Hi,

I've installed R and R-devel on one of our AIX 7.3 LPARs and now I'm hoping to install a basic set of R packages.  I'm getting a magic number error associated with libiconv and gcclib but everything is latest and all from Toolbox.  Is there a way to fix this?  Please see below.  Thanks.

Mike

> install.packages('colorspace',repos='cran.rstudio.com')
trying URL 'cran.rstudio.com/src/contrib/colorspace_2.0-3.tar.gz'
Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package 'colorspace' ...
** package 'colorspace' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -maix64 -pthread -fPIC -I"/opt/freeware/lib64/R/include" -DNDEBUG -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -mminimal-toc -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -c colorspace.c -o colorspace.o
Could not load program gcc:
Could not load module /opt/freeware/lib/libiconv.a(libiconv.so.2).
Dependent module /opt/freeware/lib/pthread/ppc64/libgcc_s.a(shr.o) could not be loaded.
The module has an invalid magic number.
Could not load module gcc-10.
Dependent module /opt/freeware/lib/libiconv.a(libiconv.so.2) could not be loaded.
make: The error code from the last command is 255.

[root@crilacs1 ~]# rpm -qa | grep -iE '(gcc|iconv)'
libgcc-10-2.ppc
gcc10-10.3.0-6.ppc
gcc10-gfortran-10.3.0-6.ppc
gcc-10-2.ppc
libiconv-1.17-1.ppc
libgcc10-10.3.0-6.ppc
gcc10-cpp-10.3.0-6.ppc
gcc-cpp-10-2.ppc
gcc-gfortran-10-2.ppc



------------------------------
Michael Metts
------------------------------

#AIXOpenSource

Looks like gcc10 pthread library " /opt/freeware/lib/pthread/ppc64/libgcc_s.a " doesn't have 32bit shared object. We are looking into it. 

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Sun November 13, 2022 01:14 PM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi,

I've installed R and R-devel on one of our AIX 7.3 LPARs and now I'm hoping to install a basic set of R packages.  I'm getting a magic number error associated with libiconv and gcclib but everything is latest and all from Toolbox.  Is there a way to fix this?  Please see below.  Thanks.

Mike

> install.packages('colorspace',repos='cran.rstudio.com')
trying URL 'cran.rstudio.com/src/contrib/colorspace_2.0-3.tar.gz'
Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package 'colorspace' ...
** package 'colorspace' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -maix64 -pthread -fPIC -I"/opt/freeware/lib64/R/include" -DNDEBUG -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -mminimal-toc -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -c colorspace.c -o colorspace.o
Could not load program gcc:
Could not load module /opt/freeware/lib/libiconv.a(libiconv.so.2).
Dependent module /opt/freeware/lib/pthread/ppc64/libgcc_s.a(shr.o) could not be loaded.
The module has an invalid magic number.
Could not load module gcc-10.
Dependent module /opt/freeware/lib/libiconv.a(libiconv.so.2) could not be loaded.
make: The error code from the last command is 255.

[root@crilacs1 ~]# rpm -qa | grep -iE '(gcc|iconv)'
libgcc-10-2.ppc
gcc10-10.3.0-6.ppc
gcc10-gfortran-10.3.0-6.ppc
gcc-10-2.ppc
libiconv-1.17-1.ppc
libgcc10-10.3.0-6.ppc
gcc10-cpp-10.3.0-6.ppc
gcc-cpp-10-2.ppc
gcc-gfortran-10-2.ppc



------------------------------
Michael Metts
------------------------------

#AIXOpenSource

Hi Ayappan,

Okay. When I installed R it seemed as though gcc10 kind of came with it. In other words it didn’t look like it was easily avoided. Thanks for looking into it. Please let me know when there’s a fix or workaround.

Best,
Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 11/14/2022 2:24:00 AM
From: Ayappan P
Subject: RE: problems with R, libiconv and gcc

Looks like gcc10 pthread library " /opt/freeware/lib/pthread/ppc64/libgcc_s.a " doesn't have 32bit shared object. We are looking into it. 

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Sun November 13, 2022 01:14 PM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi,

I've installed R and R-devel on one of our AIX 7.3 LPARs and now I'm hoping to install a basic set of R packages.  I'm getting a magic number error associated with libiconv and gcclib but everything is latest and all from Toolbox.  Is there a way to fix this?  Please see below.  Thanks.

