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Building R for AIX in 32-bit mode - as preparation for building in 64-bit mode (changed subject!) - INFO/FEEDBACK - do not read as a bug report!

aixtools
On 2015-10-15 15:02, Prof Brian Ripley wrote:
rephrase - would like to be active in keeping R binaries current for 
AIX. My interest in not in R per se (rather a colleague who has a 
project that uses R, so I hope to assist him, and others like him).
The reason for reporting old and current releases is to understand what 
is new between releases, and what has been around for "awhile".

Note: in the future I shall edit all the "you cannot build, could not 
determine ... messages" - and as much as possible, shall focus on 
R-devel "packaging".

I (attempt to) 'package' a lot of Opensource tools for AIX. Generally, 
the problems are not application code related (sometimes a function 
available on one platform, e.g. Linux, but not on AIX) - but most are, 
or can be resolved, with modifications via configure.ac, Makefile.in, etc..

Sincerely,
Michael

"Details"...

When configure does complete - config.log starts with:
It was created by R configure 3.1.3, which was
generated by GNU Autoconf 2.69.  Invocation command line was

   $ ./configure --prefix=/opt --sysconfdir=/var/R/etc 
--sharedstatedir=/var/R/com --localstatedir=/var/R 
--mandir=/usr/share/man --infodir=/opt/share/info/R --with-readline=no 
--with-x=no

As I see you are using a recent autoconf (and I shall guess a recent 
automake) I would like to try a more version of libtool and see if that 
corrects anything. However, even in R-devel I do not see, directly, how 
you are using these tools (some projects include either a setup.sh or a 
buildconf script to standardize how the project does this.) I am quite 
capable of just calling the tools in sequence, but would prefer to 
follow your procedure.
I
Starting again - fresh 3.1.3, 3.2.2 and R-devel - all in 32-bit mode, 
for the start. The goal is a 64-bit build so that memory management will 
be easier.

This is my "standard command for building a package"

CPPFLAGS="-I/opt/buildaix/include -I/opt/include" CFLAGS="-I/opt/include 
-I/opt/buildaix/include -O2" ./configure \
                 --prefix=/opt  \
                 --sysconfdir=/var/R/etc \
                 --sharedstatedir=/var/R/com \
                 --localstatedir=/var/R \
                 --mandir=/usr/share/man \
                 --infodir=/opt/share/info/R --with-readline=no --with-x=no
Results for 3.1.3
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help 
pages
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help 
pages
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
+ make > .buildaix/make.out
sys-std.c: In function 'Rstd_ChooseFile':
sys-std.c:1186:5: warning: implicit declaration of function 'isspace' 
[-Wimplicit-function-declaration]
connections.c: In function 'fifo_open':
connections.c:885:5: warning: implicit declaration of function 'open' 
[-Wimplicit-function-declaration]
main.c: In function 'dummy_ii':
main.c:1594:5: warning: function returns address of local variable 
[enabled by default]
ld: 0711-224 WARNING: Duplicate symbol: .memcpy
ld: 0711-224 WARNING: Duplicate symbol: memcpy
ld: 0711-224 WARNING: Duplicate symbol: .bcopy
ld: 0711-224 WARNING: Duplicate symbol: bcopy
ld: 0711-224 WARNING: Duplicate symbol: .strcmp
ld: 0711-224 WARNING: Duplicate symbol: strcmp
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more 
information.
Warning in solve.default(rgb) :
   unable to load shared object 
'/data/prj/cran/32/R-3.1.3/modules//lapack.so':
   rtld: 0712-001 Symbol logf was referenced
       from module /data/prj/cran/32/R-3.1.3/lib/libRlapack.so(), but a 
runtime definition
             of the symbol was not found.
Error in solve.default(rgb) : LAPACK routines cannot be loaded
Error: unable to load R code in package 'grDevices'
Execution halted
make: 1254-004 The error code from the last command is 1.

...

