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Michael Felt

2015-Oct-15 12:32 UTC

[Rd] Building R for AIX in 64-bit mode

Hi.

Just wanted to let you know I am getting close to packaging R for AIX in
64.bit mode.

One comment - the libtool.m4 I see used is quite old. The one I have on my
system is 2.4.6, and what I see in R says:

I am hoping a new libtool will clean up most of the manual work now needed.

# Which release of libtool.m4 was used?
macro_version=2.2.6
macro_revision=1.3012

This may be all that is needed to cleanup what I am doing manually.

working with gcc I have done the following for 64-bit building

export OBJECT_MODE=64
export CFLAGS="-maix64 -O2"
export FFLAGS="-maix64 -O2"
export LDFLAGS="-lpthread"

Note - it does not look as if LDFLAGS is actually being picked up, but
maybe I had a typo.

The first error I get is:

Target "libunix.a" is up to date.
        gcc -std=gnu99 -I. -I../../src/include -I../../src/include
-I/opt/buildaix/include -I/opt/include -DHAVE_CONFIG_H  -mminimal-toc
-I/opt/include -I/opt/buildaix/include -maix64 -O2  -L/usr/local/lib
-DR_HOME='"/data/prj/cran/64/R-3.2.2"'  -o Rscript ./Rscript.c
        gcc -std=gnu99 -Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x100000000
-Wl,-bpD:0x110000000 -lc   -Wl,-bE:../../etc/R.exp  -L/usr/local/lib -o
R.bin Rmain.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o
arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o
colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o
deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o
engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o
graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o
lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o
names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o
print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o
registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o
source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o
summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o
g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o
../nmath/*.o`  ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
../extra/tre/libtre.a  ../extra/xz/liblzma.a ../extra/intl/libintl.a
-lgfortran -lm /opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64/libgcc.a
-lz -lrt -ldl -lm -liconv
ld: 0711-738 ERROR: Input file /lib/crt0.o:
        XCOFF32 object files are not allowed in 64-bit mode.

This is repaired by adding the -maix64 flag again to the gcc comand used to
link.

The following steps - first cut/paste the original command, then add -maix64

root at x072:[/data/prj/cran/64/R-3.2.2]cd src/main
root at x072:[/data/prj/cran/64/R-3.2.2/src/main]ran -lm
/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64/libgcc.a     -lz -lrt -ldl
-lm -liconv               <
ld: 0711-738 ERROR: Input file /lib/crt0.o:
        XCOFF32 object files are not allowed in 64-bit mode.
collect2: error: ld returned 8 exit status
root at x072:[/data/prj/cran/64/R-3.2.2/src/main] gcc -maix64 -std=gnu99
-Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x100000000 -Wl,-bpD:0x110000000 -lc
-Wl,-bE:../../>
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: BM_norm_keep
ld: 0711-224 WARNING: Duplicate symbol: N01_kind
ld: 0711-224 WARNING: Duplicate symbol: LoadInitFile
ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.
ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_lock
ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_unlock
collect2: error: ld returned 8 exit status
root at x072:[/data/prj/cran/64/R-3.2.2/src/main]

Now add the -lpthread

gcc -maix64 -std=gnu99 -Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x100000000
-Wl,-bpD:0x110000000 -lc   -Wl,-bE:../../etc/R.exp  -L/usr/local/lib -o
R.bin Rmain.o Comma
ndLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o
array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o
connections.o
context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o
dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o
format.o gevent
s.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o
internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o
mapply.o match.o
memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o
plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o
raw.o regi
stration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o
source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o
summary.o sysuti
ls.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o
g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o`
../extra/bzip2/
libbz2.a ../extra/pcre/libpcre.a ../extra/tre/libtre.a
../extra/xz/liblzma.a ../extra/intl/libintl.a   -lgfortran -lm
/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7
.4/ppc64/libgcc.a     -lz -lrt -ldl -lm -liconv -lpthread

gcc -maix64 -std=gnu99 -Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x100000000
-Wl,-bpD:0x110000000 -lc   -Wl,-bE:../../etc/R.exp  -L/usr/local/lib -o
R.bin Rmain.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o
arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o
colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o
deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o
engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o
graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o
lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o
names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o
print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o
registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o
source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o
summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o
g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o
../nmath/*.o`  ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
../extra/tre/libtre.a  ../extra/xz/liblzma.a ../extra/intl/libintl.a
-lgfortran -lm /opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64/libgcc.a
-lz -lrt -ldl -lm -liconv -lpthread
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: BM_norm_keep
ld: 0711-224 WARNING: Duplicate symbol: N01_kind
ld: 0711-224 WARNING: Duplicate symbol: LoadInitFile
ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.