Mike

> install.packages('colorspace',repos='cran.rstudio.com')
trying URL 'cran.rstudio.com/src/contrib/colorspace_2.0-3.tar.gz'
Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package 'colorspace' ...
** package 'colorspace' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -maix64 -pthread -fPIC -I"/opt/freeware/lib64/R/include" -DNDEBUG -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -mminimal-toc -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -c colorspace.c -o colorspace.o
Could not load program gcc:
Could not load module /opt/freeware/lib/libiconv.a(libiconv.so.2).
Dependent module /opt/freeware/lib/pthread/ppc64/libgcc_s.a(shr.o) could not be loaded.
The module has an invalid magic number.
Could not load module gcc-10.
Dependent module /opt/freeware/lib/libiconv.a(libiconv.so.2) could not be loaded.
make: The error code from the last command is 255.

[root@crilacs1 ~]# rpm -qa | grep -iE '(gcc|iconv)'
libgcc-10-2.ppc
gcc10-10.3.0-6.ppc
gcc10-gfortran-10.3.0-6.ppc
gcc-10-2.ppc
libiconv-1.17-1.ppc
libgcc10-10.3.0-6.ppc
gcc10-cpp-10.3.0-6.ppc
gcc-cpp-10-2.ppc
gcc-gfortran-10-2.ppc



------------------------------
Michael Metts
------------------------------
</http:>
#AIXOpenSource

Hello,

Has there been any progress on this issue? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 11/14/2022 2:24:00 AM
From: Ayappan P
Subject: RE: problems with R, libiconv and gcc

Looks like gcc10 pthread library " /opt/freeware/lib/pthread/ppc64/libgcc_s.a " doesn't have 32bit shared object. We are looking into it. 

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Sun November 13, 2022 01:14 PM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi,

I've installed R and R-devel on one of our AIX 7.3 LPARs and now I'm hoping to install a basic set of R packages.  I'm getting a magic number error associated with libiconv and gcclib but everything is latest and all from Toolbox.  Is there a way to fix this?  Please see below.  Thanks.

Mike

> install.packages('colorspace',repos='cran.rstudio.com')
trying URL 'cran.rstudio.com/src/contrib/colorspace_2.0-3.tar.gz'
Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package 'colorspace' ...
** package 'colorspace' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -maix64 -pthread -fPIC -I"/opt/freeware/lib64/R/include" -DNDEBUG -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -mminimal-toc -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -c colorspace.c -o colorspace.o
Could not load program gcc:
Could not load module /opt/freeware/lib/libiconv.a(libiconv.so.2).
Dependent module /opt/freeware/lib/pthread/ppc64/libgcc_s.a(shr.o) could not be loaded.
The module has an invalid magic number.
Could not load module gcc-10.
Dependent module /opt/freeware/lib/libiconv.a(libiconv.so.2) could not be loaded.
make: The error code from the last command is 255.

[root@crilacs1 ~]# rpm -qa | grep -iE '(gcc|iconv)'
libgcc-10-2.ppc
gcc10-10.3.0-6.ppc
gcc10-gfortran-10.3.0-6.ppc
gcc-10-2.ppc
libiconv-1.17-1.ppc
libgcc10-10.3.0-6.ppc
gcc10-cpp-10.3.0-6.ppc
gcc-cpp-10-2.ppc
gcc-gfortran-10-2.ppc



------------------------------
Michael Metts
------------------------------
</http:>
#AIXOpenSource

Hi Mike,

As an workaround please run the below steps.

cd /opt/freeware/lib/gcc/powerpc-ibm-aix7.3.0.0/10/pthread
ar -X32 xv libgcc_s.a
ar -X32 -q ppc64/libgcc_s.a shr.o

We will continue to work on permanent solution.

------------------------------
SANGAMESH
------------------------------

Original Message:
Sent: Wed November 16, 2022 10:39 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hello,

Has there been any progress on this issue? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com
#AIXOpenSource

Hi Sangamesh,

Okay. I’ll give this a try. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 11/17/2022 8:02:00 AM
From: SANGAMESH MALLAYYA
Subject: RE: problems with R, libiconv and gcc

Hi Mike,

As an workaround please run the below steps.

cd /opt/freeware/lib/gcc/powerpc-ibm-aix7.3.0.0/10/pthread
ar -X32 xv libgcc_s.a
ar -X32 -q ppc64/libgcc_s.a shr.o

We will continue to work on permanent solution.

