rgl install problem on Solaris 10 X86

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rgl install problem on Solaris 10 X86

Dongseok Choi
Hi,
 
  Could you help me to install the rgl package on Solaris 10 x86?
  I tried and got the following error messages.
  When I compiled my R as 64bit, I used the SUN ProW compilers.
  However, gcc seems to being used below as well as missing some information.
 
Thank you in advance,
Dongseok
 
> install.packages("rgl")
--- Please select a CRAN mirror for use in this session ---
* Installing *source* package 'rgl' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for X... libraries /usr/openwin/lib, headers /usr/openwin/include
 
checking for libpng-config... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c api.cpp -o api.o
CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Background.cpp -o Background.o
CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
"Background.cpp", line 54: Warning: boundingBox hides Shape::boundingBox.
1 Warning(s) detected.
CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c BBoxDeco.cpp -o BBoxDeco.o
CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Color.cpp -o Color.oCC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
"Color.cpp", line 142: Error: The function "realloc" must have a prototype.
"Color.cpp", line 159: Error: The function "realloc" must have a prototype.
"Color.cpp", line 160: Error: The function "memcpy" must have a prototype.
"Color.cpp", line 168: Error: The function "free" must have a prototype.
"Color.cpp", line 175: Error: The function "realloc" must have a prototype.
"Color.cpp", line 196: Error: The function "realloc" must have a prototype.
"Color.cpp", line 247: Error: The function "realloc" must have a prototype.
7 Error(s) detected.
*** Error code 7
make: Fatal error: Command failed for target `Color.o'
ERROR: compilation failed for package 'rgl'
** Removing '/export/home/choid/bin/R2.2.1/lib/R/library/rgl'
 
The downloaded packages are in
        /tmp/Rtmp9Yaawc/downloaded_packages
> >



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Re: rgl install problem on Solaris 10 X86

Duncan Murdoch
On 2/3/2006 6:37 PM, Dongseok Choi wrote:
> Hi,
>  
>   Could you help me to install the rgl package on Solaris 10 x86?

No, but there have been a lot of changes to it since the last upload to
CRAN.  You might want to grab a new copy from
http://rgl.neoscientists.org/About.html by getting the latest Subversion
checkout.

Duncan Murdoch


>   I tried and got the following error messages.
>   When I compiled my R as 64bit, I used the SUN ProW compilers.
>   However, gcc seems to being used below as well as missing some information.
>  
> Thank you in advance,
> Dongseok
>  
>> install.packages("rgl")
> --- Please select a CRAN mirror for use in this session ---
> * Installing *source* package 'rgl' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for X... libraries /usr/openwin/lib, headers /usr/openwin/include
>  
> checking for libpng-config... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c api.cpp -o api.o
> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Background.cpp -o Background.o
> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
> "Background.cpp", line 54: Warning: boundingBox hides Shape::boundingBox.
> 1 Warning(s) detected.
> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c BBoxDeco.cpp -o BBoxDeco.o
> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Color.cpp -o Color.oCC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
> "Color.cpp", line 142: Error: The function "realloc" must have a prototype.
> "Color.cpp", line 159: Error: The function "realloc" must have a prototype.
> "Color.cpp", line 160: Error: The function "memcpy" must have a prototype.
> "Color.cpp", line 168: Error: The function "free" must have a prototype.
> "Color.cpp", line 175: Error: The function "realloc" must have a prototype.
> "Color.cpp", line 196: Error: The function "realloc" must have a prototype.
> "Color.cpp", line 247: Error: The function "realloc" must have a prototype.
> 7 Error(s) detected.
> *** Error code 7
> make: Fatal error: Command failed for target `Color.o'
> ERROR: compilation failed for package 'rgl'
> ** Removing '/export/home/choid/bin/R2.2.1/lib/R/library/rgl'
>  
> The downloaded packages are in
>         /tmp/Rtmp9Yaawc/downloaded_packages
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: rgl install problem on Solaris 10 X86

Brian Ripley
On Fri, 3 Feb 2006, Duncan Murdoch wrote:

> On 2/3/2006 6:37 PM, Dongseok Choi wrote:
>> Hi,
>>
>>   Could you help me to install the rgl package on Solaris 10 x86?
>
> No, but there have been a lot of changes to it since the last upload to
> CRAN.  You might want to grab a new copy from
> http://rgl.neoscientists.org/About.html by getting the latest Subversion
> checkout.

