From jason at phenogenomics.ca  Mon Nov  5 09:35:31 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 09:35:31 -0500
Subject: [MINC-development] compiling Display from github
Message-ID: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>

Howdy devs,

I just compiled Display from github head in a virtual machine running Kubuntu 12.10. I had to make a few to me odd changes to the code to get it to compile (see the bottom of the email for the diffs). The autoconf checks appeared to think I had no GL though I clearly had, so one check had to be disabled, and I had to define a few constants. It all seems to work now but it puzzled me a bit, especially the part about the constants. Any ideas?

Jason


diff --git a/configure.in b/configure.in
index fe252d3..5445dfb 100644
--- a/configure.in
+++ b/configure.in
@@ -57,7 +57,8 @@ AX_CHECK_GLU
 AX_CHECK_GLUT
 
 dnl check if we found them
-if test "$no_gl" = yes -o "$no_glu" = yes -o "$no_glut" = yes ;
+#if test "$no_gl" = yes -o "$no_glu" = yes -o "$no_glut" = yes ;
+if "$no_glu" = yes -o "$no_glut" = yes ;
 then
    AC_MSG_ERROR([
 ================================================================================
diff --git a/m4 b/m4
--- a/m4
+++ b/m4
@@ -1 +1 @@
-Subproject commit 87caf73968c8b57db276480acf85d5da8e7e48be
+Subproject commit 87caf73968c8b57db276480acf85d5da8e7e48be-dirty
diff --git a/main/main.c b/main/main.c
index 830754e..e1e4723 100644
--- a/main/main.c
+++ b/main/main.c
@@ -23,6 +23,9 @@ static char rcsid[] = "$Header: /private-cvsroot/visualization/Display/main/main
 
 #define  MAX_TITLE_LENGTH   200
 
+#define PROJECT_NAME "Display"
+#define PROJECT_VERSION 1.5
+
 /* These two globals are required for SEAL's LibSul/SULGRAPHDATA */
 int debug = 1;
 int verbose = 1;
@@ -36,7 +39,7 @@ private  void   parse_options (int argc, char *argv[],
 
 /* The first directory is set using compiler flag -D */
 /*#define  HARD_CODED_DISPLAY_DIRECTORY1    "/usr/local/mni/lib"*/
-/*#define  HARD_CODED_DISPLAY_DIRECTORY2    "/usr/local/lib"*/
+#define  HARD_CODED_DISPLAY_DIRECTORY2    "/usr/local/minc2/lib"
 #define  GLOBALS_FILENAME                 "Display.globals"
 #define  MENU_FILENAME                    "Display.menu"
 


From vladimir.fonov at gmail.com  Mon Nov  5 09:45:00 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 5 Nov 2012 09:45:00 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>

Hello Jason,


did you use devel branch? Also, I've migrated build system to cmake - can
you try it?


On Mon, Nov 5, 2012 at 9:35 AM, Jason Lerch <jason at phenogenomics.ca> wrote:

> Howdy devs,
>
> I just compiled Display from github head in a virtual machine running
> Kubuntu 12.10. I had to make a few to me odd changes to the code to get it
> to compile (see the bottom of the email for the diffs). The autoconf checks
> appeared to think I had no GL though I clearly had, so one check had to be
> disabled, and I had to define a few constants. It all seems to work now but
> it puzzled me a bit, especially the part about the constants. Any ideas?
>
> Jason
>
>
> diff --git a/configure.in b/configure.in
> index fe252d3..5445dfb 100644
> --- a/configure.in
> +++ b/configure.in
> @@ -57,7 +57,8 @@ AX_CHECK_GLU
>  AX_CHECK_GLUT
>
>  dnl check if we found them
> -if test "$no_gl" = yes -o "$no_glu" = yes -o "$no_glut" = yes ;
> +#if test "$no_gl" = yes -o "$no_glu" = yes -o "$no_glut" = yes ;
> +if "$no_glu" = yes -o "$no_glut" = yes ;
>  then
>     AC_MSG_ERROR([
>
>  ================================================================================
> diff --git a/m4 b/m4
> --- a/m4
> +++ b/m4
> @@ -1 +1 @@
> -Subproject commit 87caf73968c8b57db276480acf85d5da8e7e48be
> +Subproject commit 87caf73968c8b57db276480acf85d5da8e7e48be-dirty
> diff --git a/main/main.c b/main/main.c
> index 830754e..e1e4723 100644
> --- a/main/main.c
> +++ b/main/main.c
> @@ -23,6 +23,9 @@ static char rcsid[] = "$Header:
> /private-cvsroot/visualization/Display/main/main
>
>  #define  MAX_TITLE_LENGTH   200
>
> +#define PROJECT_NAME "Display"
> +#define PROJECT_VERSION 1.5
> +
>  /* These two globals are required for SEAL's LibSul/SULGRAPHDATA */
>  int debug = 1;
>  int verbose = 1;
> @@ -36,7 +39,7 @@ private  void   parse_options (int argc, char *argv[],
>
>  /* The first directory is set using compiler flag -D */
>  /*#define  HARD_CODED_DISPLAY_DIRECTORY1    "/usr/local/mni/lib"*/
> -/*#define  HARD_CODED_DISPLAY_DIRECTORY2    "/usr/local/lib"*/
> +#define  HARD_CODED_DISPLAY_DIRECTORY2    "/usr/local/minc2/lib"
>  #define  GLOBALS_FILENAME                 "Display.globals"
>  #define  MENU_FILENAME                    "Display.menu"
>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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From jason at phenogenomics.ca  Mon Nov  5 10:03:41 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 10:03:41 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>

No, I was using the master branch. I'll give the devel branch a try later - which I guess will include trying to understand the god forsaken cmake build system (I know that autoconf sucks and the thought of writing anything in m4 is horrid, but at least I got used to it!). I'll let you know how that works.

Jason

On 2012-11-05, at 9:45 AM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Hello Jason,
> 
> 
> did you use devel branch? Also, I've migrated build system to cmake - can you try it?
> 
> 
> On Mon, Nov 5, 2012 at 9:35 AM, Jason Lerch <jason at phenogenomics.ca> wrote:
> Howdy devs,
> 
> I just compiled Display from github head in a virtual machine running Kubuntu 12.10. I had to make a few to me odd changes to the code to get it to compile (see the bottom of the email for the diffs). The autoconf checks appeared to think I had no GL though I clearly had, so one check had to be disabled, and I had to define a few constants. It all seems to work now but it puzzled me a bit, especially the part about the constants. Any ideas?
> 
> Jason
> 
> 
> diff --git a/configure.in b/configure.in
> index fe252d3..5445dfb 100644
> --- a/configure.in
> +++ b/configure.in
> @@ -57,7 +57,8 @@ AX_CHECK_GLU
>  AX_CHECK_GLUT
> 
>  dnl check if we found them
> -if test "$no_gl" = yes -o "$no_glu" = yes -o "$no_glut" = yes ;
> +#if test "$no_gl" = yes -o "$no_glu" = yes -o "$no_glut" = yes ;
> +if "$no_glu" = yes -o "$no_glut" = yes ;
>  then
>     AC_MSG_ERROR([
>  ================================================================================
> diff --git a/m4 b/m4
> --- a/m4
> +++ b/m4
> @@ -1 +1 @@
> -Subproject commit 87caf73968c8b57db276480acf85d5da8e7e48be
> +Subproject commit 87caf73968c8b57db276480acf85d5da8e7e48be-dirty
> diff --git a/main/main.c b/main/main.c
> index 830754e..e1e4723 100644
> --- a/main/main.c
> +++ b/main/main.c
> @@ -23,6 +23,9 @@ static char rcsid[] = "$Header: /private-cvsroot/visualization/Display/main/main
> 
>  #define  MAX_TITLE_LENGTH   200
> 
> +#define PROJECT_NAME "Display"
> +#define PROJECT_VERSION 1.5
> +
>  /* These two globals are required for SEAL's LibSul/SULGRAPHDATA */
>  int debug = 1;
>  int verbose = 1;
> @@ -36,7 +39,7 @@ private  void   parse_options (int argc, char *argv[],
> 
>  /* The first directory is set using compiler flag -D */
>  /*#define  HARD_CODED_DISPLAY_DIRECTORY1    "/usr/local/mni/lib"*/
> -/*#define  HARD_CODED_DISPLAY_DIRECTORY2    "/usr/local/lib"*/
> +#define  HARD_CODED_DISPLAY_DIRECTORY2    "/usr/local/minc2/lib"
>  #define  GLOBALS_FILENAME                 "Display.globals"
>  #define  MENU_FILENAME                    "Display.menu"
> 
> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 
> 
> 
> -- 
> Best regards,
> 
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development