------------------------------
SANGAMESH
------------------------------

Original Message:
Sent: Wed November 16, 2022 10:39 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hello,

Has there been any progress on this issue? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com</http:>
#AIXOpenSource

Hi Sangamesh,

I gave that a try and the package compiles but it throws a lot of duplicate symbol warnings which makes me wonder if this is a good path to go down. Please see below and advise. Thanks.

Mike

[root@crilacs1 ~]# R

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: powerpc-ibm-aix7.1.3.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('colorspace',repos='cran.rstudio.com<http: cran.rstudio.com="">')
trying URL 'cran.rstudio.com/src/contrib/colorspace_2.0-3.tar.gz<http: cran.rstudio.com/src/contrib/colorspace_2.0-3.tar.gz="">'
Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -maix64 -pthread -fPIC -I"/opt/freeware/lib64/R/include" -DNDEBUG -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -mminimal-toc -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -c colorspace.c -o colorspace.o
gcc -maix64 -pthread -fPIC -I"/opt/freeware/lib64/R/include" -DNDEBUG -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -mminimal-toc -O2 -I/opt/freeware/include -I/usr/include -D_GETDELIM -c init.c -o init.o
gcc -maix64 -pthread -fPIC -shared -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc -L/opt/freeware/lib64/R/lib -L/opt/freeware/lib/pthread/ppc64 -L/opt/freeware/lib64 -L/opt/freeware/lib -L/usr/lib -Wl,-blibpath:/opt/freeware/lib/pthread/ppc64:/opt/freeware/lib64:/opt/freeware/lib:/usr/lib -o colorspace.so colorspace.o init.o -lm -L/opt/freeware/lib64/R/lib -lR /opt/freeware/lib64/libintl.a
ld: 0711-224 WARNING: Duplicate symbol: .strcmp
ld: 0711-224 WARNING: Duplicate symbol: strcmp
ld: 0711-224 WARNING: Duplicate symbol: .pow
ld: 0711-224 WARNING: Duplicate symbol: pow
ld: 0711-224 WARNING: Duplicate symbol: .fsav
ld: 0711-224 WARNING: Duplicate symbol: fsav
ld: 0711-224 WARNING: Duplicate symbol: .fres
ld: 0711-224 WARNING: Duplicate symbol: fres
ld: 0711-224 WARNING: Duplicate symbol: .cexp
ld: 0711-224 WARNING: Duplicate symbol: cexp
ld: 0711-224 WARNING: Duplicate symbol: .ctanh
ld: 0711-224 WARNING: Duplicate symbol: .ctan
ld: 0711-224 WARNING: Duplicate symbol: .csqrt
ld: 0711-224 WARNING: Duplicate symbol: .csinh
ld: 0711-224 WARNING: Duplicate symbol: .csin
ld: 0711-224 WARNING: Duplicate symbol: .ccosh
ld: 0711-224 WARNING: Duplicate symbol: .ccos
ld: 0711-224 WARNING: Duplicate symbol: .catan
ld: 0711-224 WARNING: Duplicate symbol: .casin
ld: 0711-224 WARNING: Duplicate symbol: .cacos
ld: 0711-224 WARNING: Duplicate symbol: .finite
ld: 0711-224 WARNING: Duplicate symbol: finite
ld: 0711-224 WARNING: Duplicate symbol: .sin
ld: 0711-224 WARNING: Duplicate symbol: sin
ld: 0711-224 WARNING: Duplicate symbol: .cos
ld: 0711-224 WARNING: Duplicate symbol: cos
ld: 0711-224 WARNING: Duplicate symbol: .sinh
ld: 0711-224 WARNING: Duplicate symbol: sinh
ld: 0711-224 WARNING: Duplicate symbol: .expm1
ld: 0711-224 WARNING: Duplicate symbol: expm1
ld: 0711-224 WARNING: Duplicate symbol: .scalb
ld: 0711-224 WARNING: Duplicate symbol: scalb
ld: 0711-224 WARNING: Duplicate symbol: .scalbn
ld: 0711-224 WARNING: Duplicate symbol: .cosh
ld: 0711-224 WARNING: Duplicate symbol: cosh
ld: 0711-224 WARNING: Duplicate symbol: .exp
ld: 0711-224 WARNING: Duplicate symbol: exp
ld: 0711-224 WARNING: Duplicate symbol: .exp__E
ld: 0711-224 WARNING: Duplicate symbol: exp__E
ld: 0711-224 WARNING: Duplicate symbol: .raise_ie
ld: 0711-224 WARNING: Duplicate symbol: raise_ie
ld: 0711-224 WARNING: Duplicate symbol: .logb
ld: 0711-224 WARNING: Duplicate symbol: logb
ld: 0711-224 WARNING: Duplicate symbol: .log
ld: 0711-224 WARNING: Duplicate symbol: log
ld: 0711-224 WARNING: Duplicate symbol: .log1p
ld: 0711-224 WARNING: Duplicate symbol: log1p
ld: 0711-224 WARNING: Duplicate symbol: .atan
ld: 0711-224 WARNING: Duplicate symbol: atan
ld: 0711-224 WARNING: Duplicate symbol: tantab
ld: 0711-224 WARNING: Duplicate symbol: .atan2
ld: 0711-224 WARNING: Duplicate symbol: atan2
ld: 0711-224 WARNING: Duplicate symbol: .atanh
ld: 0711-224 WARNING: Duplicate symbol: atanh
ld: 0711-224 WARNING: Duplicate symbol: .asin
ld: 0711-224 WARNING: Duplicate symbol: asin
ld: 0711-224 WARNING: Duplicate symbol: .asinh
ld: 0711-224 WARNING: Duplicate symbol: asinh
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information.
Target "all" is up to date.
installing to /opt/freeware/lib64/R/library/00LOCK-colorspace/00new/colorspace/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (colorspace)