I tried to reproduce this, but our Solaris box does not have GL installed.
My understanding is that the real problem seems to be that Color.cpp is
using undeclared ISO C functions and needs to include

#include <stdlib.h> // for realoc and free
#include <string.h> // for memcpy

so please try adding them.

As for the -dalign messages, I presume you included them (like -xlibmil)
in CXXFLAGS.  They are supported by our SunPro compiler, so which version
is yours?  (In any case, you need to remove it, if I guessed right.)

>
> Duncan Murdoch
>
>
>>   I tried and got the following error messages.
>>   When I compiled my R as 64bit, I used the SUN ProW compilers.
>>   However, gcc seems to being used below as well as missing some information.
>>
>> Thank you in advance,
>> Dongseok
>>
>>> install.packages("rgl")
>> --- Please select a CRAN mirror for use in this session ---
>> * Installing *source* package 'rgl' ...
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ANSI C... none needed
>> checking how to run the C preprocessor... gcc -E
>> checking for X... libraries /usr/openwin/lib, headers /usr/openwin/include
>>
>> checking for libpng-config... yes
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c api.cpp -o api.o
>> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
>> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Background.cpp -o Background.o
>> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
>> "Background.cpp", line 54: Warning: boundingBox hides Shape::boundingBox.
>> 1 Warning(s) detected.
>> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c BBoxDeco.cpp -o BBoxDeco.o
>> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
>> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Color.cpp -o Color.oCC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
>> "Color.cpp", line 142: Error: The function "realloc" must have a prototype.
>> "Color.cpp", line 159: Error: The function "realloc" must have a prototype.
>> "Color.cpp", line 160: Error: The function "memcpy" must have a prototype.
>> "Color.cpp", line 168: Error: The function "free" must have a prototype.
>> "Color.cpp", line 175: Error: The function "realloc" must have a prototype.
>> "Color.cpp", line 196: Error: The function "realloc" must have a prototype.
>> "Color.cpp", line 247: Error: The function "realloc" must have a prototype.
>> 7 Error(s) detected.
>> *** Error code 7
>> make: Fatal error: Command failed for target `Color.o'
>> ERROR: compilation failed for package 'rgl'
>> ** Removing '/export/home/choid/bin/R2.2.1/lib/R/library/rgl'
>>
>> The downloaded packages are in
>>         /tmp/Rtmp9Yaawc/downloaded_packages
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
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Re: rgl install problem on Solaris 10 X86

Dongseok Choi
In reply to this post by Dongseok Choi
Hi,
 
Thank you very much for your prompt help.
 
1)
I downloaded 'rgl' package from CRAN and its version is 0.65.
This seems to be the lasted.
 
2)
 I added those two lines and now Color.cpp is compiled OK.
 However, I have a different error as following:
 
CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c devicemanager.cpp -o devicemanager.o
CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
"devicemanager.cpp", line 19: Error: Could not find a match for std::vector<Device*>::vector(std::list<Device*>::iterator, std::list<Device*>::iterator) needed in DeviceManager::~DeviceManager().
1 Error(s) detected.
*** Error code 1
make: Fatal error: Command failed for target `devicemanager.o'
ERROR: compilation failed for package 'rgl'

 
3) I am using,
choi2100{choid}202: CC -V
CC: Sun C++ 5.7 Patch 117831-02 2005/03/30

4) Yes, -xlibmil and -dalign were used when I compiled the R with --with-lapack.
I think that I just followed the section for Sun Solaris for Sparc in "R-install" although I have Sparc x86.
I saw that they are automatically added whenever I install any add-on packages.
I'll try without them.
 
Thank you very much again,
Dongseok
 

>>> "Prof Brian Ripley" <[hidden email]> 02/04/06 12:20 AM >>>

On Fri, 3 Feb 2006, Duncan Murdoch wrote:

> On 2/3/2006 6:37 PM, Dongseok Choi wrote:
>> Hi,
>>
>>   Could you help me to install the rgl package on Solaris 10 x86?
>
> No, but there have been a lot of changes to it since the last upload to
> CRAN.  You might want to grab a new copy from
> http://rgl.neoscientists.org/About.html by getting the latest Subversion
> checkout.

I tried to reproduce this, but our Solaris box does not have GL installed.
My understanding is that the real problem seems to be that Color.cpp is
using undeclared ISO C functions and needs to include

#include <stdlib.h> // for realoc and free
#include <string.h> // for memcpy

so please try adding them.

