based OSes. For now simply we make the claim that 
freesurfer will build on centos, and will run on nearly all the major 
linux distros.

>
> I would be infinitely grateful if freesurfer could build natively on Debian
> stable! ;)  Thanks for trying.  In my case I am trying the build under jessie
> chroot (using schroot helper), so I could quickly setup/enter such environment
> while maintaining user/directory.  I will do the same now for 14.04.  If you
> would like more -- let me know I could give a bit more detailed
> instructions.
>

Working on it now. Ill be attempting the build under a vanilla jessie 
install.

>
> ;) it is an output of 'git describe --tags', which bases it on a most
> recent tag, which was 5622 commits ago and its hexsha f2d0bcd.  You
> could feed this beast to git directly -- it would swallow:
>
> $> git show stable5_branch-5622-gf3d0bcd | head
> commit f3d0bcd7c4ee8604918725de07c8736191cb1b8f
> Author: Z K 
> Date:   Tue Feb 16 17:03:00 2016 -0500
>
>  Changed to reference new GCA. -greve
>
> diff --git a/scripts/recon-all b/scripts/recon-all
> index 6e4ab62..bf35521 100755
> --- a/scripts/recon-all
> +++ b/scripts/recon-all
>

Got it! Thanks.

-Zeke
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Re: [Freesurfer] Building from source -- autoconf error

[Yaroslav Halchenko]

On Thu, 18 Feb 2016, Z K wrote:

> I beleive the .travis.yml does work but it is still under active
> development.

is there a public clone of freesurfer on github?

> The Ubuntu instructions in the linux developers page have been tested on a
> clean install and should work
> (https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page).

oh good good -- thanks.. immediate question for 14.04 ubuntu then

--disable-GUI-build  -- wouldn't it disable then building all so necessary GUI
tools?  is there  a way to overcome the shortcoming?

> However I have not yet tested a build on a Debian system. I will make an
> attempt to build today on a clean debian "jessie" install. 

I would be infinitely grateful if freesurfer could build natively on Debian
stable! ;)  Thanks for trying.  In my case I am trying the build under jessie
chroot (using schroot helper), so I could quickly setup/enter such environment
while maintaining user/directory.  I will do the same now for 14.04.  If you
would like more -- let me know I could give a bit more detailed
instructions.

> But I have one
> question, what branch are you attempting to build, because their is no
> "stable5_branch-5622-gf3d0bcd" branch in the git repo?

;) it is an output of 'git describe --tags', which bases it on a most
recent tag, which was 5622 commits ago and its hexsha f2d0bcd.  You
could feed this beast to git directly -- it would swallow:

$> git show stable5_branch-5622-gf3d0bcd | head
commit f3d0bcd7c4ee8604918725de07c8736191cb1b8f
Author: Z K 
Date:   Tue Feb 16 17:03:00 2016 -0500

Changed to reference new GCA. -greve

diff --git a/scripts/recon-all b/scripts/recon-all
index 6e4ab62..bf35521 100755
--- a/scripts/recon-all
+++ b/scripts/recon-all


-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Building from source -- autoconf error

[Z K]

Hello,

I beleive the .travis.yml does work but it is still under active 
development.

The Ubuntu instructions in the linux developers page have been tested on 
a clean install and should work 
(https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page). 


However I have not yet tested a build on a Debian system. I will make an 
attempt to build today on a clean debian "jessie" install. But I have 
one question, what branch are you attempting to build, because their is 
no "stable5_branch-5622-gf3d0bcd" branch in the git repo?