The downloaded source packages are in
‘/tmp/RtmpUvaqia/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
>


Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">

On Nov 17, 2022, at 7:19 AM, Metts, Michael < /><mailto:mmetts@cornerstone.com>> wrote:

Hi Sangamesh,

Okay. I’ll give this a try. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com/="">


Original Message:
Sent: 11/17/2022 8:02:00 AM
From: SANGAMESH MALLAYYA
Subject: RE: problems with R, libiconv and gcc

Hi Mike,

As an workaround please run the below steps.

cd /opt/freeware/lib/gcc/powerpc-ibm-aix7.3.0.0/10/pthread
ar -X32 xv libgcc_s.a
ar -X32 -q ppc64/libgcc_s.a shr.o

We will continue to work on permanent solution.

------------------------------
SANGAMESH
------------------------------

Original Message:
Sent: Wed November 16, 2022 10:39 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hello,

Has there been any progress on this issue? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
mmetts@cornerstone.com></http:></http:></http:>">www.cornerstone.com</http:></mailto:mmetts@cornerstone.com></http:></http:></http:>
#AIXOpenSource

Hi Mike,

You can ignore these errors.
While creating a shared object it's using bexpall and -lc ,-lm and -lR. With bexpall it will try to export all the libc, libm symbols coming from static .o files.
Since libR is also exporting symbols from libc & libm it's throwing an warning in this case.

------------------------------
SANGAMESH
------------------------------

Original Message:
Sent: Thu November 17, 2022 05:00 PM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Sangamesh,

I gave that a try and the package compiles but it throws a lot of duplicate symbol warnings which makes me wonder if this is a good path to go down. Please see below and advise. Thanks.

Mike

[root@crilacs1 ~]# R

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: powerpc-ibm-aix7.1.3.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('colorspace',repos='cran.rstudio.com
#AIXOpenSource

Hi Sangamesh,

I understand what you’re saying but I’m wondering whether it’s always going to throw this many warnings on every R package build. That seems problematic in my view. I guess I’m hoping that we can use R on AIX much as we do on Linux. If that’s unreasonable someone just tell me now. In other words, it’s not okay for it to spew 50 or 100 times the number of warnings when building on AIX than it otherwise would on Linux and then just call that “normal”. Right? Is it reasonable to ask that this to be fixed? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 11/18/2022 3:10:00 AM
From: SANGAMESH MALLAYYA
Subject: RE: problems with R, libiconv and gcc

Hi Mike,

You can ignore these errors.
While creating a shared object it's using bexpall and -lc ,-lm and -lR. With bexpall it will try to export all the libc, libm symbols coming from static .o files.
Since libR is also exporting symbols from libc & libm it's throwing an warning in this case.

------------------------------
SANGAMESH
------------------------------

Original Message:
Sent: Thu November 17, 2022 05:00 PM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Sangamesh,

I gave that a try and the package compiles but it throws a lot of duplicate symbol warnings which makes me wonder if this is a good path to go down. Please see below and advise. Thanks.

