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rstan warning messages

10 messages · Tom Callaway, Patrick, Larry B [CSSM], Peter Dalgaard

Original
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:tcallawa at redhat.com] 
Sent: Friday, January 29, 2016 2:46 PM
To: Patrick, Larry B [CSSM] <longplay at iastate.edu>; 'r-sig-fedora at r-project.org' <r-sig-fedora at r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages
On 01/28/2016 09:07 AM, Patrick, Larry B [CSSM] wrote:
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

==
Red Hat
Tom Callaway
#
On 02/01/2016 03:45 PM, Patrick, Larry B [CSSM] wrote:
Maybe to /usr/lib64/libgfortran.so ? You _should not_ need to do that
though. I didn't need to.
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

==
Red Hat
Patrick, Larry B [CSSM]
# 
Tom,

First of thanks for setting up your RHEL-6 VM to help me!

Until I did that link it would not install. 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.
     [root at ping /]# ls -l /usr/lib64/libgfortran*
     lrwxrwxrwx 1 root root     20 Jul 23  2015 /usr/lib64/libgfortran.so.3 -> libgfortran.so.3.0.0
     -rwxr-xr-x 1 root root 990504 Jun  1  2015 /usr/lib64/libgfortran.so.3.0.0
      [root at ping /]# ls -l /usr/lib/libgfortran*
     lrwxrwxrwx 1 root root 27 Feb  1 14:36 /usr/lib/libgfortran.so -> /usr/lib64/libgfortran.so.3

Requested information for RCurl
     [root at ping /]# rpm -qf /usr/lib64/pkgconfig/libcurl.pc
     libcurl-devel-7.19.7-46.el6.x86_64
      [root at ping /]# rpm -q pkgconfig
     pkgconfig-0.23-9.1.el6.x86_64

Attached is RCurl_logs.txt. Let me know if you would rather have it right in the email as it is extremely long log.

Thanks,
Larry



-----Original Message-----
From: Tom Callaway [mailto:tcallawa at redhat.com] 
Sent: Tuesday, February 02, 2016 10:35 AM
To: Patrick, Larry B [CSSM] <longplay at iastate.edu>; 'r-sig-fedora at r-project.org' <r-sig-fedora at r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages
On 02/01/2016 03:45 PM, Patrick, Larry B [CSSM] wrote:
Maybe to /usr/lib64/libgfortran.so ? You _should not_ need to do that though. I didn't need to.
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

==
Red Hat
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Tom Callaway
#
On 02/03/2016 09:33 AM, Patrick, Larry B [CSSM] wrote:
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

==
Red Hat
Tom Callaway
#
On 02/03/2016 09:52 AM, Tom Callaway wrote:

            

      
      
      
    

        
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

  
  


  


      

    

    

      
      

        


  

        

      Patrick, Larry B [CSSM]
    

    

      
      #
    

  


  

      
I used epel to install again. I removed the original installation that seemed from epel also.

     [root at ping /]# pkg-config --list-all |grep libcurl
      [root at ping /]#
That doesn't look good.
      [root at 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 at 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:tcallawa at redhat.com] 
Sent: Wednesday, February 03, 2016 9:02 AM
To: Patrick, Larry B [CSSM] <longplay at iastate.edu>; 'r-sig-fedora at r-project.org' <r-sig-fedora at r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

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

        

            

      
      
      
    

        
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

  
  


  


      

    

    

      
      

        


  

        

      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] <longplay at iastate.edu> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Patrick, Larry B [CSSM]
    

    

      
      #
    

  


  

      
Both RCurl and rstan seem to have installed now.

Did the following on my RHEL6 server:
     [root at ping ~]# export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/
     [root at ping ~]# /usr/bin/curl-config --libs
     -L/usr/lib64 -lcurl

Now the output from your previous commands look like:
      [root at ping ~]# pkg-config --list-all |grep libcurl
     libcurl                    libcurl - Library to transfer files with ftp, http, etc.
      [root at ping ~]# curl-config --libs
     -L/usr/lib64 -lcurl
      [root at 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

Attached are the long logs from RCurl and rstan.

Let me know if you spot something of concern. Hopefully I am good to go now.

Thanks for the assist,
Larry



-----Original Message-----
From: R-SIG-Fedora [mailto:r-sig-fedora-bounces at r-project.org] On Behalf Of Patrick, Larry B [CSSM]
Sent: Wednesday, February 03, 2016 9:06 AM
To: 'Tom Callaway' <tcallawa at redhat.com>; 'r-sig-fedora at r-project.org' <r-sig-fedora at r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

I used epel to install again. I removed the original installation that seemed from epel also.

     [root at ping /]# pkg-config --list-all |grep libcurl
      [root at ping /]#
That doesn't look good.
      [root at 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 at 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:tcallawa at redhat.com] 
Sent: Wednesday, February 03, 2016 9:02 AM
To: Patrick, Larry B [CSSM] <longplay at iastate.edu>; 'r-sig-fedora at r-project.org' <r-sig-fedora at r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

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

        

            

      
      
      
    

        
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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      Tom Callaway
    

    

      
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On 02/05/2016 09:58 AM, Patrick, Larry B [CSSM] wrote:

            

      
      
      
    

        
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

==
Red Hat

  
  


  


      

    

    

      
      

        


  

        

      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:tcallawa at redhat.com] 
Sent: Friday, February 05, 2016 9:14 AM
To: Patrick, Larry B [CSSM] <longplay at iastate.edu>; 'r-sig-fedora at r-project.org' <r-sig-fedora at r-project.org>
Subject: Re: [R-sig-Fedora] rstan warning messages

        
On 02/05/2016 09:58 AM, Patrick, Larry B [CSSM] wrote:

            

      
      
      
    

        
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

==
Red Hat