Hi all, I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html). How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux. This is the first package that I am submitting to BioConductor, so I am not aware of these issues. thanks in advance avi
[Bioc-devel] Package submission with library requirement
16 messages · avinash sahu, Dan Tenenbaum, Karim Mezhoud +4 more
Hi, Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/ Be sure that you tested it with the appropriate version of R. To work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote:
Hi all, I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html ). How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux. This is the first package that I am submitting to BioConductor, so I am not aware of these issues. thanks in advance avi [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows. Regarding third party code, bioconductor website mentions (i.e. ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor. thanks avi
On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:
Hi, Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/ Be sure that you tested it with the appropriate version of R. To work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote:
Hi all, I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html ). How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux. This is the first package that I am submitting to BioConductor, so I am not aware of these issues. thanks in advance avi [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
See my comments below. ----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com> To: "Karim Mezhoud" <kmezhoud at gmail.com> Cc: bioc-devel at r-project.org Sent: Wednesday, January 21, 2015 7:50:38 AM Subject: Re: [Bioc-devel] Package submission with library requirement Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows.
Can you please be very specific about why the package cannot be used with windows? Wherever possible we want packages to run on all the platforms we support. Have you attempted to compile it under windows and if so, what is the problem you ran into?
Regarding third party code, bioconductor website mentions (i.e. ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor.
I'm not sure you need to provide binaries for ransampl. However, can you clarify the type of dependency that your package has on ransampl and GSL? Is the dependency build-time only? If that is the case, then users on Mac and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime.
thanks avi On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:
Hi, Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/
In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not affiliated with the core team.
Be sure that you tested it with the appropriate version of R. To work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote:
Hi all, I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html ). How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux.
I will install ransampl on our build machines (GSL is already installed). Dan
This is the first package that I am submitting to BioConductor, so
I am
not
aware of these issues.
thanks in advance
avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Yes, just an error by copy/paste
Hi Dan, Thanks for the reply and quick support. I am sorry for so many issues, I am somewhat novice in bioconductor. I am replying to your comments inline. On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
See my comments below. ----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com> To: "Karim Mezhoud" <kmezhoud at gmail.com> Cc: bioc-devel at r-project.org Sent: Wednesday, January 21, 2015 7:50:38 AM Subject: Re: [Bioc-devel] Package submission with library requirement Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows.
Can you please be very specific about why the package cannot be used with windows? Wherever possible we want packages to run on all the platforms we support. Have you attempted to compile it under windows and if so, what is the problem you ran into?
Little bit of background first. GOAL is package, that will be a accompanying software for the manuscript that we are submitting to nature methods, so I would like to be as user friendly as possible. I spend couple of days to compile the package in Windows, however it is getting stuck because it uses Rcpp libraries along with third party libraries from other packages. I tried to get help from Windows regular user but it need someone expert in Windows OS to make it work. And I am no longer user of Windows so completely novice in it.
Regarding third party code, bioconductor website mentions (i.e. ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor.
I'm not sure you need to provide binaries for ransampl. However, can you clarify the type of dependency that your package has on ransampl and GSL? Is the dependency build-time only? If that is the case, then users on Mac and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime. I clarified in my dependencies that it requires ransampl and GSL. In
addition I added details in README about installation instruction of those libraries.
thanks avi On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:
Hi, Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/
In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not affiliated with the core team.
Be sure that you tested it with the appropriate version of R. To work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote:
Hi all, I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor (
). How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux.
I will install ransampl on our build machines (GSL is already installed). Dan
This is the first package that I am submitting to BioConductor, so
I am
not
aware of these issues.
thanks in advance
avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Regards Avi
On 01/21/2015 10:17 AM, avinash sahu wrote:
Hi Dan, Thanks for the reply and quick support. I am sorry for so many issues, I am somewhat novice in bioconductor. I am replying to your comments inline. On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
See my comments below. ----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com> To: "Karim Mezhoud" <kmezhoud at gmail.com> Cc: bioc-devel at r-project.org Sent: Wednesday, January 21, 2015 7:50:38 AM Subject: Re: [Bioc-devel] Package submission with library requirement Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows.