Mike

[root@crilacs1 ~]# R

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: powerpc-ibm-aix7.1.3.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('colorspace',repos='cran.rstudio.com</http:>
#AIXOpenSource

R uses "-bexpall" linker option in AIX to simplify the build process. With the libc.a & libm.a having static objects, the -bexpall option ended up re-exporting some of the symbols in the R library (libR.so). So when the R modules are compiled , during the linkage with libc, libm and libR , the linker finds the duplicate symbols and throws these warnings. 
We understand that these warnings are a menace and we will work on fixing the R build by removing the "-bexpall" option.

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Fri November 18, 2022 10:25 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Sangamesh,

I understand what you're saying but I'm wondering whether it's always going to throw this many warnings on every R package build. That seems problematic in my view. I guess I'm hoping that we can use R on AIX much as we do on Linux. If that's unreasonable someone just tell me now. In other words, it's not okay for it to spew 50 or 100 times the number of warnings when building on AIX than it otherwise would on Linux and then just call that "normal". Right? Is it reasonable to ask that this to be fixed? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com
#AIXOpenSource

Great. Thanks so much! Any idea when that and the original issue will be fixed?

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 11/21/2022 6:40:00 AM
From: Ayappan P
Subject: RE: problems with R, libiconv and gcc

R uses "-bexpall" linker option in AIX to simplify the build process. With the libc.a & libm.a having static objects, the -bexpall option ended up re-exporting some of the symbols in the R library (libR.so). So when the R modules are compiled , during the linkage with libc, libm and libR , the linker finds the duplicate symbols and throws these warnings. 
We understand that these warnings are a menace and we will work on fixing the R build by removing the "-bexpall" option.

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Fri November 18, 2022 10:25 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Sangamesh,

I understand what you're saying but I'm wondering whether it's always going to throw this many warnings on every R package build. That seems problematic in my view. I guess I'm hoping that we can use R on AIX much as we do on Linux. If that's unreasonable someone just tell me now. In other words, it's not okay for it to spew 50 or 100 times the number of warnings when building on AIX than it otherwise would on Linux and then just call that "normal". Right? Is it reasonable to ask that this to be fixed? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com</http:>
#AIXOpenSource

gcc can be easily fixed and re-published soon, perhaps next week.
But rebuilding R without "-bexpall" requires some effort. It might require couple of weeks.

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Mon November 21, 2022 10:15 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Great. Thanks so much! Any idea when that and the original issue will be fixed?

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com
#AIXOpenSource

R-4.1.2-2 is now available in AIX Toolbox with the issues fixed.

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Mon November 21, 2022 10:15 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Great. Thanks so much! Any idea when that and the original issue will be fixed?

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com
#AIXOpenSource

Great. Thanks!

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 12/23/2022 9:14:00 AM
From: Ayappan P
Subject: RE: problems with R, libiconv and gcc

R-4.1.2-2 is now available in AIX Toolbox with the issues fixed.

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Mon November 21, 2022 10:15 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Great. Thanks so much! Any idea when that and the original issue will be fixed?

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com</http:>
#AIXOpenSource

Hi Ayappan,

When I run `dnf check-update` I don’t see an update for R consistent with R-4.1.2-2 being available. I have R-4.1.2-1 installed. Is there something I should do differently? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 12/23/2022 9:14:00 AM
From: Ayappan P
Subject: RE: problems with R, libiconv and gcc

R-4.1.2-2 is now available in AIX Toolbox with the issues fixed.

------------------------------
Ayappan P
------------------------------

Original Message:
Sent: Mon November 21, 2022 10:15 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Great. Thanks so much! Any idea when that and the original issue will be fixed?

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com</http:>
#AIXOpenSource

We have updated the repository now, so you can try it again.

------------------------------
RESHMA KUMAR
------------------------------

Original Message:
Sent: Mon December 26, 2022 02:01 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Ayappan,

When I run `dnf check-update` I don't see an update for R consistent with R-4.1.2-2 being available. I have R-4.1.2-1 installed. Is there something I should do differently? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com
#AIXOpenSource

Hi Reshma,

Yes. I see them there now. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">


Original Message:
Sent: 12/26/2022 5:38:00 AM
From: RESHMA KUMAR
Subject: RE: problems with R, libiconv and gcc

We have updated the repository now, so you can try it again.