Note: this is with 3.2.2 - with 3.1.3 I did not get the Duplicate symbols.


(Using the same command in the 3.1.3 directory shows there are some other
differences)

root at x072:[/data/prj/cran/64/R-3.1.3/src/main]gcc -maix64 -std=gnu99
-Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x100000000 -Wl,-bpD:0>
gcc: error: g_alab_her.o: A file or directory in the path name does not
exist.
gcc: error: g_cntrlify.o: A file or directory in the path name does not
exist.
gcc: error: g_fontdb.o: A file or directory in the path name does not exist.
gcc: error: g_her_glyph.o: A file or directory in the path name does not
exist.

so, since I am getting farther with 3.1.3 - I shall continue this
INFORMATIONAL post.

root at x072:[/data/prj/cran/64/R-3.1.3/src/main]rm R.bin

root at x072:[/data/prj/cran/64/R-3.1.3/src/main]gcc -std=gnu99 -Wl,-brtl
-Wl,-bexpall -Wl,-bpT:0x100000000 -Wl,-bpD:0x110000000 -lc
-Wl,-bE:../../etc/R.exp  -L/usr/l>
ld: 0706-020 The number 0x100000000 is too large for the -b pT option.
        Use a value that is 4294967295 (hex FFFFFFFF) or less.
ld: 0706-020 The number 0x110000000 is too large for the -b pD option.
        Use a value that is 4294967295 (hex FFFFFFFF) or less.
collect2: error: ld returned 255 exit status
root at x072:[/data/prj/cran/64/R-3.1.3/src/main]gcc -maix64 -std=gnu99
-Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x100000000 -Wl,-bpD:0x110000000 -lc
-Wl,-bE:../../etc/R.exp  >
ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_lock
ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_unlock
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.
collect2: error: ld returned 8 exit status
root at
x072:[/data/prj/cran/64/R-3.1.3/src/main]bm-aix5.3.0.0/4.7.4/ppc64/libgcc.a
-lrt -ldl -lm -liconv -lpthread

This is a kind of error that occurs frequently - the argument -shared
causes "issues"

Target "libRlapack.so" is up to date.
/data/prj/cran/64/R-3.1.3/lib/libRlapack.so is unchanged
        gcc -std=gnu99 -shared -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry
-lc  -L/usr/local/lib -o lapack.so  Lapack.o     -L../../../lib -lRlapack
-lgfortran -lm /opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64/libgcc.a
ld: 0711-736 ERROR: Input file Lapack.o:
        XCOFF64 object files are not allowed in 32-bit mode.
collect2: error: ld returned 8 exit status
make: 1254-004 The error code from the last command is 1.

changing -shared for -maix64 has "fixed" it up to now - Now however,
back
to duplicate symbols:

gcc: error: Lapack.o: A file or directory in the path name does not exist.
root at x072:[/data/prj/cran/64/R-3.1.3/src/modules]cd lapack
root at x072:[/data/prj/cran/64/R-3.1.3/src/modules/lapack] gcc -std=gnu99
-shared -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc  -L/usr/local/lib
-o lapack.so  Lapac>
ld: 0711-736 ERROR: Input file Lapack.o:
        XCOFF64 object files are not allowed in 32-bit mode.
collect2: error: ld returned 8 exit status
root at x072:[/data/prj/cran/64/R-3.1.3/src/modules/lapack]gcc -std=gnu99
-maix64  -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc  -L/usr/local/lib
-o lapack.so  Lapac>
ld: 0711-224 WARNING: Duplicate symbol: p_xargc
ld: 0711-224 WARNING: Duplicate symbol: p_xargv
ld: 0711-224 WARNING: Duplicate symbol: p_xrcfg
ld: 0711-224 WARNING: Duplicate symbol: p_xrc
ld: 0711-224 WARNING: Duplicate symbol: end
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.
root at x072:[/data/prj/cran/64/R-3.1.3/src/modules/lapack]

