Re: [R-sig-Fedora] rstan warning messages

2016-02-05 Thread Tom Callaway 
On 02/05/2016 09:58 AM, Patrick, Larry B [CSSM] wrote:
> Did the following on my RHEL6 server:
>  [root@ping ~]# export 
> PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/
>  [root@ping ~]# /usr/bin/curl-config --libs
>  -L/usr/lib64 -lcurl

I'm glad this worked, but you should not have had to specify that. I'd
bet something else is misconfigured on your RHEL 6 system that will
likely cause problems in the future...

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-02-05 Thread Patrick, Larry B [CSSM] 
Tom,

I don't doubt it. 

Hopefully I can schedule some time to work on rebuilding this system with RHEL 
7 to help bring it up to date :) They just needed it right now and couldn't 
wait for any downtime :( I almost tossed in the towel at one point.

Thanks,
Larry


-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com] 
Sent: Friday, February 05, 2016 9:14 AM
To: Patrick, Larry B [CSSM] <longp...@iastate.edu>; 
'r-sig-fedora@r-project.org' <r-sig-fedora@r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

On 02/05/2016 09:58 AM, Patrick, Larry B [CSSM] wrote:
> Did the following on my RHEL6 server:
>  [root@ping ~]# export 
> PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/
>  [root@ping ~]# /usr/bin/curl-config --libs
>  -L/usr/lib64 -lcurl

I'm glad this worked, but you should not have had to specify that. I'd bet 
something else is misconfigured on your RHEL 6 system that will likely cause 
problems in the future...

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-02-03 Thread Tom Callaway 
On 02/03/2016 09:52 AM, Tom Callaway wrote:

> Are you trying to build R and components for i686 rather than x86_64?

Never mind. Your logs make it clear that you're building for x86_64.

Can you share the output of:

pkg-config --list-all |grep libcurl
curl-config --libs
rpm -V libcurl-devel libcurl

I'm honestly baffled as to why the configure script is failing to find
libcurl.pc on your system:

  Package libcurl was not found in the pkg-config search path.

  Perhaps you should add the directory containing `libcurl.pc'

  to the PKG_CONFIG_PATH environment variable

  No package 'libcurl' found

Do you have any files installed into /usr/local/ ?

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-02-03 Thread Patrick, Larry B [CSSM] 
I used epel to install again. I removed the original installation that seemed 
from epel also.

 [root@ping /]# pkg-config --list-all |grep libcurl
  [root@ping /]#
That doesn't look good.
  [root@ping /]# curl-config --libs
 Package libcurl was not found in the pkg-config search path.
 Perhaps you should add the directory containing `libcurl.pc'
 to the PKG_CONFIG_PATH environment variable
 No package 'libcurl' found
Again not good.
  [root@ping /]# rpm -V libcurl-devel libcurl
 prelink: /usr/lib64/libcurl.so.4.1.1: at least one of file's dependencies 
has changed since prelinking
 S.?../usr/lib64/libcurl.so.4.1.1

Something definitely not looking good here.

Thanks,
Larry


-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com] 
Sent: Wednesday, February 03, 2016 9:02 AM
To: Patrick, Larry B [CSSM] <longp...@iastate.edu>; 
'r-sig-fedora@r-project.org' <r-sig-fedora@r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

On 02/03/2016 09:52 AM, Tom Callaway wrote:

> Are you trying to build R and components for i686 rather than x86_64?

Never mind. Your logs make it clear that you're building for x86_64.

Can you share the output of:

pkg-config --list-all |grep libcurl
curl-config --libs
rpm -V libcurl-devel libcurl

I'm honestly baffled as to why the configure script is failing to find 
libcurl.pc on your system:

  Package libcurl was not found in the pkg-config search path.

  Perhaps you should add the directory containing `libcurl.pc'

  to the PKG_CONFIG_PATH environment variable

  No package 'libcurl' found

Do you have any files installed into /usr/local/ ?

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-02-03 Thread peter dalgaard 
Umm,

which curl-config

?

I.e., there might be two of them and you picking up the wrong one.
Just a hunch, I am more than rusty on Fedora these days.