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From jordigh at octave.org  Mon Nov  5 10:28:21 2012
From: jordigh at octave.org (=?UTF-8?Q?Jordi_Guti=C3=A9rrez_Hermoso?=)
Date: Mon, 5 Nov 2012 10:28:21 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
Message-ID: <CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>

On 5 November 2012 10:03, Jason Lerch <jason at phenogenomics.ca> wrote:
> No, I was using the master branch. I'll give the devel branch a try
> later - which I guess will include trying to understand the god
> forsaken cmake build system (I know that autoconf sucks and the
> thought of writing anything in m4 is horrid, but at least I got used
> to it!).

Cmake sucks too, since it's a lot more difficult to write custom tests
for it that aren't already built-in. It's less flexible than
autotools, but using it as a user should be no more difficult than
autotools. Instead of doing

    cd build-directory ## optional
    /path/to/configure
    make
    make install

do

    cd build-directory ## optional
    cmake /path/to/CMakeLists.txt
    make
    make install

As we say in IRC, "The 'suck' is a unit vector. A given foo doesn't
suck LESS, it just sucks in a direction a given hacker finds less
disagreeable."

HTH,
- Jordi G. H.

From vladimir.fonov at gmail.com  Mon Nov  5 10:39:40 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 5 Nov 2012 10:39:40 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
	<CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
Message-ID: <CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>

Are you ready to take over as official minc maintainer?

If you are not, then in this particular situation your 'suck' vector is
purely imaginary.


On Mon, Nov 5, 2012 at 10:28 AM, Jordi Guti?rrez Hermoso <jordigh at octave.org
> wrote:

> On 5 November 2012 10:03, Jason Lerch <jason at phenogenomics.ca> wrote:
> > No, I was using the master branch. I'll give the devel branch a try
> > later - which I guess will include trying to understand the god
> > forsaken cmake build system (I know that autoconf sucks and the
> > thought of writing anything in m4 is horrid, but at least I got used
> > to it!).
>
> Cmake sucks too, since it's a lot more difficult to write custom tests
> for it that aren't already built-in. It's less flexible than
> autotools, but using it as a user should be no more difficult than
> autotools. Instead of doing
>
>     cd build-directory ## optional
>     /path/to/configure
>     make
>     make install
>
> do
>
>     cd build-directory ## optional
>     cmake /path/to/CMakeLists.txt
>     make
>     make install
>
> As we say in IRC, "The 'suck' is a unit vector. A given foo doesn't
> suck LESS, it just sucks in a direction a given hacker finds less
> disagreeable."
>
> HTH,
> - Jordi G. H.
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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From jordigh at octave.org  Mon Nov  5 11:00:22 2012
From: jordigh at octave.org (=?UTF-8?Q?Jordi_Guti=C3=A9rrez_Hermoso?=)
Date: Mon, 5 Nov 2012 11:00:22 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
	<CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
	<CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>
Message-ID: <CAPHS2gwVUbvaCJ8LqgLSU2wxhd+Cm-mocPN-dh+tYSFpMKCxpA@mail.gmail.com>

On 5 November 2012 10:39, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
> On Mon, Nov 5, 2012 at 10:28 AM, Jordi Guti?rrez Hermoso
> <jordigh at octave.org> wrote:
>>
>> On 5 November 2012 10:03, Jason Lerch <jason at phenogenomics.ca> wrote:
>> > No, I was using the master branch. I'll give the devel branch a try
>> > later - which I guess will include trying to understand the god
>> > forsaken cmake build system (I know that autoconf sucks and the
>> > thought of writing anything in m4 is horrid, but at least I got used
>> > to it!).
>>
>> Cmake sucks too, since it's a lot more difficult to write custom tests
>> for it that aren't already built-in. It's less flexible than
>> autotools, but using it as a user should be no more difficult than
>> autotools. Instead of doing
>>
>>     cd build-directory ## optional
>>     /path/to/configure
>>     make
>>     make install
>>
>> do
>>
>>     cd build-directory ## optional
>>     cmake /path/to/CMakeLists.txt
>>     make
>>     make install
>>
>> As we say in IRC, "The 'suck' is a unit vector. A given foo doesn't
>> suck LESS, it just sucks in a direction a given hacker finds less
>> disagreeable."

> Are you ready to take over as official minc maintainer?

No, I didn't mean to say that CMake is a bad choice. Building is a
chore. All choices are equally annoying. For MINC, CMake may have a
'suck' vector in a better direction than autotools. I'm used to both
and I dislike both for different reasons, but I've disliked every
build system I've ever seen (ant, Scons, bjam...)

> If you are not, then in this particular situation your 'suck' vector is
> purely imaginary.

So it points straight up in the complex plane? :-)

- Jordi G. H.

From vladimir.fonov at gmail.com  Mon Nov  5 11:03:09 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 5 Nov 2012 11:03:09 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAPHS2gwVUbvaCJ8LqgLSU2wxhd+Cm-mocPN-dh+tYSFpMKCxpA@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
	<CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
	<CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>
	<CAPHS2gwVUbvaCJ8LqgLSU2wxhd+Cm-mocPN-dh+tYSFpMKCxpA@mail.gmail.com>
Message-ID: <CAMCwi7NEHVk6pW=6sCrJDiYHzrRhK42K-khU3=kNUrsiOU1Q+g@mail.gmail.com>

Exactly
On Nov 5, 2012 11:01 AM, "Jordi Guti?rrez Hermoso" <jordigh at octave.org>
wrote:

> On 5 November 2012 10:39, Vladimir S. FONOV <vladimir.fonov at gmail.com>
> wrote:
> > On Mon, Nov 5, 2012 at 10:28 AM, Jordi Guti?rrez Hermoso
> > <jordigh at octave.org> wrote:
> >>
> >> On 5 November 2012 10:03, Jason Lerch <jason at phenogenomics.ca> wrote:
> >> > No, I was using the master branch. I'll give the devel branch a try
> >> > later - which I guess will include trying to understand the god
> >> > forsaken cmake build system (I know that autoconf sucks and the
> >> > thought of writing anything in m4 is horrid, but at least I got used
> >> > to it!).
> >>
> >> Cmake sucks too, since it's a lot more difficult to write custom tests
> >> for it that aren't already built-in. It's less flexible than
> >> autotools, but using it as a user should be no more difficult than
> >> autotools. Instead of doing
> >>
> >>     cd build-directory ## optional
> >>     /path/to/configure
> >>     make
> >>     make install
> >>
> >> do
> >>
> >>     cd build-directory ## optional
> >>     cmake /path/to/CMakeLists.txt
> >>     make
> >>     make install
> >>
> >> As we say in IRC, "The 'suck' is a unit vector. A given foo doesn't
> >> suck LESS, it just sucks in a direction a given hacker finds less
> >> disagreeable."
>
> > Are you ready to take over as official minc maintainer?
>
> No, I didn't mean to say that CMake is a bad choice. Building is a
> chore. All choices are equally annoying. For MINC, CMake may have a
> 'suck' vector in a better direction than autotools. I'm used to both
> and I dislike both for different reasons, but I've disliked every
> build system I've ever seen (ant, Scons, bjam...)
>
> > If you are not, then in this particular situation your 'suck' vector is
> > purely imaginary.
>
> So it points straight up in the complex plane? :-)
>
> - Jordi G. H.
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
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From jason at phenogenomics.ca  Mon Nov  5 13:32:08 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 13:32:08 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAMCwi7NEHVk6pW=6sCrJDiYHzrRhK42K-khU3=kNUrsiOU1Q+g@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <6A3CA8E7-D374-47DE-A80A-DEA250C3A942@phenogenomics.ca>

Thanks for the cmake pointers. Two questions for the dumb ones amongst us (i.e. me):

* what's the equivalent of --prefix and our --with-build-path? 
* does everything (MINC, BICPL, etc.) have to be built with cmake or can one mix and match make and autotools?

I got the development branch, and tried running cmake, which barfs with the following error:

CMake Error at CMakeLists.txt:118 (find_package):
  By not providing "FindLIBMINC.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "LIBMINC", but
  CMake did not find one.

  Could not find a package configuration file provided by "LIBMINC" with any
  of the following names:

    LIBMINCConfig.cmake
    libminc-config.cmake

  Add the installation prefix of "LIBMINC" to CMAKE_PREFIX_PATH or set
  "LIBMINC_DIR" to a directory containing one of the above files.  If
  "LIBMINC" provides a separate development package or SDK, be sure it has
  been installed.


-- Configuring incomplete, errors occurred!

MINC and friends are compiled into /usr/local/minc2 (with autotools) with nary a .cmake file to be found under that tree. I'm sure I'm just forgetting something simple and obvious ?

Jason

On 2012-11-05, at 11:03 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:

> Exactly
> 
> On Nov 5, 2012 11:01 AM, "Jordi Guti?rrez Hermoso" <jordigh at octave.org> wrote:
> On 5 November 2012 10:39, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
> > On Mon, Nov 5, 2012 at 10:28 AM, Jordi Guti?rrez Hermoso
> > <jordigh at octave.org> wrote:
> >>
> >> On 5 November 2012 10:03, Jason Lerch <jason at phenogenomics.ca> wrote:
> >> > No, I was using the master branch. I'll give the devel branch a try
> >> > later - which I guess will include trying to understand the god
> >> > forsaken cmake build system (I know that autoconf sucks and the
> >> > thought of writing anything in m4 is horrid, but at least I got used
> >> > to it!).
> >>
> >> Cmake sucks too, since it's a lot more difficult to write custom tests
> >> for it that aren't already built-in. It's less flexible than
> >> autotools, but using it as a user should be no more difficult than
> >> autotools. Instead of doing
> >>
> >>     cd build-directory ## optional
> >>     /path/to/configure
> >>     make
> >>     make install
> >>
> >> do
> >>
> >>     cd build-directory ## optional
> >>     cmake /path/to/CMakeLists.txt
> >>     make
> >>     make install
> >>
> >> As we say in IRC, "The 'suck' is a unit vector. A given foo doesn't
> >> suck LESS, it just sucks in a direction a given hacker finds less
> >> disagreeable."
> 
> > Are you ready to take over as official minc maintainer?
> 
> No, I didn't mean to say that CMake is a bad choice. Building is a
> chore. All choices are equally annoying. For MINC, CMake may have a
> 'suck' vector in a better direction than autotools. I'm used to both
> and I dislike both for different reasons, but I've disliked every
> build system I've ever seen (ant, Scons, bjam...)
> 
> > If you are not, then in this particular situation your 'suck' vector is
> > purely imaginary.
> 
> So it points straight up in the complex plane? :-)
> 
> - Jordi G. H.
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development

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From vladimir.fonov at gmail.com  Mon Nov  5 13:34:35 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 5 Nov 2012 13:34:35 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <6A3CA8E7-D374-47DE-A80A-DEA250C3A942@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
	<CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
	<CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>
	<CAPHS2gwVUbvaCJ8LqgLSU2wxhd+Cm-mocPN-dh+tYSFpMKCxpA@mail.gmail.com>
	<CAMCwi7NEHVk6pW=6sCrJDiYHzrRhK42K-khU3=kNUrsiOU1Q+g@mail.gmail.com>
	<6A3CA8E7-D374-47DE-A80A-DEA250C3A942@phenogenomics.ca>
Message-ID: <CAMCwi7MXX7VdeKo_2xQxmJjUzKs31695qstxP9xSRMpjkEt7xA@mail.gmail.com>

Hello,

yes, basically you have to compile all the bits and pieces that Display
uses with CMake ( or just try compiling Display using
https://github.com/BIC-MNI/minc-toolkit )


On Mon, Nov 5, 2012 at 1:32 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> Thanks for the cmake pointers. Two questions for the dumb ones amongst us
> (i.e. me):
>
> * what's the equivalent of --prefix and our --with-build-path?
> * does everything (MINC, BICPL, etc.) have to be built with cmake or can
> one mix and match make and autotools?
>
> I got the development branch, and tried running cmake, which barfs with
> the following error:
>
> CMake Error at CMakeLists.txt:118 (find_package):
>   By not providing "FindLIBMINC.cmake" in CMAKE_MODULE_PATH this project
> has
>   asked CMake to find a package configuration file provided by "LIBMINC",
> but
>   CMake did not find one.
>
>   Could not find a package configuration file provided by "LIBMINC" with
> any
>   of the following names:
>
>     LIBMINCConfig.cmake
>     libminc-config.cmake
>
>   Add the installation prefix of "LIBMINC" to CMAKE_PREFIX_PATH or set
>   "LIBMINC_DIR" to a directory containing one of the above files.  If
>   "LIBMINC" provides a separate development package or SDK, be sure it has
>   been installed.
>
>
> -- Configuring incomplete, errors occurred!
>
> MINC and friends are compiled into /usr/local/minc2 (with autotools) with
> nary a .cmake file to be found under that tree. I'm sure I'm just
> forgetting something simple and obvious ?
>
> Jason
>
> On 2012-11-05, at 11:03 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com>
> wrote:
>
> Exactly
> On Nov 5, 2012 11:01 AM, "Jordi Guti?rrez Hermoso" <jordigh at octave.org>
> wrote:
>
>> On 5 November 2012 10:39, Vladimir S. FONOV <vladimir.fonov at gmail.com>
>> wrote:
>> > On Mon, Nov 5, 2012 at 10:28 AM, Jordi Guti?rrez Hermoso
>> > <jordigh at octave.org> wrote:
>> >>
>> >> On 5 November 2012 10:03, Jason Lerch <jason at phenogenomics.ca> wrote:
>> >> > No, I was using the master branch. I'll give the devel branch a try
>> >> > later - which I guess will include trying to understand the god
>> >> > forsaken cmake build system (I know that autoconf sucks and the
>> >> > thought of writing anything in m4 is horrid, but at least I got used
>> >> > to it!).
>> >>
>> >> Cmake sucks too, since it's a lot more difficult to write custom tests
>> >> for it that aren't already built-in. It's less flexible than
>> >> autotools, but using it as a user should be no more difficult than
>> >> autotools. Instead of doing
>> >>
>> >>     cd build-directory ## optional
>> >>     /path/to/configure
>> >>     make
>> >>     make install
>> >>
>> >> do
>> >>
>> >>     cd build-directory ## optional
>> >>     cmake /path/to/CMakeLists.txt
>> >>     make
>> >>     make install
>> >>
>> >> As we say in IRC, "The 'suck' is a unit vector. A given foo doesn't
>> >> suck LESS, it just sucks in a direction a given hacker finds less
>> >> disagreeable."
>>
>> > Are you ready to take over as official minc maintainer?
>>
>> No, I didn't mean to say that CMake is a bad choice. Building is a
>> chore. All choices are equally annoying. For MINC, CMake may have a
>> 'suck' vector in a better direction than autotools. I'm used to both
>> and I dislike both for different reasons, but I've disliked every
>> build system I've ever seen (ant, Scons, bjam...)
>>
>> > If you are not, then in this particular situation your 'suck' vector is
>> > purely imaginary.
>>
>> So it points straight up in the complex plane? :-)
>>
>> - Jordi G. H.
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
>


-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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From jordigh at octave.org  Mon Nov  5 13:42:35 2012
From: jordigh at octave.org (=?UTF-8?Q?Jordi_Guti=C3=A9rrez_Hermoso?=)
Date: Mon, 5 Nov 2012 13:42:35 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <6A3CA8E7-D374-47DE-A80A-DEA250C3A942@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
	<CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
	<CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>
	<CAPHS2gwVUbvaCJ8LqgLSU2wxhd+Cm-mocPN-dh+tYSFpMKCxpA@mail.gmail.com>
	<CAMCwi7NEHVk6pW=6sCrJDiYHzrRhK42K-khU3=kNUrsiOU1Q+g@mail.gmail.com>
	<6A3CA8E7-D374-47DE-A80A-DEA250C3A942@phenogenomics.ca>
Message-ID: <CAPHS2gwR6nf_W3sLaJcaCWLcNtCoW+5b08PU_+Qo4pg7eLiqBg@mail.gmail.com>

On 5 November 2012 13:32, Jason Lerch <jason at phenogenomics.ca> wrote:
> Thanks for the cmake pointers. Two questions for the dumb ones amongst us
> (i.e. me):
>
> * what's the equivalent of --prefix

    cmake -DCMAKE_INSTALL_PREFIX=/usr

Basically, you can use -D to set any CMake variable.

> and our --with-build-path?

This I don't know, but if you do "ccmake ." in your build directory,
you'll get an ncurses interface for setting other CMake variables.
They're mostly documented in the giant cmake manpage.

- Jordi G. H.

From vladimir.fonov at gmail.com  Mon Nov  5 13:54:33 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 05 Nov 2012 13:54:33 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAPHS2gwR6nf_W3sLaJcaCWLcNtCoW+5b08PU_+Qo4pg7eLiqBg@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<CAMCwi7MMnO7=R6vHMFgc94Uk-atbSw7pcp4i5o=k+p_AYYRVEQ@mail.gmail.com>
	<68E24269-977C-4004-B5EC-6D43E47A342D@phenogenomics.ca>
	<CAPHS2gzwUnq6skyn0tmiavq0GouLNSvdOqeFgEBCsm5CFvQZ2A@mail.gmail.com>
	<CAMCwi7NxdtNsm9cYypWjfxDRYBMnVyAmn6xJL23+KK5GjA=pRw@mail.gmail.com>
	<CAPHS2gwVUbvaCJ8LqgLSU2wxhd+Cm-mocPN-dh+tYSFpMKCxpA@mail.gmail.com>
	<CAMCwi7NEHVk6pW=6sCrJDiYHzrRhK42K-khU3=kNUrsiOU1Q+g@mail.gmail.com>
	<6A3CA8E7-D374-47DE-A80A-DEA250C3A942@phenogenomics.ca>
	<CAPHS2gwR6nf_W3sLaJcaCWLcNtCoW+5b08PU_+Qo4pg7eLiqBg@mail.gmail.com>
Message-ID: <50980B69.4000809@gmail.com>

Hello,

On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
> Basically, you can use -D to set any CMake variable.
>
>> and our --with-build-path?
>
> This I don't know, but if you do "ccmake ." in your build directory,
> you'll get an ncurses interface for setting other CMake variables.
> They're mostly documented in the giant cmake manpage.

Basically each MINC package which provides a library 
(libminc,ebtks,bicpl etc) creates a configuration file, and you have to 
specify it's location using CMAKE variables. So, there is no direct 
equivalent to with-build-path anymore.

-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From jason at phenogenomics.ca  Mon Nov  5 14:35:04 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 14:35:04 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <50980B69.4000809@gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <9D1CC348-FA24-4C26-A950-B005BAA74FFA@phenogenomics.ca>

Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to demonstrate my ignorance: tried to build minc from git master, and cmake produces the following:

<snip>
-- Looking for include file pwd.h - found
-- Found BISON: /usr/bin/bison (found version "2.5") 
-- Found FLEX: /usr/bin/flex (found version "2.5.35") 
CMake Error at progs/CMakeLists.txt:191 (INSTALL):
  install FILES given directory "/home/jason/git/minc/progs/minchistory" to
  install.


CMake Error at progs/CMakeLists.txt:196 (INSTALL):
  install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik" to
  install.


-- Configuring incomplete, errors occurred!

(same error whether I type 'cmake CMakeLists.txt' or whether I add the -DCMAKE_INSTALL_PREFIX)

Is there an equivalent of config.log to see what it's trying to do? Does that error ring any bells?

Jason


On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Hello,
> 
> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
>> Basically, you can use -D to set any CMake variable.
>> 
>>> and our --with-build-path?
>> 
>> This I don't know, but if you do "ccmake ." in your build directory,
>> you'll get an ncurses interface for setting other CMake variables.
>> They're mostly documented in the giant cmake manpage.
> 
> Basically each MINC package which provides a library (libminc,ebtks,bicpl etc) creates a configuration file, and you have to specify it's location using CMAKE variables. So, there is no direct equivalent to with-build-path anymore.
> 
> -- 
> Best regards,
> 
> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From vladimir.fonov at gmail.com  Mon Nov  5 14:44:11 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 05 Nov 2012 14:44:11 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <9D1CC348-FA24-4C26-A950-B005BAA74FFA@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<9D1CC348-FA24-4C26-A950-B005BAA74FFA@phenogenomics.ca>
Message-ID: <5098170B.2020706@gmail.com>

Hello,

use libminc ( https://github.com/BIC-MNI/libminc ) I just convert all 
CMakeLists to use that instead of minc.

