[BioC] BufferedMatrixMethods error

Beth Wilmot wilmotb at ohsu.edu
Fri Jun 29 00:37:10 CEST 2007 

Herve,
Thank you very much.  It works perfectly.

Beth


>>> "Herve Pages" <hpages at fhcrc.org> 6/28/2007 2:18:38 PM >>>
Hi Beth,


Note that the issue that you are reporting now is different from what
you reported earlier. It seems that you managed to solve your initial
problem:

  "init_package.c", line 5: cannot find include file:
"doubleBufferedMatrix_stubs.c"

What you show us now reveals an important difference between gcc and
your "cc" compiler.
This code (which is a simplified version of what is found in
doubleBufferedMatrix_stubs.c):

  void toto() {}

  void tutu() {
    return toto();
  }

is considered correct by gcc (so it compiles wihtout any warning on our
testing machines)
but is considered wrong by your "cc" compiler hence all those

  void function cannot return value

error messages that it generates. I've modified the code in
doubleBufferedMatrix_stubs.c
(BufferedMatrix 1.0.1 package) by replacing all the occurrences of the
above situations by:

  void toto() {}

  void tutu() {
    toto();
    return;
  }

so it should make your compiler happier ;-)

The fix will be propagated to our public repo here:

  http://bioconductor.org/packages/2.0/bioc/html/BufferedMatrix.html 

in the next 24 hours and, from here, will be available via biocLite()
(or getBioC()).

In the meantime, I've put it here for immediate download:

  http://bioconductor.org/packages/misc/BufferedMatrix_1.0.1.tar.gz 

Note that this is for R-2.5/BioC 2.0 _only_
I'm about to merge the fix to the devel version of BufferedMatrix.

Cheers,
H.


