De Xin Luan
2013-Jul-17 09:51 UTC
[R] Help: Error when installing R 2.8.1 in IBM AIX system from source code
Hi R-Help,
When we tried to install R 2.8.1 in our AIX system, we faced some error,
please help.
OS level: AIX 7.1 64 bit
R 2.8.1
We had a guide about How to install R 2.8.1 in AIX from R source code. Here
is what I did:
1. Download the R source file, for example R-2.8.1.tar.gz , from
http://www.r-project.org/ (or
ftp://ftp.stat.math.ethz.ch/Software/CRAN/src/base/R-2/) and save it to the
temporary directory.
2. cd /spss/src
tar xzf R-2.8.1.tar.gz
cd R-2.8.1
3. Download and install the patch from
http://prs.ism.ac.jp/~nakama/AIX/AIX_R-2.8.1_fix.patch.
mv AIX_R-2.8.1_fix.patch /spss/src/R-2.8.1
chown -R root:system /spss/src/R-2.8.1
chmod -R 775 /spss/src/R-2.8.1
zspssdb2was5:/spss/src/R-2.8.1# patch -p1 < AIX_R-2.8.1_fix.patch
Hmm... Looks like a unified context diff to me...
The text leading up to this was:
--------------------------
|diff -ruN R-2.8.1.orig/Makeconf.in R-2.8.1/Makeconf.in
|--- R-2.8.1.orig/Makeconf.in 2008-10-17 11:05:02.000000000 +0900
|+++ R-2.8.1/Makeconf.in 2009-02-19 17:48:17.000000000 +0900
--------------------------
Patching file Makeconf.in using Plan A...
Malformed patch at line 5: MAIN_CFLAGS = @MAIN_CFLAGS@
4. Set parameters
export ICONVINC=-I/opt/freeware/include
export PNGINC=-I/opt/freeware/include
export JPEGINC=-I/opt/freeware/include
export ZLIBINC=-I/opt/freeware/include
export ICONVLIB=-L/opt/freeware/lib
export PNGLIB=-L/opt/freeware/lib
export JPEGLIB=-L/opt/freeware/lib
export ZLIBLIB=-L/opt/freeware/lib
export CC="xlc_r -q64"
export CXX="xlC_r -q64"
export CXXFLAGS="-O -qstrict"
export CFLAGS="-O -qstrict"
export F77="xlf_r -q64"
export AR="ar -X64"
export CPPFLAGS="$ICONVINC $PNGINC $JPEGINC $ZLIBINC
-I/usr/lpp/X11/include/X11"
export LDFLAGS="$ICONVLIB $PNGLIB $JPEGLIB $ZLIBLIB -L/usr/lib
-L/usr/X11R6/lib"
export OBJECT_MODE="64"
5. ./configure --prefix=/opt/R-2.8.1 --enable-R-shlib --enable-BLAS-shlib
--with-x --with-readline=no
R is now configured for rs6000-ibm-aix
Source directory: .
Installation directory: /opt/R-2.8.1
C compiler: xlc_r -q64 -O -qstrict
Fortran 77 compiler: xlf_r -q64 -g
C++ compiler: xlC_r -q64 -O -qstrict
Fortran 90/95 compiler: gfortran
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries:
Additional capabilities: TIFF, iconv, MBCS, NLS
Options enabled: shared R library, shared BLAS, R profiling,
Java
Recommended packages: yes
configure: WARNING: you cannot build DVI versions of the R manuals
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
Issue1: during "configure" step, I faced below error in red, and I
take
below action in blue:
./configure[20510]: "${}": bad substitution
at line 20510 of ./configure file, add below line:
shlibpath_var=LD_LIBRARY_PATH
6. make
Issue: during "make" step, I faced the below error in red, I don't
know how
to fix it.
../../../bin/R[206]: "${}": bad substitution
make: The error code from the last command is 1.
Stop.
Thanks and Best Regards.
De Xin Luan (栾 德欣)
Application Developer-- Business Intelligence & = What is BAO?
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[[alternative HTML version deleted]]
Jeff Newmiller
2013-Jul-17 15:02 UTC
[R] Help: Error when installing R 2.8.1 in IBM AIX system from source code
Help with outdated versions of R, and particularly with nonstandard patch files,
are not really on topic here. Posting in HTML format is not advised (see posting
guide) since it actually makes it harder to read R code, so text coloring
doesn't come through.
It appears to me that your patch failed to make necessary changes to the R
source code to be compatible your operating system in step 3. It is possible
that you were using an incompatible version of the patch program. You may need
to obtain the version of GNU compilers and other toolchain components that were
used in developing that particular version of R. You probably need help from a
programmer who is familiar with AIX and Unix development to help you interpret
the compiler errors and warnings.
With appropriate local technical support for composing questions, you may be
able to get more focused answers on the R-devel mailing list rather than here.