-Zeke

On 02/18/2016 09:59 AM, Yaroslav Halchenko wrote:
> Hi Z K et al,
>
> What would be the recommended/tested debian/ubuntu release to approach the
> build with some guarantee of success?  Is the .travis.yml "exercised" (failed
> to quickly find a sign of it on travis-ci.org)?
>
> I have tried on debian jessie to build stable5_branch-5622-gf3d0bcd of
> the git/annex repo, using following command:
>
>  { ./setup_configure && ./configure --prefix=/usr/local/freesurfer/dev 
> --with-pkgs-dir=${PWD}/../freesurfer-packages/centos6-x86_64-packages 
> --disable-Werror --with-petsc-dir=/usr/lib/x86_64-linux-gnu && make -j3; } 
> 2>&1 | tee ../freesurfer-upstream.buildlog1.txt
>
> and before that installing various build depends and helpers through
>
>  apt-get install libtool automake gfortran libglu1-mesa-dev 
> libfreetype6-dev uuid-dev libxmu-dev libxmu-headers libxi-dev libx11-dev 
> libxt-dev libxaw7-dev liblapack-dev tcsh curl git libmpich-dev git git-annex 
> petsc-dev make
>
> but the build fails with
>
> mv -f .deps/xmlToHtml.Tpo .deps/xmlToHtml.Po
> /bin/bash ../libtool  --tag=CC   --mode=link g++-L/usr/lib64 
> -L/usr/X11R6/lib64  -fopenmp
> -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/mni/current/lib
>  
> -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/vxl/current/lib
>   
> -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/itk/current/lib/InsightToolkit
>   -o xmlToHtml xmlToHtml.o ../xml2/libxml2.a -lz
> mv -f .deps/fsPrintHelp-fsPrintHelp.Tpo .deps/fsPrintHelp-fsPrintHelp.Po
> ../libtool: line 469: CDPATH: command not found
> /bin/bash ../libtool  --tag=CC   --mode=link g++ -DBUILD_MAIN   -L/usr/lib64 
> -L/usr/X11R6/lib64  -fopenmp
> -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/mni/current/lib
>  
> -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/vxl/current/lib
>   
> -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/itk/current/lib/InsightToolkit
>   -o fsPrintHelp fsPrintHelp-fsPrintHelp.o ../xml2/libxml2.a -lz
> ../libtool: line 469: CDPATH: command not found
> libtool: Version mismatch error.  This is libtool 2.4.2 Debian-2.4.2-1.11, 
> but the
> libtool: definition of this LT_INIT comes from an older release.
> libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 
> Debian-2.4.2-1.11
> libtool: and run autoconf again.
> Makefile:1674: recipe for target 'xmlToHtml' failed
> make[3]: *** [xmlToHtml] Error 63
> make[3]: *** Waiting for unfinished jobs
> libtool: Version mismatch error.  This is libtool 2.4.2 Debian-2.4.2-1.11, 
> but the
> libtool: definition of this LT_INIT comes from an older release.
> libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 
> Debian-2.4.2-1.11
> libtool: and run autoconf again.
> Makefile:1658: recipe for target 'fsPrintHelp' failed
> make[3]: *** [fsPrintHelp] Error 63
>
> suggesting that not full auto/libtool'ification was carried out by
> ./setup_configure, but I didn't check detail yet.
>
> full log available at 
> http://www.onerussian.com/tmp/freesurfer-upstream.buildlog1.txt
>
> Thanks in advance for the hints
>
> On Tue, 02 Feb 2016, Z K wrote:
>
>> Hello Alle,
>
>> The naming of "configure.in" vs. "configure.ac" is not the issue. The
>> script is erroring out because file 'm4/autotroll.m4' does not exist. Do
>> you have that file (it should have been included in the checkout)?
>
>> I would recommend using our git repo which mirrors our CVS repo. Please
>> see the following page:
>
>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
>
>> Hope this helps,
>
>> -Zeke
>
>> On 02/02/2016 04:11 AM, Alle Meije Wink wrote:
>>> I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system.
>>> (64 bit, using g++ 4.9 for compilation)
>
>>> After
>>> $ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
>>> $ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
>>> checkout -P dev
>>> $ cd dev
>>> $ cvs update -d # just to make sure
>>> $ ./setup_configure
>
>>> I get these messages:
>
>>> rm -rf autom4te.cache
>>> libtoolize --force
>>> libtoolize: putting auxiliary files in 

Re: [Freesurfer] Building from source -- autoconf error

[Yaroslav Halchenko]

Hi Z K et al,

What would be the recommended/tested debian/ubuntu release to approach the
build with some guarantee of success?  Is the .travis.yml "exercised" (failed
to quickly find a sign of it on travis-ci.org)?