Beth Wilmot wrote:
> Herve, thank you For your response.  I am installing these packages
in
> my own directory.  I did install BufferedMatrix first and the
> doubleBufferedMatrix_stubs.c file is located in the
> BufferedMatrix/include directory.  
> 
> 
> I have tried to install the package both through GetBioC and through
R
> CMD INSTALL.  The error messages are:
> 
>> getBioC("BufferedMatrixMethods")
> Running biocinstall version 2.0.8 with R version 2.5.0 
> Your version of R requires version 2.0 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies
=
> dependencies,  : 
>          argument 'lib' is missing: using
'/mounts/users/wilmotb/libs'
> trying URL
>
'http://bioconductor.org/packages/2.0/bioc/src/contrib/BufferedMatrixMethods_1.0.0.tar.gz'
> Content type 'application/x-gzip' length 7100 bytes
> opened URL
> ==================================================
> downloaded 7100 bytes
> 
> * Installing *source* package 'BufferedMatrixMethods' ...
> ** libs
> cc -I/mounts/apps/r-project-25/lib/amd64/R/include
> -I/mounts/apps/r-project-25/lib/amd64/R/include 
> -I/mounts/devel/GNU/repoz/readline50/include
> -I/mounts/devel/GNU/repoz/ncurses54/include
> -I/mounts/devel/GNU/repoz/jpeg/include
> -I/mounts/devel/GNU/repoz/libiconv19/include
> -I/mounts/devel/GNU/repoz/gettext014/include
> -I/mounts/devel/GNU/repoz/libpng12/include
> -I/mounts/devel/GNU/repoz/zlib11/include
> -I/mounts/devel/GNU/repoz/libpcre50/include
> -I"/mounts/users/wilmotb/libs/BufferedMatrix/include"
> -D__NO_MATH_INLINES  -KPIC  -dalign -mr -Qn -xO3 -xtarget=generic64
-c
> init_package.c -o init_package.o
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 77: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 89: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 110: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 125: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 448: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 458: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 469: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 480: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 496: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 507: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 518: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 528: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 538: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 547: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 557: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 567: void function cannot return value
> cc: acomp failed for init_package.c
> gmake: *** [init_package.o] Error 2
> ERROR: compilation failed for package 'BufferedMatrixMethods'
> ** Removing '/mounts/users/wilmotb/libs/BufferedMatrixMethods'
> 
> The downloaded packages are in
>         /tmp/RtmpYtunZT/downloaded_packages
> Warning messages:
> 1: installation of package 'BufferedMatrixMethods' had non-zero exit
> status in: install.packages(pkgs = pkgs, repos = repos, dependencies
=
> dependencies,  
> 2: cannot create HTML package index in:
> tools:::unix.packages.html(.Library) 
> 
> 
> And the other is:
> 
> 
> 
> bash-3.00$ R CMD INSTALL -l $HOME/libs
> BufferedMatrixMethods_1.0.0.tar.gz
> * Installing *source* package 'BufferedMatrixMethods' ...
> ** libs
> cc -I/mounts/apps/r-project-25/lib/amd64/R/include
> -I/mounts/apps/r-project-25/lib/amd64/R/include 
> -I/mounts/devel/GNU/repoz/readline50/include
> -I/mounts/devel/GNU/repoz/ncurses54/include
> -I/mounts/devel/GNU/repoz/jpeg/include
> -I/mounts/devel/GNU/repoz/libiconv19/include
> -I/mounts/devel/GNU/repoz/gettext014/include
> -I/mounts/devel/GNU/repoz/libpng12/include
> -I/mounts/devel/GNU/repoz/zlib11/include
> -I/mounts/devel/GNU/repoz/libpcre50/include
> -I"/mounts/users/wilmotb/libs/BufferedMatrix/include"
> -D__NO_MATH_INLINES  -KPIC  -dalign -mr -Qn -xO3 -xtarget=generic64
-c
> init_package.c -o init_package.o
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 77: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 89: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 110: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 125: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 448: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 458: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 469: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 480: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 496: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 507: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 518: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 528: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 538: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 547: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 557: void function cannot return value
>
"/mounts/users/wilmotb/libs/BufferedMatrix/include/doubleBufferedMatrix_stubs.c",
> line 567: void function cannot return value
> cc: acomp failed for init_package.c
> gmake: *** [init_package.o] Error 2
> ERROR: compilation failed for package 'BufferedMatrixMethods'
> ** Removing '/mounts/users/wilmotb/libs/BufferedMatrixMethods'
> 
> 
> Thanks for your help, 
> 
> Beth
> 
> 
> 
> 
> 
> 
>>>> "Herve Pages" <hpages at fhcrc.org> 6/27/2007 2:45:34 PM >>>
> Beth Wilmot wrote:
>> Hello,
>>
>> I am running R-2.5.0 ons a 64bit Solaris 10.
>>
>> I am trying to install BufferedMatrixMethods and got the following
>> error:
>>
>> "init_package.c", line 5: cannot find include file:
>> "doubleBufferedMatrix_stubs.c"
>> cc: acomp failed for init_package.c
>>
>> I was able to successfully install this package on this machine
when
> I
>> had R-2.5.0 compiled as 32 bit but now that it's compiled as 64
bit.
>>
>> Both BufferedMatrixMethods_1.0.0 and BufferedMatrixMethods_1.1.2
> give
>> this error.
> 
> Hi Beth,
> 
> How are you trying to install BufferedMatrixMethods?
> 
> File 'doubleBufferedMatrix_stubs.c' is in the BufferedMatrix package
> so
> BufferedMatrix _must_ be installed before BufferedMatrixMethods can
be
> compiled.
> 
> - So the 1st thing to check is that BufferedMatrix is installed.
> 
> - Then check that <R_HOME>/library/BufferedMatrix/include contains
> file
>   doubleBufferedMatrix_stubs.c
> 
> - Then check that, when you try to install BufferedMatrixMethods,
your
>   compiler is invoked with something like
> 
>      -I"<R_HOME>/library/BufferedMatrix/include"
> 
>   (this is with gcc, it might be different for your compiler)
> 
> Please report which one of the 3 above steps is failing. Also the
> _complete_
> output you get during the compilation of BufferedMatrixMethods might
be
> useful.
> 
> Cheers,
> H.
> 
> 
>> Thanks,
>> Beth
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch 
>> https://stat.ethz.ch/mailman/listinfo/bioconductor 
>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/bioconductor 
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor 
> 
>

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 
https://stat.ethz.ch/mailman/listinfo/bioconductor 
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list