I think, basically what you see on the screen is your config.log

On 12-11-05 02:35 PM, Jason Lerch wrote:
> Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to demonstrate my ignorance: tried to build minc from git master, and cmake produces the following:
>
> <snip>
> -- Looking for include file pwd.h - found
> -- Found BISON: /usr/bin/bison (found version "2.5")
> -- Found FLEX: /usr/bin/flex (found version "2.5.35")
> CMake Error at progs/CMakeLists.txt:191 (INSTALL):
>    install FILES given directory "/home/jason/git/minc/progs/minchistory" to
>    install.
>
>
> CMake Error at progs/CMakeLists.txt:196 (INSTALL):
>    install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik" to
>    install.
>
>
> -- Configuring incomplete, errors occurred!
>
> (same error whether I type 'cmake CMakeLists.txt' or whether I add the -DCMAKE_INSTALL_PREFIX)
>
> Is there an equivalent of config.log to see what it's trying to do? Does that error ring any bells?
>
> Jason
>
>
> On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>
>> Hello,
>>
>> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
>>> Basically, you can use -D to set any CMake variable.
>>>
>>>> and our --with-build-path?
>>>
>>> This I don't know, but if you do "ccmake ." in your build directory,
>>> you'll get an ncurses interface for setting other CMake variables.
>>> They're mostly documented in the giant cmake manpage.
>>
>> Basically each MINC package which provides a library (libminc,ebtks,bicpl etc) creates a configuration file, and you have to specify it's location using CMAKE variables. So, there is no direct equivalent to with-build-path anymore.
>>
>> --
>> Best regards,
>>
>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From jason at phenogenomics.ca  Mon Nov  5 14:50:19 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 14:50:19 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <5098170B.2020706@gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <BC5CCF78-71F8-4892-B483-2BBFB81076AC@phenogenomics.ca>

So https://github.com/BIC-MNI/minc is deprecated? And I'm guessing the non-API bits are here: https://github.com/BIC-MNI/minc-tools?

Jason

On 2012-11-05, at 2:44 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Hello,
> 
> use libminc ( https://github.com/BIC-MNI/libminc ) I just convert all CMakeLists to use that instead of minc.
> 
> I think, basically what you see on the screen is your config.log
> 
> On 12-11-05 02:35 PM, Jason Lerch wrote:
>> Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to demonstrate my ignorance: tried to build minc from git master, and cmake produces the following:
>> 
>> <snip>
>> -- Looking for include file pwd.h - found
>> -- Found BISON: /usr/bin/bison (found version "2.5")
>> -- Found FLEX: /usr/bin/flex (found version "2.5.35")
>> CMake Error at progs/CMakeLists.txt:191 (INSTALL):
>>   install FILES given directory "/home/jason/git/minc/progs/minchistory" to
>>   install.
>> 
>> 
>> CMake Error at progs/CMakeLists.txt:196 (INSTALL):
>>   install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik" to
>>   install.
>> 
>> 
>> -- Configuring incomplete, errors occurred!
>> 
>> (same error whether I type 'cmake CMakeLists.txt' or whether I add the -DCMAKE_INSTALL_PREFIX)
>> 
>> Is there an equivalent of config.log to see what it's trying to do? Does that error ring any bells?
>> 
>> Jason
>> 
>> 
>> On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>> 
>>> Hello,
>>> 
>>> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
>>>> Basically, you can use -D to set any CMake variable.
>>>> 
>>>>> and our --with-build-path?
>>>> 
>>>> This I don't know, but if you do "ccmake ." in your build directory,
>>>> you'll get an ncurses interface for setting other CMake variables.
>>>> They're mostly documented in the giant cmake manpage.
>>> 
>>> Basically each MINC package which provides a library (libminc,ebtks,bicpl etc) creates a configuration file, and you have to specify it's location using CMAKE variables. So, there is no direct equivalent to with-build-path anymore.
>>> 
>>> --
>>> Best regards,
>>> 
>>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>> _______________________________________________
>>> MINC-development mailing list
>>> MINC-development at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
> 
> 
> -- 
> Best regards,
> 
> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From vladimir.fonov at gmail.com  Mon Nov  5 14:54:21 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 5 Nov 2012 14:54:21 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <BC5CCF78-71F8-4892-B483-2BBFB81076AC@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<9D1CC348-FA24-4C26-A950-B005BAA74FFA@phenogenomics.ca>
	<5098170B.2020706@gmail.com>
	<BC5CCF78-71F8-4892-B483-2BBFB81076AC@phenogenomics.ca>
Message-ID: <CAMCwi7Mm6cgSfVbs5n+cfU_c-fMGqwgYEbVX4Y34DVtufdcB1g@mail.gmail.com>

Yes,

that is correct.


On Mon, Nov 5, 2012 at 2:50 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> So https://github.com/BIC-MNI/minc is deprecated? And I'm guessing the
> non-API bits are here: https://github.com/BIC-MNI/minc-tools?
>
> Jason
>
> On 2012-11-05, at 2:44 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
> wrote:
>
> > Hello,
> >
> > use libminc ( https://github.com/BIC-MNI/libminc ) I just convert all
> CMakeLists to use that instead of minc.
> >
> > I think, basically what you see on the screen is your config.log
> >
> > On 12-11-05 02:35 PM, Jason Lerch wrote:
> >> Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to
> demonstrate my ignorance: tried to build minc from git master, and cmake
> produces the following:
> >>
> >> <snip>
> >> -- Looking for include file pwd.h - found
> >> -- Found BISON: /usr/bin/bison (found version "2.5")
> >> -- Found FLEX: /usr/bin/flex (found version "2.5.35")
> >> CMake Error at progs/CMakeLists.txt:191 (INSTALL):
> >>   install FILES given directory
> "/home/jason/git/minc/progs/minchistory" to
> >>   install.
> >>
> >>
> >> CMake Error at progs/CMakeLists.txt:196 (INSTALL):
> >>   install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik"
> to
> >>   install.
> >>
> >>
> >> -- Configuring incomplete, errors occurred!
> >>
> >> (same error whether I type 'cmake CMakeLists.txt' or whether I add the
> -DCMAKE_INSTALL_PREFIX)
> >>
> >> Is there an equivalent of config.log to see what it's trying to do?
> Does that error ring any bells?
> >>
> >> Jason
> >>
> >>
> >> On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <
> vladimir.fonov at gmail.com> wrote:
> >>
> >>> Hello,
> >>>
> >>> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
> >>>> Basically, you can use -D to set any CMake variable.
> >>>>
> >>>>> and our --with-build-path?
> >>>>
> >>>> This I don't know, but if you do "ccmake ." in your build directory,
> >>>> you'll get an ncurses interface for setting other CMake variables.
> >>>> They're mostly documented in the giant cmake manpage.
> >>>
> >>> Basically each MINC package which provides a library
> (libminc,ebtks,bicpl etc) creates a configuration file, and you have to
> specify it's location using CMAKE variables. So, there is no direct
> equivalent to with-build-path anymore.
> >>>
> >>> --
> >>> Best regards,
> >>>
> >>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> >>> _______________________________________________
> >>> MINC-development mailing list
> >>> MINC-development at bic.mni.mcgill.ca
> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >>
> >> _______________________________________________
> >> MINC-development mailing list
> >> MINC-development at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >>
> >
> >
> > --
> > Best regards,
> >
> > Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
-------------- next part --------------
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From jason at phenogenomics.ca  Mon Nov  5 14:55:27 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 14:55:27 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <5098170B.2020706@gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <B6B54B16-8968-4112-98EA-37AB620A0D7E@phenogenomics.ca>

libminc (git master) lets me run cmake without issues then bombs here during make:

Linking C executable test_arg_parse
Linking C executable mincapi
[ 88%] Built target test_arg_parse
Scanning dependencies of target test_mconv
[ 89%] Building C object testdir/CMakeFiles/test_mconv.dir/test_mconv.c.o
[ 89%] Built target mincapi
Scanning dependencies of target test_speed
[ 90%] Linking C executable test_mconv
Building C object testdir/CMakeFiles/test_speed.dir/test_speed.c.o
Linking C executable test_speed
[ 90%] Built target test_mconv
Scanning dependencies of target test_xfm
[ 91%] Building C object testdir/CMakeFiles/test_xfm.dir/test_xfm.c.o
Linking C executable test_xfm
[ 91%] Built target test_speed
Scanning dependencies of target fuzzy_volume_similarity
[ 92%] Building CXX object ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/fuzzy_volume_similarity.cpp.o
/home/jason/git/libminc/ezminc/examples/fuzzy_volume_similarity.cpp:15:23: fatal error: minc_1_rw.h: No such file or directory
compilation terminated.
make[2]: *** [ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/fuzzy_volume_similarity.cpp.o] Error 1
make[1]: *** [ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 92%] Built target test_xfm
make: *** [all] Error 2

Any hints? I'll dig into it if not.

