#7 Error while running "make linux-g++-64" inside build folder

[Munesh Singh Chauhan]

Hi,
I am trying to install rDock in Ubuntu 18-04 OS. I am getting the following errors:

../include/RbtContainers.h:40:20: error: redefinition of ‘template<class outputiterator,="" predicate="" inputiterator,="" class=""> OutputIterator std::copy_if(InputIterator, InputIterator, OutputIterator, Predicate)’</class>

It seems that a template class is defined twice in a cpp file as well as a header file.

Can anyone clarify on this issue?

Munesh

[Munesh Singh Chauhan]

It seems the problem is with some copatibility issues in Ubunut 18.04. I am able to install and test properly in Ubuntu 16.04 version. But is there any wayaround to install on Ubuntu 18.04?

[Sergio Ruiz]

Hi Munesh,

Thanks for reaching us and using rdock.
I have not seen this error in ubuntu 18.04.
Good that you were able to install it in 16.04, but in case you need it in
18.04, please try to install it through bioconda repository using conda:
conda install -c bioconda rdock
Cheers!

Sergio

On Mon, 18 Mar 2019 at 06:59, Munesh Singh Chauhan munesh@users.sourceforge.net wrote:

It seems the problem is with some copatibility issues in Ubunut 18.04. I
am able to install and test properly in Ubuntu 16.04 version.

---

• [tickets:#7] https://sourceforge.net/p/rdock/tickets/7/ Error while
  running "make linux-g++-64" inside build folder*

Status: open
Milestone: 1.0
Labels: Installation error
Created: Sun Mar 17, 2019 07:34 PM UTC by Munesh Singh Chauhan
Last Updated: Sun Mar 17, 2019 07:34 PM UTC
Owner: nobody

Hi,
I am trying to install rDock in Ubuntu 18-04 OS. I am getting the
following errors:

../include/RbtContainers.h:40:20: error: redefinition of ‘template<class inputiterator,="" predicate="" outputiterator,="" class=""> OutputIterator
std::copy_if(InputIterator, InputIterator, OutputIterator,
Predicate)’</class>

It seems that a template class is defined twice in a cpp file as well as a
header file.

Can anyone clarify on this issue?

Munesh

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https://sourceforge.net/p/rdock/tickets/7/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Munesh Singh Chauhan]

Hi Sergio,

Many thanks for your prompt reply.

I am looking to accelerate some features of rDock that are too slow using GPUs. So could you please suggest if possible portions of the rDock code (C++ functions) that are too slow and could benefit from multithreaded computing (I will be using CUDA to accelerate things).

Unfortunately, I am not able to intall rDock using conda. Just curious to know if any one tried compiling rDock on Ubuntu 18.04 using "make linux-g++-64" that is without using conda? If so, what were the steps?

Thanks
Munesh

[Munesh Singh Chauhan]

I am attaching the error log, while building on Ubuntu 18.04 using the following command:

make linux-g++-64

[Sergio Ruiz]

Hi Munesh,

I think it is related with your compiler version. Ubuntu 18.04 comes with
gcc 7.3 by default, so you need to install 4.8.0 or 5.4.0, which I have
succeed installing with (i will update the manual).
In any case, conda installation was straightforward with fresh Ubuntu
18.04, so I recommend you to try a bit more on that side, as all
dependencies and older versions are well managed with the conda environment.
Best,

Sergio

On Wed, 20 Mar 2019 at 15:01, Munesh Singh Chauhan munesh@users.sourceforge.net wrote:

I am attaching the error log, while building on Ubuntu 18.04 using the
following command:

make linux-g++-64

Attachments:

• error.log
  https://sourceforge.net/p/rdock/tickets/_discuss/thread/59ab3bde29/279e/5532/76fc/eff3/attachment/error.log
  (2.6 kB; text/x-log)

---

• [tickets:#7] https://sourceforge.net/p/rdock/tickets/7/ Error while
  running "make linux-g++-64" inside build folder*

Status: open
Milestone: 1.0
Labels: Installation error
Created: Sun Mar 17, 2019 07:34 PM UTC by Munesh Singh Chauhan
Last Updated: Mon Mar 18, 2019 05:15 PM UTC
Owner: nobody

Hi,
I am trying to install rDock in Ubuntu 18-04 OS. I am getting the
following errors:

../include/RbtContainers.h:40:20: error: redefinition of ‘template<class inputiterator,="" predicate="" outputiterator,="" class=""> OutputIterator
std::copy_if(InputIterator, InputIterator, OutputIterator,
Predicate)’</class>

It seems that a template class is defined twice in a cpp file as well as a
header file.

Can anyone clarify on this issue?

Munesh

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/rdock/tickets/7/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Munesh Singh Chauhan]

Hi Sergio

I am not familiar with conda installation.

Can you please outline step by step process of installing rDock using conda. I am facing the following errors. Though I must say that I tried several times with the conda isntall command.

**munesh@munesh-Lenovo-ideapad-130-15IKB:~/rDock_2013.1_src/dev/build$ conda install -c bioconda rdock
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
- rdock
Use "conda info <package>" to see the dependencies for each package.
**</package>

[Sergio Ruiz]

Hi Munesh,

It's a standard conda package installation, it will automatically download
all dependencies and install them accordingly:

$ lsb_release -a

No LSB modules are available.

Distributor ID: Ubuntu

Description: Ubuntu 18.04.1 LTS

Release: 18.04

Codename: bionic

$ conda create -n docking-rdock

Collecting package metadata: done

Solving environment: done

Package Plan

[...]

To activate this environment, use

$ conda activate docking-rdock

To deactivate an active environment, use

$ conda deactivate

$ conda activate docking-rdock
(docking-rdock) $ conda install -c bioconda rdock

Collecting package metadata: done

Solving environment: done

[...]

The following packages will be downloaded:

package                    |            build

---------------------------|-----------------

certifi-2019.3.9           |           py36_0         149 KB

conda-forge

fontconfig-2.13.1          |    he4413a7_1000         327 KB

conda-forge

[...]

xorg-libsm-1.2.3 | 25 KB |

| 100%

xorg-libxrender-0.9. | 31 KB |

| 100%

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

(docking-rdock)$ rbdock

---

The rDock program is licensed under GNU-LGPLv3.0.
http://rdock.sourceforge.net/

Executable: rbdock ($Id:
//depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)

Library: libRbt.so/2013.1/901 2013/11/27

RBT_ROOT:
/home/sruizcarmona/miniconda3/envs/docking-rdock/share/rdock-2013.1-1

RBT_HOME: /home/sruizcarmona

Current dir: /home/sruizcarmona

Date: Thu Mar 21 10:09:23 2019

---

Usage:

rbdock -i <sdfile> -o <outputroot> -r <recepprmfile> -p <protoprmfile> [-n
<nruns>]</nruns> [-ap] [-an] [-allH]</protoprmfile></recepprmfile></outputroot></sdfile>

   [-t <targetScore|targetFilterFile>] [-c] [-T <traceLevel>] [-s

<rndseed>]</rndseed>

Options: -i <sdfile> - input ligand SD file</sdfile>

-o <outputroot> - root name for output file(s)</outputroot>

-r <recepprmfile> - receptor parameter file</recepprmfile>

-p <protoprmfile> - docking protocol parameter file</protoprmfile>

-n <nruns> - number of runs/ligand (default=1)</nruns>

-ap - protonate all neutral amines, guanidines, imidazoles
(default=disabled)

-an - deprotonate all carboxylic, sulphur and phosphorous acid groups
(default=disabled)

-allH - read all hydrogens present (default=polar hydrogens only)

-t - score threshold OR filter file name

-c - continue if score threshold is met (use with -t <targetscore>,
default=terminate ligand)</targetscore>

-T <tracelevel> - controls output level for debugging (0 = minimal, >0 =
more verbose)</tracelevel>

-s <rndseed> - random number seed (default=from sys clock)</rndseed>

It takes around 5 min to install.

Let me know if it works!

Cheers,

Sergio

On Thu, 21 Mar 2019 at 02:07, Munesh Singh Chauhan munesh@users.sourceforge.net wrote:

Hi Sergio

I am not familiar with conda installation.

Can you please outline step by step process of installing rDock using
conda. I am facing the following errors. Though I must say that I tried
several times with the conda isntall command.

**munesh@munesh-Lenovo-ideapad-130-15IKB:~/rDock_2013.1_src/dev/build$
conda install -c bioconda rdock
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in
conflict:
- rdock
Use "conda info <package>" to see the dependencies for each package.
**</package>

---

• [tickets:#7] https://sourceforge.net/p/rdock/tickets/7/ Error while
  running "make linux-g++-64" inside build folder*

Status: open
Milestone: 1.0
Labels: Installation error
Created: Sun Mar 17, 2019 07:34 PM UTC by Munesh Singh Chauhan
Last Updated: Wed Mar 20, 2019 04:01 AM UTC
Owner: nobody

Hi,
I am trying to install rDock in Ubuntu 18-04 OS. I am getting the
following errors:

../include/RbtContainers.h:40:20: error: redefinition of ‘template<class inputiterator,="" predicate="" outputiterator,="" class=""> OutputIterator
std::copy_if(InputIterator, InputIterator, OutputIterator,
Predicate)’</class>

It seems that a template class is defined twice in a cpp file as well as a
header file.

Can anyone clarify on this issue?

Munesh

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/rdock/tickets/7/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Anonymous]

Hi. I recently joined the SourceForge communityy as I want to install rDOCK for my project. I also had aa "make linux-g++-64" error. I have attached the error code. I have XUbuntu Linux. To try and correct the error, I downloaded popt into my Downloads directory. This is where the rDOCK folder is downloaderd and unzipped. I navigated to the build folder and followed the instructions to install. I get the same same error. DO i need to install additional dependencies? If so, where should they be saved so that rDOck can access them? Thanks in advance.

[Sergio Ruiz]

Hi,
All the dependencies are detailed in the manual and the installation webpages. Based on the error log that you attached, looks like you dont have popt and popt-devel installed (or correctly pointed). Please check that and rerun rdock installation.
You can also try installation with conda, which already manages all dependencies: conda install -c bioconda rdock
Thanks,
Sergio

[Anonymous]

[Anonymous]

Hi Sergio

Thanks for your help.

I finally decided to freshly install Ubuntu 16.04, which supports CUDA as well as rDock. The reason for not continuing with Ubuntu 18.04 was that I feared that downgrading the gcc version (to support rDock) might adversely affect other programs.

Thanks once again.

Munesh

[Anonymous]

[Anonymous]

[Anonymous]