------------------------------
RESHMA KUMAR
------------------------------

Original Message:
Sent: Mon December 26, 2022 02:01 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Ayappan,

When I run `dnf check-update` I don't see an update for R consistent with R-4.1.2-2 being available. I have R-4.1.2-1 installed. Is there something I should do differently? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com</http:>
#AIXOpenSource

I am getting the below error message when trying to build the CRAN package `stringi` . Does anyone have thoughts on how to fix or avoid this? Please advise. Thanks.

cu69/i18n/ztrans.o icu69/stubdata/stubdata.o -lm -L/opt/freeware/lib64/R/lib -lR /opt/freeware/lib64/libintl.a
ld: 0711-781 ERROR: TOC overflow. TOC size: 108984 Maximum size: 65536
collect2: error: ld returned 12 exit status
make: The error code from the last command is 1.

Stop.
ERROR: compilation failed for package ‘stringi’
* removing ‘/opt/freeware/lib64/R/library/stringi’


Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">

On Dec 26, 2022, at 8:19 AM, Metts, Michael < /><mailto:mmetts@cornerstone.com>> wrote:

Hi Reshma,

Yes. I see them there now. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com/="">


Original Message:
Sent: 12/26/2022 5:38:00 AM
From: RESHMA KUMAR
Subject: RE: problems with R, libiconv and gcc

We have updated the repository now, so you can try it again.

------------------------------
RESHMA KUMAR
------------------------------

Original Message:
Sent: Mon December 26, 2022 02:01 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Ayappan,

When I run `dnf check-update` I don't see an update for R consistent with R-4.1.2-2 being available. I have R-4.1.2-1 installed. Is there something I should do differently? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
mmetts@cornerstone.com></http:>">www.cornerstone.com</http:></mailto:mmetts@cornerstone.com></http:>
#AIXOpenSource

Okay, I created this file:

[root@crilacs1 ~]# cat .R/Makevars
LDFLAGS += -Wl,-bbigtoc

Then I attempted to build `broom` again which depends on `stringi` and it worked. If there are other things like this that you know if please let me know. In other words, if there are things you haven’t told me about making sure I have a viable R package build environment, please let me know what those things are. My goal is to have a reasonably function R installation on one of our AIX 7.3 machines. In my view, that doesn’t seem unreasonable. Thanks.

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com="">

On Dec 26, 2022, at 12:02 PM, Metts, Michael < /><mailto:mmetts@cornerstone.com>> wrote:

I am getting the below error message when trying to build the CRAN package `stringi` . Does anyone have thoughts on how to fix or avoid this? Please advise. Thanks.

cu69/i18n/ztrans.o icu69/stubdata/stubdata.o -lm -L/opt/freeware/lib64/R/lib -lR /opt/freeware/lib64/libintl.a
ld: 0711-781 ERROR: TOC overflow. TOC size: 108984 Maximum size: 65536
collect2: error: ld returned 12 exit status
make: The error code from the last command is 1.

Stop.
ERROR: compilation failed for package ‘stringi’
* removing ‘/opt/freeware/lib64/R/library/stringi’


Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com/="">

On Dec 26, 2022, at 8:19 AM, Metts, Michael < /><mailto:mmetts@cornerstone.com>> wrote:

Hi Reshma,

Yes. I see them there now. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
www.cornerstone.com<http: www.cornerstone.com/="">


Original Message:
Sent: 12/26/2022 5:38:00 AM
From: RESHMA KUMAR
Subject: RE: problems with R, libiconv and gcc

We have updated the repository now, so you can try it again.

------------------------------
RESHMA KUMAR
------------------------------

Original Message:
Sent: Mon December 26, 2022 02:01 AM
From: Michael Metts
Subject: problems with R, libiconv and gcc

Hi Ayappan,

When I run `dnf check-update` I don't see an update for R consistent with R-4.1.2-2 being available. I have R-4.1.2-1 installed. Is there something I should do differently? Please advise. Thanks.

Mike

Michael L. Metts (he/him/his)
/ˈmaɪkəɫ ˈɛɫ ˈmɛts/
Principal Data Engineer
CORNERSTONE RESEARCH
1000 El Camino Real, Suite 250
Menlo Park, CA 94025-4327
650.470.7171 direct
650.740.8551 mobile
mmetts@cornerstone.com></http:></mailto:mmetts@cornerstone.com></http:>">www.cornerstone.com</http:></mailto:mmetts@cornerstone.com></http:></mailto:mmetts@cornerstone.com></http:>
#AIXOpenSource