Can you please be very specific about why the package cannot be used with windows? Wherever possible we want packages to run on all the platforms we support. Have you attempted to compile it under windows and if so, what is the problem you ran into?
Little bit of background first. GOAL is package, that will be a accompanying software for the manuscript that we are submitting to nature methods, so I would like to be as user friendly as possible. I spend couple of days to compile the package in Windows, however it is getting stuck because it uses Rcpp libraries along with third party libraries from other packages. I tried to get help from Windows regular user but it need someone expert in Windows OS to make it work. And I am no longer user of Windows so completely novice in it.
have you thought carefully about the need for third-party libraries? For
instance, R has extensive random number facilities, and these are available at
the C level. This is documented in section 6 of RShowDoc("R-exts")
Martin
Regarding third party code, bioconductor website mentions (i.e. ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor.
I'm not sure you need to provide binaries for ransampl. However, can you clarify the type of dependency that your package has on ransampl and GSL? Is the dependency build-time only? If that is the case, then users on Mac and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime. I clarified in my dependencies that it requires ransampl and GSL. In
addition I added details in README about installation instruction of those libraries.
thanks avi On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:
Hi, Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/
In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not affiliated with the core team.
Be sure that you tested it with the appropriate version of R. To work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote:
Hi all, I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor (
). How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux.
I will install ransampl on our build machines (GSL is already installed). Dan
This is the first package that I am submitting to BioConductor, so
I am
not
aware of these issues.
thanks in advance
avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Regards Avi [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
Yes. I tried R internal libraries for random number generator also those provided by Rcpp but they are were not thread safe so it with multi-threading. I can try using other libraries, if anyone know random generator that are thread safe and not slow. thanks avi On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 01/21/2015 10:17 AM, avinash sahu wrote:
Hi Dan, Thanks for the reply and quick support. I am sorry for so many issues, I am somewhat novice in bioconductor. I am replying to your comments inline. On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote: See my comments below.
----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com> To: "Karim Mezhoud" <kmezhoud at gmail.com> Cc: bioc-devel at r-project.org Sent: Wednesday, January 21, 2015 7:50:38 AM Subject: Re: [Bioc-devel] Package submission with library requirement Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows.
Can you please be very specific about why the package cannot be used with windows? Wherever possible we want packages to run on all the platforms we support. Have you attempted to compile it under windows and if so, what is the problem you ran into?
Little bit of background first. GOAL is package, that will be a accompanying software for the manuscript that we are submitting to nature methods, so I would like to be as user friendly as possible. I spend couple of days to compile the package in Windows, however it is getting stuck because it uses Rcpp libraries along with third party libraries from other packages. I tried to get help from Windows regular user but it need someone expert in Windows OS to make it work. And I am no longer user of Windows so completely novice in it.
have you thought carefully about the need for third-party libraries? For
instance, R has extensive random number facilities, and these are available
at the C level. This is documented in section 6 of RShowDoc("R-exts")
Martin
Regarding third party code, bioconductor website mentions (i.e.
ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor.
I'm not sure you need to provide binaries for ransampl. However, can you clarify the type of dependency that your package has on ransampl and GSL? Is the dependency build-time only? If that is the case, then users on Mac and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime. I clarified in my dependencies that it requires ransampl and GSL. In
addition I added details in README about installation instruction of those libraries.
thanks
avi On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote: Hi,
Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/
In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not affiliated with the core team. Be sure that you tested it with the appropriate version of R. To
work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote: Hi all,
I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_
buildreport_20150121045701.html
).
How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux.
I will install ransampl on our build machines (GSL is already installed). Dan This is the first package that I am submitting to BioConductor, so
I am
not
aware of these issues.
thanks in advance
avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Regards
Avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
Does the boost RNGs qualify? He's a vignette showing how to use them through R/Rcpp http://gallery.rcpp.org/articles/timing-normal-rngs/ Boost headers are provided via the BH library: https://github.com/eddelbuettel/bh -steve
On Wed, Jan 21, 2015 at 10:48 AM, avinash sahu <avinash.sahu at gmail.com> wrote:
Yes. I tried R internal libraries for random number generator also those provided by Rcpp but they are were not thread safe so it with multi-threading. I can try using other libraries, if anyone know random generator that are thread safe and not slow. thanks avi On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 01/21/2015 10:17 AM, avinash sahu wrote:
Hi Dan, Thanks for the reply and quick support. I am sorry for so many issues, I am somewhat novice in bioconductor. I am replying to your comments inline. On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote: See my comments below.