I have tried on debian jessie to build stable5_branch-5622-gf3d0bcd of
the git/annex repo, using following command:

{ ./setup_configure && ./configure --prefix=/usr/local/freesurfer/dev 
--with-pkgs-dir=${PWD}/../freesurfer-packages/centos6-x86_64-packages 
--disable-Werror --with-petsc-dir=/usr/lib/x86_64-linux-gnu && make -j3; } 2>&1 
| tee ../freesurfer-upstream.buildlog1.txt

and before that installing various build depends and helpers through

apt-get install libtool automake gfortran libglu1-mesa-dev libfreetype6-dev 
uuid-dev libxmu-dev libxmu-headers libxi-dev libx11-dev libxt-dev libxaw7-dev 
liblapack-dev tcsh curl git libmpich-dev git git-annex petsc-dev make

but the build fails with

mv -f .deps/xmlToHtml.Tpo .deps/xmlToHtml.Po
/bin/bash ../libtool  --tag=CC   --mode=link g++-L/usr/lib64 
-L/usr/X11R6/lib64  -fopenmp
-L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/mni/current/lib
 
-L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/vxl/current/lib
  
-L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/itk/current/lib/InsightToolkit
  -o xmlToHtml xmlToHtml.o ../xml2/libxml2.a -lz 
mv -f .deps/fsPrintHelp-fsPrintHelp.Tpo .deps/fsPrintHelp-fsPrintHelp.Po
../libtool: line 469: CDPATH: command not found
/bin/bash ../libtool  --tag=CC   --mode=link g++ -DBUILD_MAIN   -L/usr/lib64 
-L/usr/X11R6/lib64  -fopenmp
-L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/mni/current/lib
 
-L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/vxl/current/lib
  
-L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/itk/current/lib/InsightToolkit
  -o fsPrintHelp fsPrintHelp-fsPrintHelp.o ../xml2/libxml2.a -lz 
../libtool: line 469: CDPATH: command not found
libtool: Version mismatch error.  This is libtool 2.4.2 Debian-2.4.2-1.11, but 
the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 
Debian-2.4.2-1.11
libtool: and run autoconf again.
Makefile:1674: recipe for target 'xmlToHtml' failed
make[3]: *** [xmlToHtml] Error 63
make[3]: *** Waiting for unfinished jobs
libtool: Version mismatch error.  This is libtool 2.4.2 Debian-2.4.2-1.11, but 
the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 
Debian-2.4.2-1.11
libtool: and run autoconf again.
Makefile:1658: recipe for target 'fsPrintHelp' failed
make[3]: *** [fsPrintHelp] Error 63

suggesting that not full auto/libtool'ification was carried out by
./setup_configure, but I didn't check detail yet.

full log available at 
http://www.onerussian.com/tmp/freesurfer-upstream.buildlog1.txt

Thanks in advance for the hints

On Tue, 02 Feb 2016, Z K wrote:

> Hello Alle,

> The naming of "configure.in" vs. "configure.ac" is not the issue. The 
> script is erroring out because file 'm4/autotroll.m4' does not exist. Do 
> you have that file (it should have been included in the checkout)?

