IBM Power vs Markdown

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IBM Power vs Markdown

adkin8

Hi, folks.

I was wondering if any of you could point me in the right direction.

Using R 3.3.3 (and later), on an IBM Power LPAR, Red Hat 7 PPC64le, markdown build fails as below.

> install.packages("markdown")
trying URL 'https://cloud.r-project.org/src/contrib/markdown_0.8.tar.gz'
Content type 'unknown' length 80583 bytes (78 KB) ==================================================
downloaded 78 KB

installing source package 'markdown' ...
** package 'markdown' successfully unpacked and MD5 sums checked
** libs
/opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rbase64.c -o Rbase64.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rinit.c -o Rinit.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rmarkdown.c -o Rmarkdown.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c autolink.c -o autolink.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c buffer.c -o buffer.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c houdini_href_e.c -o houdini_href_e.o /opt/ibm/xlC/13.1.
 6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c houdini_html_e.c -o houdini_html_e.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c html.c -o html.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c html_smartypants.c -o html_smartypants.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c markdown.c -o markdown.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c stack.c -o stack.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -qmkshrobj -shared -L/usr/local/lib64/R/lib -L/usr/local/lib64 -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdin
 i_html_e.o html.o html_smartypants.o markdown.o stack.o -L/usr/local/lib64/R/lib -lR
markdown.o: In function find_block_tag': /tmp/RtmpqYsbzz/R.INSTALL1cb764af1cf/markdown/src/./html_blocks.h:206: undefined reference tofind_block_tag$AF85_1'
/usr/bin/ld: markdown.so: internal symbol `find_block_tag$AF85_1' isn't defined
/usr/bin/ld: final link failed: Bad value
make: *** [markdown.so] Error 1
ERROR: compilation failed for package 'markdown'
removing '/usr/local/lib64/R/library/markdown'
The downloaded source packages are in
'/tmp/Rtmpl7vFYx/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("markdown") :
installation of package 'markdown' had non-zero exit status

...

It looks like the issue can be traced down to, "!gperf_case_strncmp (str, s, len)" ... is there a way to trace this down further?

# tail markdown/src/html_blocks.h
      if (key <= MAX_HASH_VALUE && key >= 0)
        {
          register const char *s = wordlist[key];

          if ((((unsigned char)*str ^ (unsigned char)*s) & ~32) == 0 && !gperf_case_strncmp (str, s, len) && s[len] == '\0')
            return s;
        }
    }
  return 0;
}

Any assistance is appreciated.

A. Daniel King
Haverty Furniture Companies, Inc.

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Re: IBM Power vs Markdown

Marc Schwartz-3
Hi,

As I was doing some searching, it would appear that you also posted to the package's GitHub repo and obtained a solution there:

  https://github.com/rstudio/markdown/issues/88

For specific packages, in situations like this, contacting the package maintainer as you did, is a good first step.

For future reference, since you are running on RH, there is the R-SIG-Fedora list, which covers issues associated with running R on RH and Fedora based distros:

  https://stat.ethz.ch/mailman/listinfo/r-sig-fedora

Regards,

Marc Schwartz


> On Jan 19, 2018, at 9:57 AM, Daniel King <[hidden email]> wrote:
>
>
> Hi, folks.
>
> I was wondering if any of you could point me in the right direction.
>
> Using R 3.3.3 (and later), on an IBM Power LPAR, Red Hat 7 PPC64le, markdown build fails as below.
>
>> install.packages("markdown")
> trying URL 'https://cloud.r-project.org/src/contrib/markdown_0.8.tar.gz'
> Content type 'unknown' length 80583 bytes (78 KB) ==================================================
> downloaded 78 KB
>
> installing source package 'markdown' ...
> ** package 'markdown' successfully unpacked and MD5 sums checked
> ** libs
> /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rbase64.c -o Rbase64.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rinit.c -o Rinit.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rmarkdown.c -o Rmarkdown.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c autolink.c -o autolink.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c buffer.c -o buffer.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c houdini_href_e.c -o houdini_href_e.o /opt/ibm/xlC/13.
 1.
> 6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c houdini_html_e.c -o houdini_html_e.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c html.c -o html.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c html_smartypants.c -o html_smartypants.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c markdown.c -o markdown.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c stack.c -o stack.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -qmkshrobj -shared -L/usr/local/lib64/R/lib -L/usr/local/lib64 -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdi
 n

> i_html_e.o html.o html_smartypants.o markdown.o stack.o -L/usr/local/lib64/R/lib -lR
> markdown.o: In function find_block_tag': /tmp/RtmpqYsbzz/R.INSTALL1cb764af1cf/markdown/src/./html_blocks.h:206: undefined reference tofind_block_tag$AF85_1'
> /usr/bin/ld: markdown.so: internal symbol `find_block_tag$AF85_1' isn't defined
> /usr/bin/ld: final link failed: Bad value
> make: *** [markdown.so] Error 1
> ERROR: compilation failed for package 'markdown'
> removing '/usr/local/lib64/R/library/markdown'
> The downloaded source packages are in
> '/tmp/Rtmpl7vFYx/downloaded_packages'
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("markdown") :
> installation of package 'markdown' had non-zero exit status
>
> ...
>
> It looks like the issue can be traced down to, "!gperf_case_strncmp (str, s, len)" ... is there a way to trace this down further?
>
> # tail markdown/src/html_blocks.h
>      if (key <= MAX_HASH_VALUE && key >= 0)
>        {
>          register const char *s = wordlist[key];
>
>          if ((((unsigned char)*str ^ (unsigned char)*s) & ~32) == 0 && !gperf_case_strncmp (str, s, len) && s[len] == '\0')
>            return s;
>        }
>    }
>  return 0;
> }
>
> Any assistance is appreciated.
>
> A. Daniel King
> Haverty Furniture Companies, Inc.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.