However, the issue of asking questions about an old version of the R source code
may still prove unpopular, so it may be better to study the intent of your
existing patch files and try to adapt them to a v3.0.x version before asking for
help there.
---------------------------------------------------------------------------
Jeff Newmiller The ..... ..... Go Live...
DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.
De Xin Luan <luandex at cn.ibm.com> wrote:
>
>Hi R-Help,
>
>When we tried to install R 2.8.1 in our AIX system, we faced some
>error,
>please help.
>
>OS level: AIX 7.1 64 bit
>R 2.8.1
>
>We had a guide about How to install R 2.8.1 in AIX from R source code.
>Here
>is what I did:
>
>1.??Download the R source file, for example R-2.8.1.tar.gz , from
>http://www.r-project.org/ (or
>ftp://ftp.stat.math.ethz.ch/Software/CRAN/src/base/R-2/) and save it to
>the
>temporary directory.
>
>2. cd /spss/src
>tar xzf R-2.8.1.tar.gz
>cd R-2.8.1
>
>3.??Download and install the patch from
>http://prs.ism.ac.jp/~nakama/AIX/AIX_R-2.8.1_fix.patch.
>
>mv??AIX_R-2.8.1_fix.patch??/spss/src/R-2.8.1
>chown -R root:system??/spss/src/R-2.8.1
>chmod -R 775??/spss/src/R-2.8.1
>
>zspssdb2was5:/spss/src/R-2.8.1# patch -p1 < AIX_R-2.8.1_fix.patch
>Hmm... ??Looks like a unified context diff to me...
>The text leading up to this was:
>--------------------------
>|diff -ruN R-2.8.1.orig/Makeconf.in R-2.8.1/Makeconf.in
>|--- R-2.8.1.orig/Makeconf.in ?? 2008-10-17 11:05:02.000000000 +0900
>|+++ R-2.8.1/Makeconf.in ?? ?? ?? ??2009-02-19 17:48:17.000000000 +0900
>--------------------------
>Patching file Makeconf.in using Plan A...
>Malformed patch at line 5: ??MAIN_CFLAGS = @MAIN_CFLAGS@
>
>4. Set parameters
>
>export ICONVINC=-I/opt/freeware/include
>export PNGINC=-I/opt/freeware/include
>export JPEGINC=-I/opt/freeware/include
>export ZLIBINC=-I/opt/freeware/include
>export ICONVLIB=-L/opt/freeware/lib
>export PNGLIB=-L/opt/freeware/lib
>export JPEGLIB=-L/opt/freeware/lib
>export ZLIBLIB=-L/opt/freeware/lib
>
>export CC="xlc_r -q64"
>export CXX="xlC_r -q64"
>export CXXFLAGS="-O -qstrict"
>export CFLAGS="-O -qstrict"
>export F77="xlf_r -q64"
>export AR="ar -X64"
>export CPPFLAGS="$ICONVINC $PNGINC $JPEGINC $ZLIBINC
>-I/usr/lpp/X11/include/X11"
>export LDFLAGS="$ICONVLIB $PNGLIB $JPEGLIB $ZLIBLIB -L/usr/lib
>-L/usr/X11R6/lib"
>export OBJECT_MODE="64"
>
>
>
>5. ./configure --prefix=/opt/R-2.8.1??--enable-R-shlib
>--enable-BLAS-shlib
>--with-x --with-readline=no
>
>R is now configured for rs6000-ibm-aix
>
>?? Source directory: ?? ?? ?? ?? ??.
>?? Installation directory: ?? ??/opt/R-2.8.1
>
>?? C compiler: ?? ?? ?? ?? ?? ?? ?? ??xlc_r -q64 ??-O -qstrict
>?? Fortran 77 compiler: ?? ?? ?? xlf_r -q64 ??-g
>
>?? C++ compiler: ?? ?? ?? ?? ?? ?? ??xlC_r -q64 ??-O -qstrict
>?? Fortran 90/95 compiler: ?? ??gfortran
>?? Obj-C compiler:
>
>?? Interfaces supported: ?? ?? ??X11, tcltk
>?? External libraries:
>?? Additional capabilities: ?? TIFF, iconv, MBCS, NLS
>?? Options enabled: ?? ?? ?? ?? ?? shared R library, shared BLAS, R
>profiling,
>Java
>
>?? Recommended packages: ?? ?? ??yes
>
>configure: WARNING: you cannot build DVI versions of the R manuals
>configure: WARNING: you cannot build info or HTML versions of the R
>manuals
>configure: WARNING: you cannot build PDF versions of the R manuals
>configure: WARNING: I could not determine a browser
>configure: WARNING: I could not determine a PDF viewer
>
>
>Issue1: during "configure" step, I faced below error in red, and I
take
>below action in blue:
>./configure[20510]: "${}": bad substitution
>at line 20510 of ./configure file, add below line:
>shlibpath_var=LD_LIBRARY_PATH
>
>
>6. make
>
>Issue: during "make" step, I faced the below error in red, I
don't know
>how
>to fix it.