-pd


On 03 Feb 2016, at 16:06 , Patrick, Larry B [CSSM] <longp...@iastate.edu> wrote:

> I used epel to install again. I removed the original installation that seemed 
> from epel also.
> 
> [root@ping /]# pkg-config --list-all |grep libcurl
>  [root@ping /]#
> That doesn't look good.
>  [root@ping /]# curl-config --libs
> Package libcurl was not found in the pkg-config search path.
> Perhaps you should add the directory containing `libcurl.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'libcurl' found
> Again not good.
>  [root@ping /]# rpm -V libcurl-devel libcurl
> prelink: /usr/lib64/libcurl.so.4.1.1: at least one of file's dependencies 
> has changed since prelinking
> S.?../usr/lib64/libcurl.so.4.1.1
> 
> Something definitely not looking good here.
> 
> Thanks,
> Larry
> 
> 
> -Original Message-
> From: Tom Callaway [mailto:tcall...@redhat.com] 
> Sent: Wednesday, February 03, 2016 9:02 AM
> To: Patrick, Larry B [CSSM] <longp...@iastate.edu>; 
> 'r-sig-fedora@r-project.org' <r-sig-fedora@r-project.org>
> Subject: Re: [R-sig-Fedora] rstan warning messages
> 
> On 02/03/2016 09:52 AM, Tom Callaway wrote:
> 
>> Are you trying to build R and components for i686 rather than x86_64?
> 
> Never mind. Your logs make it clear that you're building for x86_64.
> 
> Can you share the output of:
> 
> pkg-config --list-all |grep libcurl
> curl-config --libs
> rpm -V libcurl-devel libcurl
> 
> I'm honestly baffled as to why the configure script is failing to find 
> libcurl.pc on your system:
> 
>  Package libcurl was not found in the pkg-config search path.
> 
>  Perhaps you should add the directory containing `libcurl.pc'
> 
>  to the PKG_CONFIG_PATH environment variable
> 
>  No package 'libcurl' found
> 
> Do you have any files installed into /usr/local/ ?
> 
> ~tom
> 
> ==
> Red Hat
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-sig-Fedora] rstan warning messages

2016-02-03 Thread Tom Callaway 
On 02/03/2016 09:33 AM, Patrick, Larry B [CSSM] wrote:
> I didn't have any libgfortran files in /usr/lib so I did that soft link. 
> Maybe something didn't fully install or configure. I have inherited this 
> machine from another admin and it is not a fresh installation.

So, here's oddity number one:

You're clearly on an x86_64 system, which should store (and look for)
all libraries in /usr/lib64. /usr/lib should only be used for 32bit
libraries.

Are you trying to build R and components for i686 rather than x86_64?

Was R built from source on that system?

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-02-02 Thread Tom Callaway 
On 02/01/2016 03:45 PM, Patrick, Larry B [CSSM] wrote:
> Got past my libgfortran issue
>  ln -s  /usr/lib64/libgfortran.so.3 /usr/lib/libgfortran.so

Maybe to /usr/lib64/libgfortran.so ? You _should not_ need to do that
though. I didn't need to.

> Now if I could get RCurl and rstan installed.

This one is perplexing. I can't reproduce your failures from my RHEL-6 VM.

Can you provide me the output from:

   rpm -qf /usr/lib64/pkgconfig/libcurl.pc
   rpm -q pkgconfig

Also, if you can run the install.packages again and send me the full
log, that might be helpful.

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-02-01 Thread Patrick, Larry B [CSSM] 
Got past my libgfortran issue
 ln -s  /usr/lib64/libgfortran.so.3 /usr/lib/libgfortran.so

Now if I could get RCurl and rstan installed.

Thanks,
Larry


-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com] 
Sent: Friday, January 29, 2016 2:46 PM
To: Patrick, Larry B [CSSM] <longp...@iastate.edu>; 
'r-sig-fedora@r-project.org' <r-sig-fedora@r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

On 01/28/2016 09:07 AM, Patrick, Larry B [CSSM] wrote:
> Looks to have libgfortran installed.
>  yum list installed | grep libgfortran
>  libgfortran.x86_644.4.7-16.el6 
> @rhel-x86_64-server-6
> What else could I check?
> 
> Installed libcurl-devel and libidn-devel.
>  yum list installed | grep libcurl
>  libcurl.x86_647.19.7-46.el6
> @rhel-x86_64-server-6
>  libcurl-devel.x86_64  7.19.7-46.el6
> @rhel-x86_64-server-6
> Still getting warning for RCurl.
>  2: In install.packages("rstan", dependencies = TRUE, repos = 
> "http://cran.r-project.org/;) :  installation of package 'RCurl' had non-zero 
> exit status Now this log is way different and I have tried to pick through 
> the warning and error messages.
> Any thoughts here?