As for the -dalign messages, I presume you included them (like -xlibmil)
in CXXFLAGS.  They are supported by our SunPro compiler, so which version
is yours?  (In any case, you need to remove it, if I guessed right.)



        [[alternative HTML version deleted]]

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Re: rgl install problem on Solaris 10 X86

Duncan Murdoch
On 2/5/2006 10:25 AM, Dongseok Choi wrote:
> Hi,
>  
> Thank you very much for your prompt help.
>  
> 1)
> I downloaded 'rgl' package from CRAN and its version is 0.65.
> This seems to be the lasted.

That's the latest on CRAN, but not the latest available.  See my message
below.  I have put Brian's suggested changes into the repository.

I can't help you with the other problems; I don't have any experience on
Solaris.

Duncan Murdoch

>  
> 2)
>  I added those two lines and now Color.cpp is compiled OK.
>  However, I have a different error as following:
>  
> CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include   -KPIC  -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c devicemanager.cpp -o devicemanager.o
> CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise
> "devicemanager.cpp", line 19: Error: Could not find a match for std::vector<Device*>::vector(std::list<Device*>::iterator, std::list<Device*>::iterator) needed in DeviceManager::~DeviceManager().
> 1 Error(s) detected.
> *** Error code 1
> make: Fatal error: Command failed for target `devicemanager.o'
> ERROR: compilation failed for package 'rgl'
>
>  
> 3) I am using,
> choi2100{choid}202: CC -V
> CC: Sun C++ 5.7 Patch 117831-02 2005/03/30
>
> 4) Yes, -xlibmil and -dalign were used when I compiled the R with --with-lapack.
> I think that I just followed the section for Sun Solaris for Sparc in "R-install" although I have Sparc x86.
> I saw that they are automatically added whenever I install any add-on packages.
> I'll try without them.
>  
> Thank you very much again,
> Dongseok
>  
>
>>>> "Prof Brian Ripley" <[hidden email]> 02/04/06 12:20 AM >>>
>
> On Fri, 3 Feb 2006, Duncan Murdoch wrote:
>
>> On 2/3/2006 6:37 PM, Dongseok Choi wrote:
>>> Hi,
>>>
>>>   Could you help me to install the rgl package on Solaris 10 x86?
>> No, but there have been a lot of changes to it since the last upload to
>> CRAN.  You might want to grab a new copy from
>> http://rgl.neoscientists.org/About.html by getting the latest Subversion
>> checkout.
>
> I tried to reproduce this, but our Solaris box does not have GL installed.
> My understanding is that the real problem seems to be that Color.cpp is
> using undeclared ISO C functions and needs to include
>
> #include <stdlib.h> // for realoc and free
> #include <string.h> // for memcpy
>
> so please try adding them.
>
> As for the -dalign messages, I presume you included them (like -xlibmil)
> in CXXFLAGS.  They are supported by our SunPro compiler, so which version
> is yours?  (In any case, you need to remove it, if I guessed right.)
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Cluster Analysis

John Janmaat
Hello,

I'm trying some cluster analysis, using the hclust command.  I am looking for
some help in selecting the 'best' number of clusters.  Some software reports
pseudo-F and pseudo-T^2 statistics, for each cluster merge.  Is there any way
to generate such statistics simply in R?

Thanks,

John.
============================================================================
Dr. John Janmaat                       Tel: 902-585-1461
Department of Economics                Fax: 902-585-1461
Acadia University,                     Email: [hidden email]
Wolfville, Nova Scotia, Canada.        Web: ace.acadiau.ca/~jjanmaat/
B4P 1H5

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Re: Cluster Analysis

Romain François
Le 05.02.2006 17:50, John Janmaat a écrit :

>Hello,
>
>I'm trying some cluster analysis, using the hclust command.  I am looking for
>some help in selecting the 'best' number of clusters.  Some software reports
>pseudo-F and pseudo-T^2 statistics, for each cluster merge.  Is there any way
>to generate such statistics simply in R?
>
>Thanks,
>
>John.
>============================================================================
>Dr. John Janmaat                       Tel: 902-585-1461
>Department of Economics                Fax: 902-585-1461
>Acadia University,                     Email: [hidden email]
>Wolfville, Nova Scotia, Canada.        Web: ace.acadiau.ca/~jjanmaat/
>B4P 1H5
>  
>
Hi,

The package fpc have things like that.

Romain

--
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+---------------------------------------------------------------+
| Romain FRANCOIS - http://francoisromain.free.fr               |
| Doctorant INRIA Futurs / EDF                                  |
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