So, for today, my story ends with
gcc -Wl,-bloadmap:aixtools -std=gnu99 -maix64  -Wl,-brtl -Wl,-G
-Wl,-bexpall -Wl,-bnoentry -lc  -L/usr/local/lib -o lapack.so  Lapack.o
-L../../../lib -lRlapack  -lgfortran -lm
/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64/libgcc.a

ld: 0711-228 WARNING: Duplicate symbols were found while resolving symbols.
        The following duplicates were found:
 Symbol                    Source-File(Object) OR Import-File{Shared-object}
 ------------------------- -------------------------------------------------
 p_xargc                   crt0_64.s(/lib/crt0_64.o)
    ** Duplicate **        {../../../lib/libRlapack.so}
 p_xargv                   crt0_64.s(/lib/crt0_64.o)
    ** Duplicate **        {../../../lib/libRlapack.so}
 p_xrcfg                   crt0_64.s(/lib/crt0_64.o)
    ** Duplicate **        {../../../lib/libRlapack.so}
 p_xrc                     crt0_64.s(/lib/crt0_64.o)
    ** Duplicate **        {../../../lib/libRlapack.so}
 end                       crt0_64.s(/lib/crt0_64.o)
    ** Duplicate **        {../../../lib/libRlapack.so}
 .memcpy                   moveeq.s(/usr/lib/libc.a[moveeq_64.o])
    ** Duplicate **        {../../../lib/libRlapack.so}
 memcpy                    moveeq.s(/usr/lib/libc.a[moveeq_64.o])
    ** Duplicate **        {../../../lib/libRlapack.so}
 .bcopy                    moveeq.s(/usr/lib/libc.a[moveeq_64.o])
    ** Duplicate **        {../../../lib/libRlapack.so}
 bcopy                     moveeq.s(/usr/lib/libc.a[moveeq_64.o])
    ** Duplicate **        {../../../lib/libRlapack.so}
 .strcmp                   strcmp.s(/usr/lib/libc.a[strcmp_64.o])
    ** Duplicate **        {../../../lib/libRlapack.so}
 strcmp                    strcmp.s(/usr/lib/libc.a[strcmp_64.o])
    ** Duplicate **        {../../../lib/libRlapack.so}

	[[alternative HTML version deleted]]

Prof Brian Ripley

2015-Oct-15 13:02 UTC

head link

[Rd] Building R for AIX in 64-bit mode

On 15/10/2015 13:32, Michael Felt wrote:> Hi.
>
> Just wanted to let you know I am getting close to packaging R for AIX in
> 64.bit mode.
Which version? (You mentioned 3.1.3 and 3.2.2 far below.)  There is 
little value in reporting on frozen branches, and most value in 
reporting on R-devel where all the current changes have been incorporated.
> One comment - the libtool.m4 I see used is quite old. The one I have on my
> system is 2.4.6, and what I see in R says:
R-devel has 2.4.6 .
> I am hoping a new libtool will clean up most of the manual work now needed.
But libtool is hardly used in building R.
> # Which release of libtool.m4 was used?
> macro_version=2.2.6
> macro_revision=1.3012
>
> This may be all that is needed to cleanup what I am doing manually.
>
> working with gcc I have done the following for 64-bit building
>
> export OBJECT_MODE=64
> export CFLAGS="-maix64 -O2"
> export FFLAGS="-maix64 -O2"
See the manual: flags such as -maix64 should be part of CC, not CFLAGS. 
  That explains a lot of what was reported.
Specifically, 
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries
and https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#AIX .

It is safer to put such things on the configure command line or in a 
config.site file (they will be found when updating if you do).

[Lots of test output removed.]

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK

aixtools

2015-Oct-18 19:06 UTC

head link

[Rd] 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!