Stop.
make returned an error
root at x072:[/data/prj/cran/32/R-3.1.3]
++++++
Notes: Last April I was successful with building R - I do not recall 
specifically how I changed the release. I shall determine what I did to 
get it to build normally.
++++++
Results for 3.2.2
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help 
pages
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help 
pages
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
+ make > .buildaix/make.out
sys-std.c: In function 'Rstd_ChooseFile':
sys-std.c:1189:5: warning: implicit declaration of function 'isspace' 
[-Wimplicit-function-declaration]
connections.c: In function 'fifo_open':
connections.c:876:5: warning: implicit declaration of function 'open' 
[-Wimplicit-function-declaration]
main.c: In function 'dummy_ii':
main.c:1598:5: warning: function returns address of local variable 
[enabled by default]
ld: 0711-415 WARNING: Symbol BM_norm_keep is already exported.
ld: 0711-415 WARNING: Symbol LoadInitFile is already exported.
ld: 0711-415 WARNING: Symbol N01_kind is already exported.
ld: 0711-415 WARNING: Symbol R_ReadItemDepth is already exported.
ld: 0711-224 WARNING: Duplicate symbol: LoadInitFile
ld: 0711-224 WARNING: Duplicate symbol: BM_norm_keep
ld: 0711-224 WARNING: Duplicate symbol: N01_kind
ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more 
information.
ld: 0711-415 WARNING: Symbol BM_norm_keep is already exported.
ld: 0711-415 WARNING: Symbol LoadInitFile is already exported.
ld: 0711-415 WARNING: Symbol N01_kind is already exported.
ld: 0711-415 WARNING: Symbol R_ReadItemDepth is already exported.
ld: 0711-224 WARNING: Duplicate symbol: LoadInitFile
ld: 0711-224 WARNING: Duplicate symbol: BM_norm_keep
ld: 0711-224 WARNING: Duplicate symbol: N01_kind
ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more 
information.
ld: 0711-224 WARNING: Duplicate symbol: .memcpy
ld: 0711-224 WARNING: Duplicate symbol: memcpy
ld: 0711-224 WARNING: Duplicate symbol: .bcopy
ld: 0711-224 WARNING: Duplicate symbol: bcopy
ld: 0711-224 WARNING: Duplicate symbol: .strcmp
ld: 0711-224 WARNING: Duplicate symbol: strcmp
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more 
information.
/bin/sh: There is no process to read data written to a pipe.
Warning in solve.default(rgb) :
   unable to load shared object 
'/data/prj/cran/32/R-3.2.2/modules//lapack.so':
   rtld: 0712-001 Symbol logf was referenced
       from module /data/prj/cran/32/R-3.2.2/lib/libRlapack.so(), but a 
runtime definition
             of the symbol was not found.
Error in solve.default(rgb) : LAPACK routines cannot be loaded
Error: unable to load R code in package 'grDevices'
Execution halted
make: 1254-004 The error code from the last command is 1.

...
make returned an error
+++++
Here there are similiar - and new problems. The error re: rtld is 
usually a compiler (actually ld) flag error - a routine is expected to 
be exported in a shared object, but the object is still "static".
I have seen this same problem with at least one R module.

I still am unsure why some functions are being defined double - that 
info will come later
root at x072:[/data/prj/cran/32/R-3.2.2]

+++++
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help 
pages
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
configure: error: bzip2 library and headers are required
buildaix: ./configure ... returned an error

try doing "grep configure: config.log | tail" for possible explanation

try "./configure --help" for additional arguments to buildaix
++++ config.log configure: comments are ++++
configure:35647: checking bzlib.h presence
configure:35647: gcc -E -I/opt/buildaix/include -I/opt/include  conftest.c
configure:35647: $? = 1
configure: failed program was:
configure:35647: result: no
configure:35647: checking for bzlib.h
configure:35647: result: no
configure:35712: checking whether bzip2 support suffices
configure:35719: error: bzip2 library and headers are required
configure: exit 1
++++ ++++
Here is a completely new kind of "problem" - a demand for an include 
file. bzip2 is available, but configure is looking for it in a different 
way and now configure fails.

Thread (5 messages)

Michael Felt Building R for AIX in 64-bit mode Oct 15 Brian Ripley Building R for AIX in 64-bit mode Oct 15 aixtools Building R for AIX in 32-bit mode - as preparation for building in 64-bit mode (changed subject!) - INFO/FEEDBACK - do not read as a bug report! Oct 18 Michael Felt Building R for AIX in 32-bit mode - as preparation for building in 64-bit mode (changed subject!) - INFO/FEEDBACK - do not read as a bug report! Oct 24 Michael Felt Building R for AIX in 32-bit mode - as preparation for building in 64-bit mode (changed subject!) - INFO/FEEDBACK - do not read as a bug report! Oct 24