[BioC] BufferedMatrixMethods error
Beth Wilmot
wilmotb at ohsu.edu
Thu Jun 28 01:28:43 CEST 2007
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
>
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