Jason

On 2012-11-05, at 2:44 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Hello,
> 
> use libminc ( https://github.com/BIC-MNI/libminc ) I just convert all CMakeLists to use that instead of minc.
> 
> I think, basically what you see on the screen is your config.log
> 
> On 12-11-05 02:35 PM, Jason Lerch wrote:
>> Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to demonstrate my ignorance: tried to build minc from git master, and cmake produces the following:
>> 
>> <snip>
>> -- Looking for include file pwd.h - found
>> -- Found BISON: /usr/bin/bison (found version "2.5")
>> -- Found FLEX: /usr/bin/flex (found version "2.5.35")
>> CMake Error at progs/CMakeLists.txt:191 (INSTALL):
>>   install FILES given directory "/home/jason/git/minc/progs/minchistory" to
>>   install.
>> 
>> 
>> CMake Error at progs/CMakeLists.txt:196 (INSTALL):
>>   install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik" to
>>   install.
>> 
>> 
>> -- Configuring incomplete, errors occurred!
>> 
>> (same error whether I type 'cmake CMakeLists.txt' or whether I add the -DCMAKE_INSTALL_PREFIX)
>> 
>> Is there an equivalent of config.log to see what it's trying to do? Does that error ring any bells?
>> 
>> Jason
>> 
>> 
>> On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>> 
>>> Hello,
>>> 
>>> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
>>>> Basically, you can use -D to set any CMake variable.
>>>> 
>>>>> and our --with-build-path?
>>>> 
>>>> This I don't know, but if you do "ccmake ." in your build directory,
>>>> you'll get an ncurses interface for setting other CMake variables.
>>>> They're mostly documented in the giant cmake manpage.
>>> 
>>> Basically each MINC package which provides a library (libminc,ebtks,bicpl etc) creates a configuration file, and you have to specify it's location using CMAKE variables. So, there is no direct equivalent to with-build-path anymore.
>>> 
>>> --
>>> Best regards,
>>> 
>>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>> _______________________________________________
>>> MINC-development mailing list
>>> MINC-development at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
> 
> 
> -- 
> Best regards,
> 
> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From jason at phenogenomics.ca  Mon Nov  5 15:00:06 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 15:00:06 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <B6B54B16-8968-4112-98EA-37AB620A0D7E@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <AC8B71A6-7EF7-46E2-A249-134FCDB2F4FE@phenogenomics.ca>

Related cmake question - how does one get it to accept CPPFLAGS (or other similar environment variables)? And how can I get cmake/make to show me the actual arguments used by gcc/g++?

Thanks,

Jason

On 2012-11-05, at 2:55 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> libminc (git master) lets me run cmake without issues then bombs here during make:
> 
> Linking C executable test_arg_parse
> Linking C executable mincapi
> [ 88%] Built target test_arg_parse
> Scanning dependencies of target test_mconv
> [ 89%] Building C object testdir/CMakeFiles/test_mconv.dir/test_mconv.c.o
> [ 89%] Built target mincapi
> Scanning dependencies of target test_speed
> [ 90%] Linking C executable test_mconv
> Building C object testdir/CMakeFiles/test_speed.dir/test_speed.c.o
> Linking C executable test_speed
> [ 90%] Built target test_mconv
> Scanning dependencies of target test_xfm
> [ 91%] Building C object testdir/CMakeFiles/test_xfm.dir/test_xfm.c.o
> Linking C executable test_xfm
> [ 91%] Built target test_speed
> Scanning dependencies of target fuzzy_volume_similarity
> [ 92%] Building CXX object ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/fuzzy_volume_similarity.cpp.o
> /home/jason/git/libminc/ezminc/examples/fuzzy_volume_similarity.cpp:15:23: fatal error: minc_1_rw.h: No such file or directory
> compilation terminated.
> make[2]: *** [ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/fuzzy_volume_similarity.cpp.o] Error 1
> make[1]: *** [ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs....
> [ 92%] Built target test_xfm
> make: *** [all] Error 2
> 
> Any hints? I'll dig into it if not.
> 
> Jason
> 
> On 2012-11-05, at 2:44 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
> 
>> Hello,
>> 
>> use libminc ( https://github.com/BIC-MNI/libminc ) I just convert all CMakeLists to use that instead of minc.
>> 
>> I think, basically what you see on the screen is your config.log
>> 
>> On 12-11-05 02:35 PM, Jason Lerch wrote:
>>> Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to demonstrate my ignorance: tried to build minc from git master, and cmake produces the following:
>>> 
>>> <snip>
>>> -- Looking for include file pwd.h - found
>>> -- Found BISON: /usr/bin/bison (found version "2.5")
>>> -- Found FLEX: /usr/bin/flex (found version "2.5.35")
>>> CMake Error at progs/CMakeLists.txt:191 (INSTALL):
>>>  install FILES given directory "/home/jason/git/minc/progs/minchistory" to
>>>  install.
>>> 
>>> 
>>> CMake Error at progs/CMakeLists.txt:196 (INSTALL):
>>>  install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik" to
>>>  install.
>>> 
>>> 
>>> -- Configuring incomplete, errors occurred!
>>> 
>>> (same error whether I type 'cmake CMakeLists.txt' or whether I add the -DCMAKE_INSTALL_PREFIX)
>>> 
>>> Is there an equivalent of config.log to see what it's trying to do? Does that error ring any bells?
>>> 
>>> Jason
>>> 
>>> 
>>> On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>>> 
>>>> Hello,
>>>> 
>>>> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
>>>>> Basically, you can use -D to set any CMake variable.
>>>>> 
>>>>>> and our --with-build-path?
>>>>> 
>>>>> This I don't know, but if you do "ccmake ." in your build directory,
>>>>> you'll get an ncurses interface for setting other CMake variables.
>>>>> They're mostly documented in the giant cmake manpage.
>>>> 
>>>> Basically each MINC package which provides a library (libminc,ebtks,bicpl etc) creates a configuration file, and you have to specify it's location using CMAKE variables. So, there is no direct equivalent to with-build-path anymore.
>>>> 
>>>> --
>>>> Best regards,
>>>> 
>>>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>>> _______________________________________________
>>>> MINC-development mailing list
>>>> MINC-development at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>> 
>>> _______________________________________________
>>> MINC-development mailing list
>>> MINC-development at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>> 
>> 
>> 
>> -- 
>> Best regards,
>> 
>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From vladimir.fonov at gmail.com  Mon Nov  5 15:00:42 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 05 Nov 2012 15:00:42 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <B6B54B16-8968-4112-98EA-37AB620A0D7E@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<B6B54B16-8968-4112-98EA-37AB620A0D7E@phenogenomics.ca>
Message-ID: <50981AEA.7020007@gmail.com>

Hello,

looks like you found a bug.