On 2015-10-15 15:02, Prof Brian Ripley wrote:> On 15/10/2015 13:32, Michael Felt wrote:
>> Hi.
>>
>> Just wanted to let you know I am getting close to packaging R for AIX
inrephrase - 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).>
> Which version? (You mentioned 3.1.3 and 3.2.2 far below.)  There is 
> little value in reporting on frozen branches, and most value in 
> reporting on R-devel where all the current changes have been 
> incorporated.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]

+++++>From  R-devel_2015-10-17.tar.bz2configure: 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.
>
>> One comment - the libtool.m4 I see used is quite old. The one I have 
>> on my
>> system is 2.4.6, and what I see in R says:
>
> R-devel has 2.4.6 .
>
>> I am hoping a new libtool will clean up most of the manual work now 
>> needed.
>
> But libtool is hardly used in building R.
>
>> # Which release of libtool.m4 was used?
>> macro_version=2.2.6
>> macro_revision=1.3012
>>
>> This may be all that is needed to cleanup what I am doing manually.
>>
>> working with gcc I have done the following for 64-bit building
>>
>> export OBJECT_MODE=64
>> export CFLAGS="-maix64 -O2"
>> export FFLAGS="-maix64 -O2"
>
> See the manual: flags such as -maix64 should be part of CC, not 
> CFLAGS.  That explains a lot of what was reported.
> Specifically, 
>
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries
> and https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#AIX .
>
> It is safer to put such things on the configure command line or in a 
> config.site file (they will be found when updating if you do).
>
> [Lots of test output removed.]
>

aixtools

2015-Nov-04 15:51 UTC

head link

[Rd] Building R for AIX in 64-bit mode

On 2015-10-15 15:02, Prof Brian Ripley wrote:> On 15/10/2015 13:32, Michael Felt wrote:
>> Hi.
>>
>> Just wanted to let you know I am getting close to packaging R for AIX
in
>> 64.bit mode.
>
> Which version? (You mentioned 3.1.3 and 3.2.2 far below.)  There is 
> little value in reporting on frozen branches, and most value in 
> reporting on R-devel where all the current changes have been 
> incorporated.This report is based on R-3.2.2 I shall repeat asap with R-devel and 
report any significant differences.
compiler is:
root at x072:[/data/prj/cran/64/R-3.2.2/src/main]gcc --version
gcc (GCC) 4.7.4
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

root at x072:[/data/prj/cran/64/R-3.2.2/src/main]gfortran --version
GNU Fortran (GCC) 4.7.4
Copyright (C) 2012 Free Software Foundation, Inc.

AIX level:
root at x072:[/data/prj/cran/64/R-3.2.2/src/main]oslevel -s
7100-03-05-1524

Non-IBM filesets installed:
root at x072:[/data/prj/cran/64/R-3.2.2/src/main]lslpp -L | grep aixtools
   aixtools.buildaix.man      2.0.1.0    C     F    man pages
   aixtools.buildaix.man.en_US
   aixtools.buildaix.rte      2.0.3.1    C     F    1540 1007 2004
   aixtools.gmp.rte           5.0.5.0    C     F    gmp version 5.0.5 
for powerpc
   aixtools.gmp.share         5.0.5.0    C     F    gmp share and 
documentation
   aixtools.gnu.bash.man.en_US
   aixtools.gnu.bash.rte     4.3.42.0    C     F    1537 0913 1505
   aixtools.gnu.bash.share   4.3.42.0    C     F    universal pages
   aixtools.gnu.coreutils.rte
   aixtools.gnu.gettext.rte  0.19.5.0    C     F    1531 0807 0000
   aixtools.gnu.gettext.share
   aixtools.gnu.make.rte      4.1.0.0    C     F    1523 0613 1158
   aixtools.gnu.wget.man.en_US
   aixtools.gnu.wget.rte     1.16.3.0    C     F    1530 0731 0651
   aixtools.gnu.wget.share   1.16.3.0    C     F    universal pages
   aixtools.libiconv.man     1.14.0.0    C     F    built 1447 1127 1728
   aixtools.libiconv.rte     1.14.0.0    C     F    libiconv 1447 1127 1728
   aixtools.libiconv.share   1.14.0.0    C     F    built 1447 1127 1728
   aixtools.mpc.rte           1.0.2.0    C     F    mpc 2014.Oct.31 
15.44 CUT
   aixtools.mpc.share         1.0.2.0    C     F    share and documentation
   aixtools.mpfr.rte          2.4.2.0    C     F    mpfr 2014.Oct.31 
15.19 CUT
   aixtools.mpfr.share        2.4.2.0    C     F    share and documentation
   aixtools.obj.gcc.man       4.7.4.0    C     F    man pages
   aixtools.obj.gcc.rte       4.7.4.0    C     F    1515 0416 2134
   aixtools.obj.gcc.share     4.7.4.0    C     F    universal pages
   aixtools64.gnu.libiconv.rte
>> export OBJECT_MODE=64
>> export CFLAGS="-maix64 -O2"
>> export FFLAGS="-maix64 -O2"
>
> See the manual: flags such as -maix64 should be part of CC, not 
> CFLAGS.  That explains a lot of what was reported.
> Specifically, 
>
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries
> and https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#AIX .
>
> It is safer to put such things on the configure command line or in a 
> config.site file (they will be found when updating if you do).
>Not sure what you mean by a config.site file - perhaps what I use as a 
"setup.env" script.

