[MINC-users] MINC-users Digest, Vol 93, Issue 7

Sun Apr 14 13:32:34 EDT 2013

Thanks guys!

I installed automake with homebrew and reran the command to install RMINC.
It installed and seems to work, although I haven't tested it fully.
However, the install process gave the following warnings, is that normal?

Jon

minc_anova.c: In function ‘test_slice_loop’:
minc_anova.c:109: warning: assignment from incompatible pointer type
minc_anova.c:121: warning: passing argument 4 of ‘fill_slice_buffer’ from
incompatible pointer type
minc_anova.c:132: warning: passing argument 3 of ‘free_slice_buffer’ from
incompatible pointer type
minc_anova.c:88: warning: unused variable ‘num_files’
minc_anova.c:86: warning: unused variable ‘i’
minc_anova.c: In function ‘per_voxel_anova’:
minc_anova.c:240: warning: passing argument 5 of ‘get_indices’ from
incompatible pointer type
minc_anova.c:240: warning: passing argument 6 of ‘get_indices’ from
incompatible pointer type
llvm-gcc-4.2 -arch x86_64 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/bic/include -Wall -I/usr/local/include    -fPIC  -mtune=core2
-g -O2  -c minc_reader.c -o minc_reader.o
minc_reader.c: In function ‘minc2_apply’:
minc_reader.c:285: warning: unused variable ‘R_fcall’
llvm-gcc-4.2 -arch x86_64 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/bic/include -Wall -I/usr/local/include    -fPIC  -mtune=core2
-g -O2  -c modelling_functions.c -o modelling_functions.o
modelling_functions.c: In function ‘t_test’:
modelling_functions.c:104: warning: unused variable ‘s_p’
modelling_functions.c: In function ‘voxel_sum’:
modelling_functions.c:241: warning: unused variable ‘subjects_per_group’
modelling_functions.c: In function ‘voxel_lm’:
modelling_functions.c:431: warning: implicit declaration of function
‘dqrls_’
modelling_functions.c:471: warning: implicit declaration of function
‘ch2inv_’
modelling_functions.c: In function ‘minc2_model’:
modelling_functions.c:685: warning: assignment discards qualifiers from
pointer target type
modelling_functions.c:679: warning: unused variable ‘index’
modelling_functions.c:679: warning: unused variable ‘rdf’
modelling_functions.c:679: warning: unused variable ‘j’
modelling_functions.c:679: warning: unused variable ‘rank’
modelling_functions.c:679: warning: unused variable ‘ny’
modelling_functions.c:678: warning: unused variable ‘resvar’
modelling_functions.c:678: warning: unused variable ‘rss’
modelling_functions.c:678: warning: unused variable ‘tol’
modelling_functions.c:676: warning: unused variable ‘x’
modelling_functions.c:676: warning: unused variable ‘y’
modelling_functions.c:674: warning: unused variable ‘R_fcall’
modelling_functions.c:667: warning: unused variable ‘xn’

On Sun, Apr 14, 2013 at 12:00 PM, <minc-users-request at bic.mni.mcgill.ca>wrote:

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> Today's Topics:
>
>    1. Trouble installing RMINC (Jonathan DuBois)
>    2. Re: Trouble installing RMINC (Vladimir S. Fonov)
>    3. Re: Trouble installing RMINC (Jason Lerch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 13 Apr 2013 17:17:13 -0400
> From: Jonathan DuBois <jonathan.m.dubois at gmail.com>
> To: minc-users at bic.mni.mcgill.ca
> Subject: [MINC-users] Trouble installing RMINC
> Message-ID:
>         <CA+E6mRsp4ouC-W9EFdGysLHa7sVnjGm3G=
> T6FKHMCKb9x0nR+Q at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Hi Minc Users,
>
> I am having some trouble installing RMINC on my Mac. I followed the
> direction here: https://github.com/mcvaneede/RMINC. The specific commands
> and errors are below. Any help would be appreciated.
>
> Alternatively, is there a minc function to export the values and
> coordinates of a minc file to a csv or text file that could imported into
> R, manipulated, and written back to a minc file?
>
> ######################
> :/usr/local$ export R_LIBS=/usr/local/
> :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC
> :/usr/local$ cd RMINC
> :/usr/local/RMINC$ ./autogen.sh
> ./autogen.sh: line 1: aclocal: command not found
> ./autogen.sh: line 2: autoconf: command not found
> :/usr/local/RMINC$ cd ..
> :/usr/local$ sudo R CMD INSTALL RMINC
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library
> --configure-args='--with-build-path=/usr/local/bic'
> Warning: invalid package
> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> * installing to library
> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> * installing *source* package ?RMINC? ...
> ERROR: a 'NAMESPACE' file is required
> * removing
> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC?
> ######################
>
> Thanks
> Jon DuBois
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 13 Apr 2013 17:21:02 -0400
> From: "Vladimir S. Fonov" <vladimir.fonov at gmail.com>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Trouble installing RMINC
> Message-ID: <5169CC3E.50207 at gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hello,
>
>
> looks like you don't have autoconf/automake installed on your system -
>  > ./autogen.sh: line 1: aclocal: command not found
>  > ./autogen.sh: line 2: autoconf: command not found
> indicates that these commands are missing
>
> On 13-04-13 05:17 PM, Jonathan DuBois wrote:
> > Hi Minc Users,
> >
> > I am having some trouble installing RMINC on my Mac. I followed the
> > direction here: https://github.com/mcvaneede/RMINC. The specific
> commands
> > and errors are below. Any help would be appreciated.
> >
> > Alternatively, is there a minc function to export the values and
> > coordinates of a minc file to a csv or text file that could imported into
> > R, manipulated, and written back to a minc file?
> >
> > ######################
> > :/usr/local$ export R_LIBS=/usr/local/
> > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC
> > :/usr/local$ cd RMINC
> > :/usr/local/RMINC$ ./autogen.sh
> > ./autogen.sh: line 1: aclocal: command not found
> > ./autogen.sh: line 2: autoconf: command not found
> > :/usr/local/RMINC$ cd ..
> > :/usr/local$ sudo R CMD INSTALL RMINC
> > /Library/Frameworks/R.framework/Versions/3.0/Resources/library
> > --configure-args='--with-build-path=/usr/local/bic'
> > Warning: invalid package
> > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> > * installing to library
> > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> > * installing *source* package ?RMINC? ...
> > ERROR: a 'NAMESPACE' file is required
> > * removing
> > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC?
>
>
> --
> Best regards,
>   Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 13 Apr 2013 17:24:47 -0400
> From: Jason Lerch <jason at phenogenomics.ca>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Trouble installing RMINC
> Message-ID: <FD624F16-2DFE-431D-A015-7E4A29952335 at phenogenomics.ca>
> Content-Type: text/plain;       charset="utf-8"
>
> It looks like you are missing some of the automagic tools (autoconf, etc).
>
> Jason
>
> On 2013-04-13, at 5:17 PM, Jonathan DuBois <jonathan.m.dubois at gmail.com>
> wrote:
>
> > Hi Minc Users,
> >
> > I am having some trouble installing RMINC on my Mac. I followed the
> > direction here: https://github.com/mcvaneede/RMINC. The specific
> commands
> > and errors are below. Any help would be appreciated.
> >
> > Alternatively, is there a minc function to export the values and
> > coordinates of a minc file to a csv or text file that could imported into
> > R, manipulated, and written back to a minc file?
> >
> > ######################
> > :/usr/local$ export R_LIBS=/usr/local/
> > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC
> > :/usr/local$ cd RMINC
> > :/usr/local/RMINC$ ./autogen.sh
> > ./autogen.sh: line 1: aclocal: command not found
> > ./autogen.sh: line 2: autoconf: command not found
> > :/usr/local/RMINC$ cd ..
> > :/usr/local$ sudo R CMD INSTALL RMINC
> > /Library/Frameworks/R.framework/Versions/3.0/Resources/library
> > --configure-args='--with-build-path=/usr/local/bic'
> > Warning: invalid package
> > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> > * installing to library
> > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> > * installing *source* package ?RMINC? ...
> > ERROR: a 'NAMESPACE' file is required
> > * removing
> > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC?
> > ######################
> >
> > Thanks
> > Jon DuBois
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
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>
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> End of MINC-users Digest, Vol 93, Issue 7
> *****************************************
>