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

Jason Lerch jason at phenogenomics.ca
Mon Apr 15 15:51:28 EDT 2013 

These warnings are indeed "normal" - if I remember they come out in part because some variable are initialized in the R session, which the C compiler does not know about and thus complains. I could be wrong on that part though; anyway, they do appear on every system, not just yours.

Jason

On 2013-04-14, at 1:32 PM, Jonathan DuBois <jonathan.m.dubois at gmail.com> wrote:

> 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
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> MINC-users mailing list
>> MINC-users at bic.mni.mcgill.ca
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>> 
>> End of MINC-users Digest, Vol 93, Issue 7
>> *****************************************
>> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

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