I followed the suggestion to move the flag -maix64 from CFLAGS and 
FFLAGS (where I think it belongs) to the compiler defintions. It does 
build better, but, still many concerns.

Details - too many lines of duplicate symbol references to paste (not 
wishing to spam the list - for details see 
http://download.aixtools.net/test/R/R-3.2.2-main-nohup.out> [Lots of test output removed.]
>The summary is:
ld: 0711-318 ERROR: Undefined symbols were found.
         The following symbols are in error:
  Symbol                    Inpndx  TY CL Source-File(Object-File) OR 
Import-File{Shared-object}
                               RLD: Address  Section  Rld-type 
Referencing Symbol
 
----------------------------------------------------------------------------------------------
  .pthread_mutex_lock       [24]    ER PR 
pcre_jit_compile.c(../extra/pcre/libpcre.a[pcre_jit_compile.o])
                                    000076f8 .text    R_RBR    [118] 
<.sljit_free_exec>
                                    00007940 .text    R_RBR    [120] 
<.sljit_generate_code>
                                    00028c30 .text    R_RBR    [230]   
.pcre_jit_free_unused_memory
  .pthread_mutex_unlock     [26]    ER PR 
pcre_jit_compile.c(../extra/pcre/libpcre.a[pcre_jit_compile.o])
                                    0000777c .text    R_RBR    [118] 
<.sljit_free_exec>
                                    000079cc .text    R_RBR    [120] 
<.sljit_generate_code>
                                    00007b94 .text    R_RBR    [120] 
<.sljit_generate_code>
                                    00008038 .text    R_RBR    [120] 
<.sljit_generate_code>
                                    00028cc4 .text    R_RBR    [230]   
.pcre_jit_free_unused_memory
ER: The return code is 8.
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: BM_norm_keep
ld: 0711-224 WARNING: Duplicate symbol: N01_kind
ld: 0711-224 WARNING: Duplicate symbol: LoadInitFile
ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth
ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_lock
ld: 0711-317 ERROR: Undefined symbol: .pthread_mutex_unlock
collect2: error: ld returned 8 exit status

The undefined sysbols can be resolved by adding -lpthread to the gcc 
command (and can be automated by adding that to LDFLAGS I expect, but 
imho - better if that gets caught by configure).

It then ends with:

RESOLVE: 6793 of 18448 symbols were kept.
RESOLVE: The return code is 4.
(ld): addgl /usr/lib/glink64.o
ADDGL: Glink code added for 212 symbols.
(ld): er full
ER: There are no unresolved symbols.
(ld): mismatch
MISMATCH: No type mismatches exist.
(ld): comprld
COMPRLD: Kept 52596 of 52596 relocation entries.
(ld): origin page 0x100000000 0x110000000
(ld): libpath 
/usr/local/lib:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/../../../ppc64:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/../../..:/usr/lib:/lib
LIBPATH: Library path set to 
/usr/local/lib:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/ppc64:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/../../../ppc64:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4:/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/../../..:/usr/lib:/lib
(ld): save 1L .
SAVE: Section sizes = 3374479+365673+669656 (0x337D8F+0x59469+0xA37D8 hex)
SAVE: Size of TOC: 5208 (0x1458 hex)
SAVE: No .loader section relocation entries exist for the .text section.
(ld): rc
RC: Highest return code was 4.
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: BM_norm_keep
ld: 0711-224 WARNING: Duplicate symbol: N01_kind
ld: 0711-224 WARNING: Duplicate symbol: LoadInitFile
ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth

a) There is still a non-zero status (rc=4)
b) unhappy about all the duplications, even double exports

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