> I would recommend using our git repo which mirrors our CVS repo. Please 
> see the following page:


> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

> Hope this helps,

> -Zeke

> On 02/02/2016 04:11 AM, Alle Meije Wink wrote:
> > I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system.
> > (64 bit, using g++ 4.9 for compilation)

> > After
> > $ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
> > $ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
> > checkout -P dev
> > $ cd dev
> > $ cvs update -d # just to make sure
> > $ ./setup_configure

> > I get these messages:

> > rm -rf autom4te.cache
> > libtoolize --force
> > libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'.
> > libtoolize: linking file `config/ltmain.sh'
> > libtoolize: putting macros in `m4'.
> > libtoolize: linking file `m4/libtool.m4'
> > libtoolize: linking file `m4/ltoptions.m4'
> > libtoolize: linking file `m4/ltsugar.m4'
> > libtoolize: linking file `m4/ltversion.m4'
> > libtoolize: linking file `m4/lt~obsolete.m4'
> > libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and
> > libtoolize: rerunning libtoolize, to keep the correct libtool macros 
> > in-tree.
> > aclocal
> > aclocal: warning: autoconf input should be named 'configure.ac', not
> > 'configure.in'
> > aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist

> > Which looks like a not-(anymore)supported use of autoconf?
> 

[Freesurfer] Building from source -- autoconf error

[Alle Meije Wink]

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system.
(64 bit, using g++ 4.9 for compilation)

After
$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
checkout -P dev
$ cd dev
$ cvs update -d # just to make sure
$ ./setup_configure

I get these messages:

rm -rf autom4te.cache
libtoolize --force
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'.
libtoolize: linking file `config/ltmain.sh'
libtoolize: putting macros in `m4'.
libtoolize: linking file `m4/libtool.m4'
libtoolize: linking file `m4/ltoptions.m4'
libtoolize: linking file `m4/ltsugar.m4'
libtoolize: linking file `m4/ltversion.m4'
libtoolize: linking file `m4/lt~obsolete.m4'
libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and
libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
aclocal
aclocal: warning: autoconf input should be named 'configure.ac', not
'configure.in'
aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist

Which looks like a not-(anymore)supported use of autoconf?
I found one previous message on the list about autotroll
  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.html
that provided another version of configure.in which might solve the issue.

And it did in the original case but sadly not for me. I get the same
error message also with the new configure.in -- there should probably
be a configure.ac?

If anyone knows how to make this work (e.g. by modifying the configure
script) that would be fantastic.
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Building from source -- autoconf error

[Z K]

Hello Alle,

The naming of "configure.in" vs. "configure.ac" is not the issue. The 
script is erroring out because file 'm4/autotroll.m4' does not exist. Do 
you have that file (it should have been included in the checkout)?

I would recommend using our git repo which mirrors our CVS repo. Please 
see the following page:

 
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

Hope this helps,

-Zeke

On 02/02/2016 04:11 AM, Alle Meije Wink wrote:
> I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system.
> (64 bit, using g++ 4.9 for compilation)
>
> After
> $ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login
> $ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
> checkout -P dev
> $ cd dev
> $ cvs update -d # just to make sure
> $ ./setup_configure
>
> I get these messages:
>
> rm -rf autom4te.cache
> libtoolize --force
> libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'.
> libtoolize: linking file `config/ltmain.sh'
> libtoolize: putting macros in `m4'.
> libtoolize: linking file `m4/libtool.m4'
> libtoolize: linking file `m4/ltoptions.m4'
> libtoolize: linking file `m4/ltsugar.m4'
> libtoolize: linking file `m4/ltversion.m4'
> libtoolize: linking file `m4/lt~obsolete.m4'
> libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and
> libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
> aclocal
> aclocal: warning: autoconf input should be named 'configure.ac', not
> 'configure.in'
> aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist
>
> Which looks like a not-(anymore)supported use of autoconf?
> I found one previous message on the list about autotroll
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.html
> that provided another version of configure.in which might solve the issue.
>
> And it did in the original case but sadly not for me. I get the same
> error message also with the new configure.in -- there should probably
> be a configure.ac?
>
> If anyone knows how to make this work (e.g. by modifying the configure
> script) that would be fantastic.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.