>../../../bin/R[206]: "${}": bad substitution
>make: The error code from the last command is 1.
>
>
>Stop.
>
>
>
>Thanks and Best Regards.
>
>
>
>De Xin Luan (??? ??????)
>
>Application Developer-- Business Intelligence & = What is BAO?
>
>Performance Management = Global BAO Wiki
>
>BAO Service Line, As Delivery = China GDC BAO
>Wiki
>China Global Delivery = Japan BAO Wiki
>
>Office: +86,411,88151485 T/L: 61901 Mobile: = GCG BAO Wiki
>
>+86,186,4342,5156 = Sales &
>Delivery
>E-mail: luandex at cn.ibm.com = BOSS (BAO
>Offerings and Solutions Store)
> = GBS Solutions and Assets
>BAO can provide you below products and services: = BAO University
>
>BAO-BIPM: Cognos, BI Reporting Tools, TM1, = BAO University
>Virtual Campus
>OpenPages, Algorithmic = Smarter
>Analytics University
>BAO-EIM: DataStage, Informatica, MDM, Netezza, = BAO Tube
>
>Data Modeler = Practitioner
>Portal
>BAO-DBA: DB2 DBA, Oracle DBA, Sybase DBA = IBM CareerSmart
>
>BAO-Advanced Analytics & ECM: SPSS, iLog, BigData
>
>and FileNet
>
>BAO-Strategy & CoC : BAO Strategy, BAO CoC, and
>
>BAO Consulting Community
>
>
>
>
>Click here for BAO Service Area contact point.
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
>------------------------------------------------------------------------
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
Duncan Murdoch
2013-Jul-19 13:35 UTC
[R] Help: Error when installing R 2.8.1 in IBM AIX system from source code
On 19/07/2013 9:27 AM, De Xin Luan wrote:> > Hello, > > They can't solve the problem of R installation and direct me to > contact R help. I want to follow your standard way to install R 2.8.1 > in AIX 7.1 64bit system. Please guide me to install R 2.8.1. Thank you. >Presumably you're paying them, so if they can't figure out how to solve your problem, you should stop paying them. You're not paying us, but we will continue to offer help as long as you follow our advice, which is to upgrade to R 3.0.1. There might be someone on this list who would offer tech support for 2.8.1 for a fee, but I doubt it. Duncan Murdoch> > > Inactive hide details for Duncan Murdoch ---07/19/2013 09:11:52 > PM---On 19/07/2013 6:16 AM, De Xin Luan wrote: > Hi Jeff,Duncan > Murdoch ---07/19/2013 09:11:52 PM---On 19/07/2013 6:16 AM, De Xin Luan > wrote: > Hi Jeff, > > From: Duncan Murdoch <murdoch.duncan at gmail.com> > To: De Xin Luan/China/IBM at IBMCN, > Cc: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>, r-help at r-project.org > Date: 07/19/2013 09:11 PM > Subject: Re: [R] Help: Error when installing R 2.8.1 in IBM AIX system > from source code > > ------------------------------------------------------------------------ > > > > On 19/07/2013 6:16 AM, De Xin Luan wrote: > > Hi Jeff, > > > > Thanks for your quick response. Let me describe more about my situation. > > > > 1. Patch file - Yes, I found patch didn't change any file, so I manually > > changed 4 files(R-2.8.1/configure, R-2.8.1/configure.ac, > > R-2.8.1/Makeconf.in, R-2.8.1/src/main/Makefile.in) by reading the patch > > file. > > > > 2. why I use old version R 2.8.1 - We want to use SPSS Statistics to > call R > > in our server and have to install "Statistics essentials for R" > after R is > > installed successfully. In Statistics 20 document, it only supports > R 2.8.1 > > and provide that install guidance. > > In that case, you should be contacting SPSS tech support for help. > > Duncan Murdoch > > > > > 3. I don't know how to disable HTML format in my mail client. Sorry for > > that. I rewrite colorful part again here as 3.1 and 3.2 : > > > > 3.1 Issue1: during "configure" step, I faced this error:"./configure > > [20510]: "${}": bad substitution". > > And I took action to solve it, the action is :add > > "shlibpath_var=LD_LIBRARY_PATH" before line 20510 of configure file. > > > > 3.2 Issue2: during "make" step, I faced the below error but I don't know > > how to fix it: > > > > ../../../bin/R[206]: "${}": bad substitution > > make: The error code from the last command is 1. > > > > Stop. > > > > 4. Since you said it's not a standard patch, do you have a standard > patch > > for R 2.8.1 installation in AIX 7.1 64bit system? > > > > Best regards, > > > > Dexin Luan (??????) > > > > [[alternative HTML version deleted]] > > > > > > > > ______________________________________________ > > R-help at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > >