[R-pkg-devel] set PKG_CONFIG_PATH before installing a package

I am using this command to set an environment variable ` Sys.setenv(PKG_CONFIG_PATH=paste(Sys.getenv('PKG_CONFIG_PATH'),paste(.libPaths(),'my_package/lib/pkgconfig',sep='/',collapse=':'),sep=':'));’ before install my package. It works fine if I run it before installing my package. How can I do

[R-pkg-devel] Problem with using parallel runtime system with R

Hi, I have a C package which includes the usage of the StarPU runtime system to allow running my code on different HW architectures. I included this to an R-package and I found that R is using only one core and all the thread initiated by the runtime system is assigned to a single core which

Re: [R-pkg-devel] Problem with using parallel runtime system with R

Actually not yet. It is on Github but in a private repo. If it helps I can fork it for public access for now. Sameh Get Outlook for iOS<https://aka.ms/o0ukef> On Fri, May 10, 2019 at 5:55 PM +0300, "Iñaki Ucar" mailto:iu...@fedoraproject.org>> wrote: On Fri, 10 May

Re: [R-pkg-devel] Problem with using parallel runtime system with R

he virtual memory usage of the R package is doubled which we cannot Understand or even know if it is related to the performance issue or not --Sameh On 5/10/19, 6:12 PM, "Iñaki Ucar" wrote: On Fri, 10 May 2019 at 17:06, Sameh M. Abdulah wrote: > > Actuall

Re: [R-pkg-devel] Problem with using parallel runtime system with R

I meant for anyone who can help :). —Sameh Get Outlook for iOS<https://aka.ms/o0ukef> On Fri, May 10, 2019 at 6:48 PM +0300, "Iñaki Ucar" mailto:iu...@fedoraproject.org>> wrote: On Fri, 10 May 2019 at 17:38, Sameh M. Abdulah wrote: > > I will try to talk to

Re: [R-pkg-devel] set PKG_CONFIG_PATH before installing a package

Thanks Travers and Dirk for your feedbacks. —Sameh From: Travers Ching Sent: Monday, April 8, 2019 10:52 PM To: Dirk Eddelbuettel Cc: Sameh M. Abdulah; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] set PKG_CONFIG_PATH before installing a package What

Re: [R-pkg-devel] Linking with software dependencies

uettel Sent: Saturday, August 24, 2019 9:48 PM To: Sameh M. Abdulah Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Linking with software dependencies On 24 August 2019 at 18:16, Sameh M. Abdulah wrote: | (1) My package requires a pre-installation of Intel MKL. Is there any way to i

[R-pkg-devel] Linking with software dependencies

Hi, First, I am inviting all of you to try our recent package at https://github.com/ecrc/exageostatR. This package involves MLE estimation in large scale using leading-edge hardware architectures. I have multiple questions: (1) My package requires a pre-installation of Intel MKL. Is there any

[R-pkg-devel] set pkg_config for 3rd party software

Hi, I recently asked some questions about my R package which were well responded by Dirk. I have another question related to pkg_config path, I am using this command to add the installation path to the PKG_CONFIG_PATH so that all cmake commands can get the required libraries from this path,

[R-pkg-devel] Linking with OpenBLAS complains lapacke not found

I am linking my package against openblas but it complains that lapacke is not found which I need for the installation. I have another alternative to linking against MKL but I cannot find it using MKLROOT variable on CRAN servers. —Sameh Get Outlook for iOS

Re: [R-pkg-devel] Linking with OpenBLAS complains lapacke not found

NFIG_PATH variable" echo "" err=1 fi fi fi It works great but when OpenBLAS is using, my application cannot find lapacke library. On 9/8/19, 2:28 PM, "Brian G. Peterson" wrote: On Sun, 2019-09-08 at 10:04 +, Sameh M. Abdulah wr

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

the installation directory of my R package and set PKG_CONFIG_PATH to this path. Do I need to set any other paths so that R can see my new OpenBLAS which include LAPACKE? --Sameh On 9/26/19, 4:34 PM, "Ralf Stubner" wrote: On Wed, Sep 25, 2019 at 3:34 PM Sameh M. Abdulah

[R-pkg-devel] Package or namespace load failed: undefined symbol

Hi, I am uploading my R package to CRAN. One of the dynamic libraries the package requires depends on LAPACKE library which usually integrated with BLAS and CBLAS in the same .so file (as I understand). CRAN has OpenBLAS already installed on the system. However, this OpenBLAS library does not

[R-pkg-devel] Set env variables for cmake

I am using CMake command inside the configure file to install some dependencies for my package. These CMake commands require setting an environment variable. When I set it inside the configure file, it does not work!. Thus, I have used .Renviron file to set my env variables. This solution works

Re: [R-pkg-devel] Use LAPACK, BLAS and CBLAS paths in configure file

My package requires LAPACK, LAPACKE, BLAS, and CBLAS, this why I think OpenBLAS should be available to support all these libraries. --Sameh On 11/5/19, 1:09 PM, "Ralf Stubner" wrote: On Tue, Nov 5, 2019 at 10:12 AM Sameh M. Abdulah wrote: > 1- Use LAPACK, BLAS, an

[R-pkg-devel] Use LAPACK, BLAS and CBLAS paths in configure file

Hi, I would like to 1- Use LAPACK, BLAS, and CBLAS paths in my configure file. What is the command to use or what are the environment variables to read? 2- Check if OpenBLAS is installed on the system or not. I tried to use pkg-config but it doesn't work with CRAN servers, any alternatives?

[R-pkg-devel] Cannot find -ludev

I am getting this error on CRAN, /usr/bin/ld: cannot find -ludev --Sameh [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Cannot find -ludev

on Unix systems. �Sameh Get Outlook for iOS<https://aka.ms/o0ukef> From: Rolf Turner Sent: Monday, December 9, 2019 12:30 PM To: Sameh M. Abdulah; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Cannot find -ludev On 9/12/19 9:25 pm, Sameh M. A

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

:23 AM, "Ralf Stubner" wrote: On Tue, Sep 24, 2019 at 12:10 PM Sameh M. Abdulah wrote: > I am uploading my R package to CRAN. One of the dynamic libraries the package requires depends on LAPACKE library which usually integrated with BLAS and CBLAS in the same .so file (as

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

ubner" wrote: On Wed, Sep 25, 2019 at 10:29 AM Sameh M. Abdulah wrote: > I am installing OpenBLAS because I need LAPACKE libraries which I cannot find on the current version of OpenBLAS on CRAN. > > I add the libraries directory in my package to the PKG_CONFIG_PA

[R-pkg-devel] missing wget, cmake, pkg-config,..etc

Hi, I am using some tools through my package installation such as wget, cmake, pkg-config. The users complain that the installation failed because of missing such tools on their system. They need to install them separately before installation my package. Is this normal, or I need to include

Re: [R-pkg-devel] missing wget, cmake, pkg-config,..etc

Thanks Dirk, this is what I thought too. --Sameh On 10/7/19, 3:29 PM, "Dirk Eddelbuettel" wrote: On 7 October 2019 at 11:42, Sameh M. Abdulah wrote: | I am using some tools through my package installation such as wget, cmake, pkg-config. The user

[R-pkg-devel] Problem uploading my package to CRAN

Dear All, I have a problem uploading my package to CRAN for more than a month now even my package can be downloaded and installed successfully from GitHub. The problem happens when loading the package after the installation where R complains that some functions are not defined.

[R-pkg-devel] Missing R.h file

I am getting this error when uploading my package to CRAN, MLE_misc.h:52:10: fatal error: R.h: No such file or directory 52 | #include On my system I have to export the R include directory to my CPATH “export CPATH=/usr/share/R/include:$CPATH” to avoid this error. Could anyone tell me

[R-pkg-devel] /usr/bin/ld: cannot find -ludev

I am getting this error when trying to install my package on CRAN. Do I need to contact CRAN to include it on the CRAN system? or there is another solution. /usr/bin/ld: cannot find -ludev collect2: error: ld returned 1 exit status --Sameh [[alternative HTML version deleted]]

Re: [R-pkg-devel] /usr/bin/ld: cannot find -ludev

> listed in your SystemRequirements entry in your DESCRIPTION file? > >> On April 26, 2020 6:41:27 AM PDT, "Sameh M. Abdulah" >> wrote: >> I am getting this error when trying to install my package on CRAN. Do I >> need to contact >> CRAN to incl

[R-pkg-devel] exit and 'stderr' warning

I am getting this warning which I need to get rid of. Found 'exit', possibly from 'exit' (C) Found 'stderr', possibly from 'stderr' (C) I am depending on several C-based software that has many calls for 'exit' and 'stderr'. In this case, how can I avoid this warning?

[R-pkg-devel] R CMD INSTALL -l /path/lib

If a user is using this command to install my package, R CMD INSTALL -l /path/lib package_r.tar.gz How can I get the lib value within the configure file? --Sameh [[alternative HTML version deleted]] __ R-package-devel@r-project.org

[R-pkg-devel] install_git +submodules

I am using install_git to download my package from Github. The problem that I am using submodule on my repo and install_git always uses the master branch of this submodule. I defined mu submodules to uses a specific commit, not the master. I tried to used args="--recursive" but the same