You can disable building this thing by setting 
LIBMINC_BUILD_EZMINC_EXAMPLES to OFF

i.e -DLIBMINC_BUILD_EZMINC_EXAMPLES=OFF

what version of CMake is included in this version of Ubuntu ?

On 12-11-05 02:55 PM, Jason Lerch wrote:
> /home/jason/git/libminc/ezminc/examples/fuzzy_volume_similarity.cpp:15:23: fatal error: minc_1_rw.h: No such file or directory


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From jason at phenogenomics.ca  Mon Nov  5 15:02:15 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 15:02:15 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <AC8B71A6-7EF7-46E2-A249-134FCDB2F4FE@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <DAA5550D-E5CB-443B-9117-DF6573AAA0FD@phenogenomics.ca>

Answered my own question - this lets libminc build:

cmake -DCMAKE_INSTALL_PREFIX=/usr/local/minc2 -DCMAKE_CXX_FLAGS="-I/home/jason/git/libminc/ezminc" CMakeLists.txt

Jason

On 2012-11-05, at 3:00 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> Related cmake question - how does one get it to accept CPPFLAGS (or other similar environment variables)? And how can I get cmake/make to show me the actual arguments used by gcc/g++?
> 
> Thanks,
> 
> Jason
> 
> On 2012-11-05, at 2:55 PM, Jason Lerch <jason at phenogenomics.ca> wrote:
> 
>> libminc (git master) lets me run cmake without issues then bombs here during make:
>> 
>> Linking C executable test_arg_parse
>> Linking C executable mincapi
>> [ 88%] Built target test_arg_parse
>> Scanning dependencies of target test_mconv
>> [ 89%] Building C object testdir/CMakeFiles/test_mconv.dir/test_mconv.c.o
>> [ 89%] Built target mincapi
>> Scanning dependencies of target test_speed
>> [ 90%] Linking C executable test_mconv
>> Building C object testdir/CMakeFiles/test_speed.dir/test_speed.c.o
>> Linking C executable test_speed
>> [ 90%] Built target test_mconv
>> Scanning dependencies of target test_xfm
>> [ 91%] Building C object testdir/CMakeFiles/test_xfm.dir/test_xfm.c.o
>> Linking C executable test_xfm
>> [ 91%] Built target test_speed
>> Scanning dependencies of target fuzzy_volume_similarity
>> [ 92%] Building CXX object ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/fuzzy_volume_similarity.cpp.o
>> /home/jason/git/libminc/ezminc/examples/fuzzy_volume_similarity.cpp:15:23: fatal error: minc_1_rw.h: No such file or directory
>> compilation terminated.
>> make[2]: *** [ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/fuzzy_volume_similarity.cpp.o] Error 1
>> make[1]: *** [ezminc/examples/CMakeFiles/fuzzy_volume_similarity.dir/all] Error 2
>> make[1]: *** Waiting for unfinished jobs....
>> [ 92%] Built target test_xfm
>> make: *** [all] Error 2
>> 
>> Any hints? I'll dig into it if not.
>> 
>> Jason
>> 
>> On 2012-11-05, at 2:44 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>> 
>>> Hello,
>>> 
>>> use libminc ( https://github.com/BIC-MNI/libminc ) I just convert all CMakeLists to use that instead of minc.
>>> 
>>> I think, basically what you see on the screen is your config.log
>>> 
>>> On 12-11-05 02:35 PM, Jason Lerch wrote:
>>>> Thanks Jordi and Vlad for the cmake tips! Onwards in my attempt to demonstrate my ignorance: tried to build minc from git master, and cmake produces the following:
>>>> 
>>>> <snip>
>>>> -- Looking for include file pwd.h - found
>>>> -- Found BISON: /usr/bin/bison (found version "2.5")
>>>> -- Found FLEX: /usr/bin/flex (found version "2.5.35")
>>>> CMake Error at progs/CMakeLists.txt:191 (INSTALL):
>>>> install FILES given directory "/home/jason/git/minc/progs/minchistory" to
>>>> install.
>>>> 
>>>> 
>>>> CMake Error at progs/CMakeLists.txt:196 (INSTALL):
>>>> install PROGRAMS given directory "/home/jason/git/minc/progs/mincpik" to
>>>> install.
>>>> 
>>>> 
>>>> -- Configuring incomplete, errors occurred!
>>>> 
>>>> (same error whether I type 'cmake CMakeLists.txt' or whether I add the -DCMAKE_INSTALL_PREFIX)
>>>> 
>>>> Is there an equivalent of config.log to see what it's trying to do? Does that error ring any bells?
>>>> 
>>>> Jason
>>>> 
>>>> 
>>>> On 2012-11-05, at 1:54 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
>>>> 
>>>>> Hello,
>>>>> 
>>>>> On 12-11-05 01:42 PM, Jordi Guti?rrez Hermoso wrote:
>>>>>> Basically, you can use -D to set any CMake variable.
>>>>>> 
>>>>>>> and our --with-build-path?
>>>>>> 
>>>>>> This I don't know, but if you do "ccmake ." in your build directory,
>>>>>> you'll get an ncurses interface for setting other CMake variables.
>>>>>> They're mostly documented in the giant cmake manpage.
>>>>> 
>>>>> Basically each MINC package which provides a library (libminc,ebtks,bicpl etc) creates a configuration file, and you have to specify it's location using CMAKE variables. So, there is no direct equivalent to with-build-path anymore.
>>>>> 
>>>>> --
>>>>> Best regards,
>>>>> 
>>>>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>>>> _______________________________________________
>>>>> MINC-development mailing list
>>>>> MINC-development at bic.mni.mcgill.ca
>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>>> 
>>>> _______________________________________________
>>>> MINC-development mailing list
>>>> MINC-development at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>>> 
>>> 
>>> 
>>> -- 
>>> Best regards,
>>> 
>>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>> _______________________________________________
>>> MINC-development mailing list
>>> MINC-development at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From jason at phenogenomics.ca  Mon Nov  5 15:02:52 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 15:02:52 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <50981AEA.7020007@gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <B6280E17-607E-4BEF-B872-D006A0AA9996@phenogenomics.ca>

cmake version 2.8.9



Jason

On 2012-11-05, at 3:00 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Hello,
> 
> looks like you found a bug.
> 
> You can disable building this thing by setting LIBMINC_BUILD_EZMINC_EXAMPLES to OFF
> 
> i.e -DLIBMINC_BUILD_EZMINC_EXAMPLES=OFF
> 
> what version of CMake is included in this version of Ubuntu ?
> 
> On 12-11-05 02:55 PM, Jason Lerch wrote:
>> /home/jason/git/libminc/ezminc/examples/fuzzy_volume_similarity.cpp:15:23: fatal error: minc_1_rw.h: No such file or directory
> 
> 
> -- 
> Best regards,
> 
> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From jason at phenogenomics.ca  Mon Nov  5 15:19:58 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 15:19:58 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <B6280E17-607E-4BEF-B872-D006A0AA9996@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <F61D43D2-1919-4ADB-86CC-E65C26767BD6@phenogenomics.ca>

BTW, minc-tools (git master) has the exact same issue I described earlier:

-- Looking for include file pwd.h - found
-- Found BISON: /usr/bin/bison (found version "2.5") 
-- Found FLEX: /usr/bin/flex (found version "2.5.35") 
CMake Error at progs/CMakeLists.txt:191 (INSTALL):
  install FILES given directory "/home/jason/git/minctools/progs/minchistory"
  to install.


CMake Error at progs/CMakeLists.txt:196 (INSTALL):
  install PROGRAMS given directory "/home/jason/git/minctools/progs/mincpik"
  to install.


-- Configuring incomplete, errors occurred!

(after running: cmake -DCMAKE_INSTALL_PREFIX=/usr/local/minc2 -DCMAKE_PREFIX_PATH=/usr/local/minc2/lib CMakeLists.txt)

Jason


On 2012-11-05, at 3:02 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> cmake version 2.8.9
> 
> 
> 
> Jason
> 
> On 2012-11-05, at 3:00 PM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:
> 
>> Hello,
>> 
>> looks like you found a bug.
>> 
>> You can disable building this thing by setting LIBMINC_BUILD_EZMINC_EXAMPLES to OFF
>> 
>> i.e -DLIBMINC_BUILD_EZMINC_EXAMPLES=OFF
>> 
>> what version of CMake is included in this version of Ubuntu ?
>> 
>> On 12-11-05 02:55 PM, Jason Lerch wrote:
>>> /home/jason/git/libminc/ezminc/examples/fuzzy_volume_similarity.cpp:15:23: fatal error: minc_1_rw.h: No such file or directory
>> 
>> 
>> -- 
>> Best regards,
>> 
>> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From a.janke at gmail.com  Mon Nov  5 15:23:28 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 6 Nov 2012 06:23:28 +1000
Subject: [MINC-development] compiling Display from github
In-Reply-To: <F61D43D2-1919-4ADB-86CC-E65C26767BD6@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<B6280E17-607E-4BEF-B872-D006A0AA9996@phenogenomics.ca>
	<F61D43D2-1919-4ADB-86CC-E65C26767BD6@phenogenomics.ca>
Message-ID: <CAG0CB22nBXHAbvjX46CaxEtwPVU2pEJRqV3FC_ATPKeOqC9ffw@mail.gmail.com>

BTW, at this juncture I should point out that there are now two
"official" build systems for MINC autoconf and cmake. Vlad has put a
lot of work into cmake so that things work for MINC+ITK.
I am still maintaining the autoconf builds.

If there is something wrong with either of them you know who to bug now.


a

On 6 November 2012 06:19, Jason Lerch <jason at phenogenomics.ca> wrote:
> BTW, minc-tools (git master) has the exact same issue I described earlier:

From jason at phenogenomics.ca  Mon Nov  5 15:31:07 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 5 Nov 2012 15:31:07 -0500
Subject: [MINC-development] compiling Display from github
In-Reply-To: <CAG0CB22nBXHAbvjX46CaxEtwPVU2pEJRqV3FC_ATPKeOqC9ffw@mail.gmail.com>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
Message-ID: <108F5FF8-F6B3-4E2B-BF76-BCFCE46B4862@phenogenomics.ca>

Ah, excellent!! Is that the plan for the indefinite future (two build-systems) or is one of them on the way out?

Jason

On 2012-11-05, at 3:23 PM, Andrew Janke <a.janke at gmail.com> wrote:

> BTW, at this juncture I should point out that there are now two
> "official" build systems for MINC autoconf and cmake. Vlad has put a
> lot of work into cmake so that things work for MINC+ITK.
> I am still maintaining the autoconf builds.
> 
> If there is something wrong with either of them you know who to bug now.
> 
> 
> a
> 
> On 6 November 2012 06:19, Jason Lerch <jason at phenogenomics.ca> wrote:
>> BTW, minc-tools (git master) has the exact same issue I described earlier:
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


From a.janke at gmail.com  Mon Nov  5 16:01:39 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 6 Nov 2012 07:01:39 +1000
Subject: [MINC-development] compiling Display from github
In-Reply-To: <108F5FF8-F6B3-4E2B-BF76-BCFCE46B4862@phenogenomics.ca>
References: <7B922B92-6354-44B7-B0D9-E04D1F3C1D42@phenogenomics.ca>
	<B6280E17-607E-4BEF-B872-D006A0AA9996@phenogenomics.ca>
	<F61D43D2-1919-4ADB-86CC-E65C26767BD6@phenogenomics.ca>
	<CAG0CB22nBXHAbvjX46CaxEtwPVU2pEJRqV3FC_ATPKeOqC9ffw@mail.gmail.com>
	<108F5FF8-F6B3-4E2B-BF76-BCFCE46B4862@phenogenomics.ca>
Message-ID: <CAG0CB20kio3ekdBr-pm_KqsYxt2Tjbxjc1QOdZeyCosgA=KHbg@mail.gmail.com>

Horses for courses.

I will maintain the autoconf build for linbminc and minc-tools
indefinitely (or at least until cmake supports libtool for library
versioning and Debian agrees to use it!). Other tools that don't make
libraries will be more up to whoever takes the orphans on.

Certainly there is no plans for autoconf for vlads extra stuff written in ITK!

a


On 6 November 2012 06:31, Jason Lerch <jason at phenogenomics.ca> wrote:
> Ah, excellent!! Is that the plan for the indefinite future (two build-systems) or is one of them on the way out?

From vladimir.fonov at gmail.com  Wed Nov 28 14:42:21 2012
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 28 Nov 2012 14:42:21 -0500
Subject: [MINC-development] MINC2 api - hidden treasures
Message-ID: <50B6691D.90604@gmail.com>

Hello Everybody,

I've been trying to make MINC2 API, NETCDF independent recently. And I 
have to say that it's been very frustrating experience so far.

Occasionally I come across pieces of code like this:
https://github.com/BIC-MNI/libminc/blob/master/libsrc2/volume.c#L98 
(written in 2004):

     if (volume->has_slice_scaling) {
       /* TODO: Find the slowest-varying spatial dimension; that forms
       * the basis for the image-min and image-max variables.  Right
       * now this is an oversimplification!
       */
       ndims = volume->number_of_dims - 2;
       dataspace_id = H5Screate_simple(ndims, hdf_size, NULL);
     } else {
       ndims = 0;
       dataspace_id = H5Screate(H5S_SCALAR);
     }

Which means that MINC2 files created with MINC2 API are always assumed 
to have more then 2 dimensions if slice normalization is enabled. And 
only provide 2D slice normalization.

-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From a.janke at gmail.com  Wed Nov 28 23:39:15 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 29 Nov 2012 14:39:15 +1000
Subject: [MINC-development] MINC2 api - hidden treasures
In-Reply-To: <50B6691D.90604@gmail.com>
References: <50B6691D.90604@gmail.com>
Message-ID: <CAG0CB23yk2FKqUFcy7Bub-kHt2P95wwywNPYU-JT3V3JxkuQiA@mail.gmail.com>

Ack!  I wonder if our scheme of simply re-implementing MINC in HDF5
from scratch we mused about while I was in Montreal has any legs.. :)

a



On 29 November 2012 05:42, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
> Hello Everybody,
>
> I've been trying to make MINC2 API, NETCDF independent recently. And I have
> to say that it's been very frustrating experience so far.
>
> Occasionally I come across pieces of code like this:
> https://github.com/BIC-MNI/libminc/blob/master/libsrc2/volume.c#L98 (written
> in 2004):
>
>     if (volume->has_slice_scaling) {
>       /* TODO: Find the slowest-varying spatial dimension; that forms
>       * the basis for the image-min and image-max variables.  Right
>       * now this is an oversimplification!
>       */
>       ndims = volume->number_of_dims - 2;
>       dataspace_id = H5Screate_simple(ndims, hdf_size, NULL);
>     } else {
>       ndims = 0;
>       dataspace_id = H5Screate(H5S_SCALAR);
>     }
>
> Which means that MINC2 files created with MINC2 API are always assumed to
> have more then 2 dimensions if slice normalization is enabled. And only
> provide 2D slice normalization.
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development