RHEL-6 is getting long in the tooth, at almost six years old. It's quite 
possible that these R modules are checking for modern dependencies and not 
finding them.

That said, something strange is definitely happening here. You're getting this 
error message:

   No package 'libcurl' found

That normally means that it could not find the pkgconfig file for 'libcurl', 
but I've pulled down the libcurl-devel package that you installed and it 
definitely has:

   /usr/lib64/pkgconfig/libcurl.pc

I think the only way I'm going to be able to troubleshoot this is to bring up a 
RHEL 6 VM and try it myself.

~tom

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Re: [R-sig-Fedora] rstan warning messages

2016-01-28 Thread Patrick, Larry B [CSSM] 
URLINFO_CERTINFO=1 
-DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 
-DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 
-DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 
-DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 
-DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 
-DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 
-DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 
-DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 
-DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 
-DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 
-DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 
-DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLO!
 PT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_H
OST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 
-DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 
-DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 
-DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 
-DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 
-DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 
-DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 
-DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 
-DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 
-DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 
-DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 
-DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 
-DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 
-DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 
-I/usr/local/include-fpic  -O2 -g -pipe -Wall -Wp,-D_!
 FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 
-mtune=generic  -c myUTF8.c -o myUTF8.o
 myUTF8.c: In function 'StringValue':
 myUTF8.c:284:5: warning: passing argument 1 of 'Rf_mkCharLenCE' from 
incompatible pointer type [enabled by default]
  yylval = mkCharLenCE(wcs, wcnt, CE_UTF8); /* include terminator */
  ^
 In file included from /usr/include/R/Rdefines.h:29:0,
  from myUTF8.c:3:
 /usr/include/R/Rinternals.h:890:6: note: expected 'const char *' but 
argument is of type 'ucs_t *'
  SEXP Rf_mkCharLenCE(const char *, int, cetype_t);
   ^
 myUTF8.c:112:34: warning: variable 'use_wcs' set but not used 
[-Wunused-but-set-variable]
  Rboolean oct_or_hex = FALSE, use_wcs = FALSE;
   ^
 myUTF8.c:112:14: warning: variable 'oct_or_hex' set but not used 
[-Wunused-but-set-variable]
  Rboolean oct_or_hex = FALSE, use_wcs = FALSE;
   ^
 myUTF8.c:101:14: warning: unused variable 'mbcslocale' [-Wunused-variable]
  Rboolean mbcslocale = TRUE;
   ^
 *** installing help indices
   converting help for package 'RCurl'
 finding HTML links ... done
 ...
binaryBufferhtml
 Rd warning: 
/tmp/RtmpaLgRR9/R.INSTALL33a830da853e/RCurl/man/binaryBuffer.Rd:15: missing 
file link 'writeBin'
 chunkToLineReader   html
...
 getCurlErrorClassNames  html
 Rd warning: 
/tmp/RtmpaLgRR9/R.INSTALL33a830da853e/RCurl/man/getCurlErrorClassNames.Rd:25: 
missing file link 'tryCatch'
 getCurlHandle   html
...
 url.exists  html
 Rd warning: 
/tmp/RtmpaLgRR9/R.INSTALL33a830da853e/RCurl/man/url.exists.Rd:5: missing file 
link 'file.exists'
 ** building package indices
 ...
 Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object '/usr/lib64/R/library/RCurl/libs/RCurl.so':
   /usr/lib64/R/library/RCurl/libs/RCurl.so: undefined symbol: 
curl_multi_remove_handle
 Error: loading failed
 Execution halted
 ERROR: loading failed
 * removing '/usr/lib64/R/library/RCurl'

Thanks,
Larry



-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com] 
Sent: Wednesday, January 27, 2016 1:02 PM
To: Patrick, Larry B [CSSM] <longp...@iastate.edu>; 
'r-sig-fedora@r-project.org' <r-sig-fedora@r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

On 01/27/2016 01:55 PM, Patrick, Larry B [CSSM] wrote:
> Confirmed that gcc-gfortran is installed
>  Package gcc-gfortran-4.4.7-16.el6.x86_64 already installed and 
> latest version What could I check next?

Hm. Do you have libgfortran installed?

~tom

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