----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com> To: "Karim Mezhoud" <kmezhoud at gmail.com> Cc: bioc-devel at r-project.org Sent: Wednesday, January 21, 2015 7:50:38 AM Subject: Re: [Bioc-devel] Package submission with library requirement Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows.
Can you please be very specific about why the package cannot be used with windows? Wherever possible we want packages to run on all the platforms we support. Have you attempted to compile it under windows and if so, what is the problem you ran into?
Little bit of background first. GOAL is package, that will be a accompanying software for the manuscript that we are submitting to nature methods, so I would like to be as user friendly as possible. I spend couple of days to compile the package in Windows, however it is getting stuck because it uses Rcpp libraries along with third party libraries from other packages. I tried to get help from Windows regular user but it need someone expert in Windows OS to make it work. And I am no longer user of Windows so completely novice in it.
have you thought carefully about the need for third-party libraries? For
instance, R has extensive random number facilities, and these are available
at the C level. This is documented in section 6 of RShowDoc("R-exts")
Martin
Regarding third party code, bioconductor website mentions (i.e.
ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor.
I'm not sure you need to provide binaries for ransampl. However, can you clarify the type of dependency that your package has on ransampl and GSL? Is the dependency build-time only? If that is the case, then users on Mac and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime. I clarified in my dependencies that it requires ransampl and GSL. In
addition I added details in README about installation instruction of those libraries.
thanks
avi On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote: Hi,
Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/
In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not affiliated with the core team. Be sure that you tested it with the appropriate version of R. To
work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote: Hi all,
I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_
buildreport_20150121045701.html
).
How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux.
I will install ransampl on our build machines (GSL is already installed). Dan This is the first package that I am submitting to BioConductor, so
I am
not
aware of these issues.
thanks in advance
avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Regards
Avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Steve Lianoglou Computational Biologist Genentech
Both the libraries are not thread safe. Although boost random genrator in limited situation can be thread safe. I have tried them earlier they were failing with multi-threading. One way out might be, if I include the source code of ransampl with package source code. There license allows this, I can also mail ask the developer of Ransampl about the permission. Will this be acceptable to bioconductor folks? thanks avi On Wed, Jan 21, 2015 at 7:57 PM, Steve Lianoglou <lianoglou.steve at gene.com> wrote:
Does the boost RNGs qualify? He's a vignette showing how to use them through R/Rcpp http://gallery.rcpp.org/articles/timing-normal-rngs/ Boost headers are provided via the BH library: https://github.com/eddelbuettel/bh -steve On Wed, Jan 21, 2015 at 10:48 AM, avinash sahu <avinash.sahu at gmail.com> wrote:
Yes. I tried R internal libraries for random number generator also those provided by Rcpp but they are were not thread safe so it with multi-threading. I can try using other libraries, if anyone know random generator that are thread safe and not slow. thanks avi On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 01/21/2015 10:17 AM, avinash sahu wrote:
Hi Dan, Thanks for the reply and quick support. I am sorry for so many issues,
I
am somewhat novice in bioconductor. I am replying to your comments
inline.
On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org
wrote: See my comments below.
----- Original Message -----
From: "avinash sahu" <avinash.sahu at gmail.com> To: "Karim Mezhoud" <kmezhoud at gmail.com> Cc: bioc-devel at r-project.org Sent: Wednesday, January 21, 2015 7:50:38 AM Subject: Re: [Bioc-devel] Package submission with library requirement Thanks for mail Karim. I have GOAL staisfies all guidelines. However, GOAL is not compiling in windows and because of its heavy computational requirement its cannot be used with Windows.
Can you please be very specific about why the package cannot be used
with
windows? Wherever possible we want packages to run on all the
platforms
we support. Have you attempted to compile it under windows and if so,
what
is the problem you ran into?
Little bit of background first. GOAL is package, that will be a accompanying software for the manuscript that we are submitting to
nature
methods, so I would like to be as user friendly as possible. I spend couple of days to compile the package in Windows, however it is getting stuck because it uses Rcpp libraries along with third party libraries from
other
packages. I tried to get help from Windows regular user but it need someone expert in Windows OS to make it work. And I am no longer user of
Windows
so completely novice in it.
have you thought carefully about the need for third-party libraries? For instance, R has extensive random number facilities, and these are
available
at the C level. This is documented in section 6 of RShowDoc("R-exts")
Martin
Regarding third party code, bioconductor website mentions (i.e.
ransampl): "In cases where the external library is complex the author may need to supply pre-built binary versions for some platforms." How to provide such binaries for linux and Mac to bioconductor.
I'm not sure you need to provide binaries for ransampl. However, can
you
clarify the type of dependency that your package has on ransampl and
GSL?
Is the dependency build-time only? If that is the case, then users on
Mac
and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime. I clarified in my dependencies that it requires ransampl and GSL. In
addition I added details in README about installation instruction of
those
libraries.
thanks
avi On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote: Hi,
Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package?guidelines/
In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not
affiliated
with the core team. Be sure that you tested it with the appropriate version of R. To
work out which version that is, please have a look at this site here: http://www.bioconductor.org/developers/how?to/useDevel/ Then use our tracking system for package submission (which can be found here): https://tracker.bioconductor.org/ recommended video: https://www.youtube.com/watch?v=QfqaK_BHebU Karim ?__ c/ /'_;~~~~kmezhoud (*) \(*) ????? ?????? http://bioinformatics.tn/ On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu <avinash.sahu at gmail.com> wrote: Hi all,
I am trying to submit a package (https://github.com/vinash85/GOAL) in bioconductor. It requires a ransampl ( http://sourceforge.net/projects/ransampl/) and gsl libraries already installed in system. The package is failing to install at automated package installer of bioconductor ( http://bioconductor.org/spb_reports/GOAL_0.99.0_
buildreport_20150121045701.html
).
How to take care of additional Libraries? Further, the package is meant for Linux and Mac ( it is NOT currently compiling in windows). Is it possible to submit the package in pre-compiled binaries form for Mac and Linux.
I will install ransampl on our build machines (GSL is already
installed).
Dan This is the first package that I am submitting to BioConductor, so
I am
not
aware of these issues.
thanks in advance
avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Regards
Avi
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Steve Lianoglou Computational Biologist Genentech
On Wed, Jan 21, 2015 at 2:16 PM, avinash sahu <avinash.sahu at gmail.com> wrote:
Both the libraries are not thread safe. Although boost random genrator in limited situation can be thread safe. I have tried them earlier they were failing with multi-threading.
I like the rlecuyer package for parallel random number generation: http://cran.r-project.org/web/packages/rlecuyer/index.html
Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org
1 day later
On 01/21/2015 11:16 AM, avinash sahu wrote:
Both the libraries are not thread safe. Although boost random genrator in limited situation can be thread safe. I have tried them earlier they were failing with multi-threading. One way out might be, if I include the source code of ransampl with package source code. There license allows this, I can also mail ask the developer of Ransampl about the permission. Will this be acceptable to bioconductor folks?
yes, provided the license of the library allows for it, it is a good solution.
There is guidance in RShowDoc("R-exts") on acknowledging this in the
DESCRIPTION (and possibly LICENSE) file.
Martin
thanks
avi
On Wed, Jan 21, 2015 at 7:57 PM, Steve Lianoglou <lianoglou.steve at gene.com
<mailto:lianoglou.steve at gene.com>> wrote:
Does the boost RNGs qualify?
He's a vignette showing how to use them through R/Rcpp
http://gallery.rcpp.org/articles/timing-normal-rngs/
Boost headers are provided via the BH library:
https://github.com/eddelbuettel/bh
-steve
On Wed, Jan 21, 2015 at 10:48 AM, avinash sahu <avinash.sahu at gmail.com
<mailto:avinash.sahu at gmail.com>> wrote:
> Yes. I tried R internal libraries for random number generator also those
> provided by Rcpp but they are were not thread safe so it with
> multi-threading. I can try using other libraries, if anyone know random
> generator that are thread safe and not slow.
>
> thanks
> avi
>
> On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan <mtmorgan at fredhutch.org
<mailto:mtmorgan at fredhutch.org>>
> wrote:
>
>> On 01/21/2015 10:17 AM, avinash sahu wrote:
>>
>>> Hi Dan,
>>>
>>> Thanks for the reply and quick support. I am sorry for so many issues, I
>>> am
>>> somewhat novice in bioconductor. I am replying to your comments inline.
>>>
>>>
>>> On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org
<mailto:dtenenba at fredhutch.org>>
>>> wrote:
>>>
>>> See my comments below.
>>>>
>>>> ----- Original Message -----
>>>>
>>>>> From: "avinash sahu" <avinash.sahu at gmail.com
<mailto:avinash.sahu at gmail.com>>
>>>>> To: "Karim Mezhoud" <kmezhoud at gmail.com <mailto:kmezhoud at gmail.com>>
>>>>> Cc: bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>
>>>>> Sent: Wednesday, January 21, 2015 7:50:38 AM
>>>>> Subject: Re: [Bioc-devel] Package submission with library requirement
>>>>>
>>>>> Thanks for mail Karim.
>>>>>
>>>>> I have GOAL staisfies all guidelines.
>>>>> However, GOAL is not compiling in windows and because of its heavy
>>>>> computational requirement its cannot be used with Windows.
>>>>>
>>>>
>>>> Can you please be very specific about why the package cannot be used with
>>>> windows? Wherever possible we want packages to run on all the platforms
>>>> we
>>>> support. Have you attempted to compile it under windows and if so, what
>>>> is
>>>> the problem you ran into?
>>>>
>>>>
>>> Little bit of background first. GOAL is package, that will be a
>>> accompanying software for the manuscript that we are submitting to nature
>>> methods, so I would like to be as user friendly as possible. I spend
>>> couple
>>> of days to compile the package in Windows, however it is getting stuck
>>> because it uses Rcpp libraries along with third party libraries from other
>>> packages. I tried to get help from Windows regular user but it need
>>> someone
>>> expert in Windows OS to make it work. And I am no longer user of Windows
>>> so completely novice in it.
>>>
>>
>> have you thought carefully about the need for third-party libraries? For
>> instance, R has extensive random number facilities, and these are available
>> at the C level. This is documented in section 6 of RShowDoc("R-exts")
>>
>> Martin
>>
>>
>>
>>>
>>>> Regarding third party code, bioconductor website mentions (i.e.
>>>>> ransampl):
>>>>> "In cases where the external library is complex the author may need
>>>>> to
>>>>> supply pre-built binary versions for some platforms." How to provide
>>>>> such
>>>>> binaries for linux and Mac to bioconductor.
>>>>>
>>>>>
>>>> I'm not sure you need to provide binaries for ransampl. However, can you
>>>> clarify the type of dependency that your package has on ransampl and GSL?
>>>> Is the dependency build-time only? If that is the case, then users on Mac
>>>> and Windows will not need to have ransampl and GSL installed, but they
>>>> will
>>>> if they need them at runtime.
>>>>
>>>> I clarified in my dependencies that it requires ransampl and GSL. In
>>>>
>>> addition I added details in README about installation instruction of those
>>> libraries.
>>>
>>>
>>>>
>>>> thanks
>>>>> avi
>>>>>
>>>>> On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com
<mailto:kmezhoud at gmail.com>>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>>
>>>>>> Before you submit your package, please make sure that it satisfies
>>>>>> all our
>>>>>>
>>>>>> guidelines here.
>>>>>>
>>>>>> http://www.bioconductor.org/developers/package?guidelines/
>>>>>>
>>>>>>
>>>>
>>>> In the sense that Bioconductor is open source and belongs to everyone,
>>>> these are 'our' guidelines, but just to be clear, Karim is not affiliated
>>>> with the core team.
>>>>
>>>>
>>>> Be sure that you tested it with the appropriate version of R. To
>>>>>> work
>>>>>>
>>>>>> out which version that is, please have a look at this site here:
>>>>>>
>>>>>> http://www.bioconductor.org/developers/how?to/useDevel/
>>>>>>
>>>>>> Then use our tracking system for package submission (which can be
>>>>>>
>>>>>> found here):
>>>>>>
>>>>>> https://tracker.bioconductor.org/
>>>>>>
>>>>>> recommended video:
>>>>>> https://www.youtube.com/watch?v=QfqaK_BHebU
>>>>>>
>>>>>> Karim
>>>>>>
>>>>>> ?__
>>>>>> c/ /'_;~~~~kmezhoud
>>>>>> (*) \(*) ????? ??????
>>>>>> http://bioinformatics.tn/
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu
>>>>>> <avinash.sahu at gmail.com <mailto:avinash.sahu at gmail.com>>
>>>>>> wrote:
>>>>>>
>>>>>> Hi all,
>>>>>>>
>>>>>>> I am trying to submit a package (https://github.com/vinash85/GOAL)
>>>>>>> in
>>>>>>> bioconductor. It requires a ransampl (
>>>>>>> http://sourceforge.net/projects/ransampl/) and gsl libraries
>>>>>>> already
>>>>>>> installed in system.
>>>>>>> The package is failing to install at automated package installer
>>>>>>> of
>>>>>>> bioconductor (
>>>>>>>
>>>>>>>
>>>>>>> http://bioconductor.org/spb_reports/GOAL_0.99.0_
>>>> buildreport_20150121045701.html
>>>>
>>>>> ).
>>>>>>> How to take care of additional Libraries?
>>>>>>>
>>>>>>> Further, the package is meant for Linux and Mac ( it is NOT
>>>>>>> currently
>>>>>>> compiling in windows). Is it possible to submit the package in
>>>>>>> pre-compiled
>>>>>>> binaries form for Mac and Linux.
>>>>>>>
>>>>>>>
>>>> I will install ransampl on our build machines (GSL is already installed).
>>>>
>>>> Dan
>>>>
>>>>
>>>> This is the first package that I am submitting to BioConductor, so
>>>>>>> I am
>>>>>>> not
>>>>>>> aware of these issues.
>>>>>>>
>>>>>>> thanks in advance
>>>>>>> avi
>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>>
>>>>
>>> Regards
>>> Avi
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Steve Lianoglou
Computational Biologist
Genentech
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
----- Original Message -----
From: "Martin Morgan" <mtmorgan at fredhutch.org> To: "avinash sahu" <avinash.sahu at gmail.com>, "Steve Lianoglou" <lianoglou.steve at gene.com> Cc: bioc-devel at r-project.org Sent: Friday, January 23, 2015 10:52:32 AM Subject: Re: [Bioc-devel] Package submission with library requirement On 01/21/2015 11:16 AM, avinash sahu wrote:
Both the libraries are not thread safe. Although boost random genrator in limited situation can be thread safe. I have tried them earlier they were failing with multi-threading. One way out might be, if I include the source code of ransampl with package source code. There license allows this, I can also mail ask the developer of Ransampl about the permission. Will this be acceptable to bioconductor folks?
yes, provided the license of the library allows for it, it is a good
solution.
There is guidance in RShowDoc("R-exts") on acknowledging this in the
DESCRIPTION (and possibly LICENSE) file.
However, you should consider using Rlecuyer as it has no external dependencies (see Levi's post to this thread). Then your package should build on windows. Dan
Martin
thanks
avi
On Wed, Jan 21, 2015 at 7:57 PM, Steve Lianoglou
<lianoglou.steve at gene.com
<mailto:lianoglou.steve at gene.com>> wrote:
Does the boost RNGs qualify?
He's a vignette showing how to use them through R/Rcpp
http://gallery.rcpp.org/articles/timing-normal-rngs/
Boost headers are provided via the BH library:
https://github.com/eddelbuettel/bh
-steve
On Wed, Jan 21, 2015 at 10:48 AM, avinash sahu
<avinash.sahu at gmail.com
<mailto:avinash.sahu at gmail.com>> wrote:
> Yes. I tried R internal libraries for random number
> generator also those
> provided by Rcpp but they are were not thread safe so it
> with
> multi-threading. I can try using other libraries, if anyone
> know random
> generator that are thread safe and not slow.
>
> thanks
> avi
>
> On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan
> <mtmorgan at fredhutch.org
<mailto:mtmorgan at fredhutch.org>>
> wrote:
>
>> On 01/21/2015 10:17 AM, avinash sahu wrote:
>>
>>> Hi Dan,
>>>
>>> Thanks for the reply and quick support. I am sorry for so
>>> many issues, I
>>> am
>>> somewhat novice in bioconductor. I am replying to your
>>> comments inline.
>>>
>>>
>>> On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum
>>> <dtenenba at fredhutch.org
<mailto:dtenenba at fredhutch.org>>
>>> wrote:
>>>
>>> See my comments below.
>>>>
>>>> ----- Original Message -----
>>>>
>>>>> From: "avinash sahu" <avinash.sahu at gmail.com
<mailto:avinash.sahu at gmail.com>>
>>>>> To: "Karim Mezhoud" <kmezhoud at gmail.com
>>>>> <mailto:kmezhoud at gmail.com>>
>>>>> Cc: bioc-devel at r-project.org
>>>>> <mailto:bioc-devel at r-project.org>
>>>>> Sent: Wednesday, January 21, 2015 7:50:38 AM
>>>>> Subject: Re: [Bioc-devel] Package submission with
>>>>> library requirement
>>>>>
>>>>> Thanks for mail Karim.
>>>>>
>>>>> I have GOAL staisfies all guidelines.
>>>>> However, GOAL is not compiling in windows and because of
>>>>> its heavy
>>>>> computational requirement its cannot be used with
>>>>> Windows.
>>>>>
>>>>
>>>> Can you please be very specific about why the package
>>>> cannot be used with
>>>> windows? Wherever possible we want packages to run on all
>>>> the platforms
>>>> we
>>>> support. Have you attempted to compile it under windows
>>>> and if so, what
>>>> is
>>>> the problem you ran into?
>>>>
>>>>
>>> Little bit of background first. GOAL is package, that will
>>> be a
>>> accompanying software for the manuscript that we are
>>> submitting to nature
>>> methods, so I would like to be as user friendly as
>>> possible. I spend
>>> couple
>>> of days to compile the package in Windows, however it is
>>> getting stuck
>>> because it uses Rcpp libraries along with third party
>>> libraries from other
>>> packages. I tried to get help from Windows regular user
>>> but it need
>>> someone
>>> expert in Windows OS to make it work. And I am no longer
>>> user of Windows
>>> so completely novice in it.
>>>
>>
>> have you thought carefully about the need for third-party
>> libraries? For
>> instance, R has extensive random number facilities, and
>> these are available
>> at the C level. This is documented in section 6 of
>> RShowDoc("R-exts")
>>
>> Martin
>>
>>
>>
>>>
>>>> Regarding third party code, bioconductor website
>>>> mentions (i.e.
>>>>> ransampl):
>>>>> "In cases where the external library is complex the
>>>>> author may need
>>>>> to
>>>>> supply pre-built binary versions for some platforms."
>>>>> How to provide
>>>>> such
>>>>> binaries for linux and Mac to bioconductor.
>>>>>
>>>>>
>>>> I'm not sure you need to provide binaries for ransampl.
>>>> However, can you
>>>> clarify the type of dependency that your package has on
>>>> ransampl and GSL?
>>>> Is the dependency build-time only? If that is the case,
>>>> then users on Mac
>>>> and Windows will not need to have ransampl and GSL
>>>> installed, but they
>>>> will
>>>> if they need them at runtime.
>>>>
>>>> I clarified in my dependencies that it requires ransampl
>>>> and GSL. In
>>>>
>>> addition I added details in README about installation
>>> instruction of those
>>> libraries.
>>>
>>>
>>>>
>>>> thanks
>>>>> avi
>>>>>
>>>>> On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud
>>>>> <kmezhoud at gmail.com
<mailto:kmezhoud at gmail.com>>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>>
>>>>>> Before you submit your package, please make sure that
>>>>>> it satisfies
>>>>>> all our
>>>>>>
>>>>>> guidelines here.
>>>>>>
>>>>>> http://www.bioconductor.org/developers/package?guidelines/
>>>>>>
>>>>>>
>>>>
>>>> In the sense that Bioconductor is open source and belongs
>>>> to everyone,
>>>> these are 'our' guidelines, but just to be clear, Karim
>>>> is not affiliated
>>>> with the core team.
>>>>
>>>>
>>>> Be sure that you tested it with the appropriate version
>>>> of R. To
>>>>>> work
>>>>>>
>>>>>> out which version that is, please have a look at this
>>>>>> site here:
>>>>>>
>>>>>> http://www.bioconductor.org/developers/how?to/useDevel/
>>>>>>
>>>>>> Then use our tracking system for package submission
>>>>>> (which can be
>>>>>>
>>>>>> found here):
>>>>>>
>>>>>> https://tracker.bioconductor.org/
>>>>>>
>>>>>> recommended video:
>>>>>> https://www.youtube.com/watch?v=QfqaK_BHebU
>>>>>>
>>>>>> Karim
>>>>>>
>>>>>> ?__
>>>>>> c/ /'_;~~~~kmezhoud
>>>>>> (*) \(*) ????? ??????
>>>>>> http://bioinformatics.tn/
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu
>>>>>> <avinash.sahu at gmail.com
>>>>>> <mailto:avinash.sahu at gmail.com>>
>>>>>> wrote:
>>>>>>
>>>>>> Hi all,
>>>>>>>
>>>>>>> I am trying to submit a package
>>>>>>> (https://github.com/vinash85/GOAL)
>>>>>>> in
>>>>>>> bioconductor. It requires a ransampl (
>>>>>>> http://sourceforge.net/projects/ransampl/) and gsl
>>>>>>> libraries
>>>>>>> already
>>>>>>> installed in system.
>>>>>>> The package is failing to install at automated package
>>>>>>> installer
>>>>>>> of
>>>>>>> bioconductor (
>>>>>>>
>>>>>>>
>>>>>>> http://bioconductor.org/spb_reports/GOAL_0.99.0_
>>>> buildreport_20150121045701.html
>>>>
>>>>> ).
>>>>>>> How to take care of additional Libraries?
>>>>>>>
>>>>>>> Further, the package is meant for Linux and Mac ( it
>>>>>>> is NOT
>>>>>>> currently
>>>>>>> compiling in windows). Is it possible to submit the
>>>>>>> package in
>>>>>>> pre-compiled
>>>>>>> binaries form for Mac and Linux.
>>>>>>>
>>>>>>>
>>>> I will install ransampl on our build machines (GSL is
>>>> already installed).
>>>>
>>>> Dan
>>>>
>>>>
>>>> This is the first package that I am submitting to
>>>> BioConductor, so
>>>>>>> I am
>>>>>>> not
>>>>>>> aware of these issues.
>>>>>>>
>>>>>>> thanks in advance
>>>>>>> avi
>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org
>>>>>>> <mailto:Bioc-devel at r-project.org> mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org
>>>>> <mailto:Bioc-devel at r-project.org> mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>>
>>>>
>>> Regards
>>> Avi
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research
>> Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Steve Lianoglou
Computational Biologist
Genentech
-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Fri, Jan 23, 2015 at 1:58 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
However, you should consider using Rlecuyer as it has no external dependencies (see Levi's post to this thread). Then your package should build on windows.
I think so too - it's also a standard solution in R, implemented natively in r-core's parallel library and suggested by the snow library. I used it in my pensim library before transitioning to parallel, and have tested its streams on hyperthreaded CPUs and clusters.
Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org
2 days later
Hi Dan, Now I have included source code of the rsampl.h in the GOAL package. Although, rlecuyer is good candidate for random number generator, I currently avoid using it because I wanted results of our submitted manuscript to be completely reproducible. I can reproduce the results using ransampl library by setting seed that I have stored. Changing to other random generator libraries will imply that I have recheck results of the manuscript are reproducible and possibly change some of them which is not possible at this stage. I will reserve that inclusion for the future. I have resubmitted the GOAL package. thanks avi On Fri, Jan 23, 2015 at 9:37 PM, Levi Waldron <levi.waldron at hunter.cuny.edu> wrote:
On Fri, Jan 23, 2015 at 1:58 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
However, you should consider using Rlecuyer as it has no external
dependencies (see Levi's post to this thread). Then your package should build on windows. I think so too - it's also a standard solution in R, implemented natively in r-core's parallel library and suggested by the snow library. I used it in my pensim library before transitioning to parallel, and have tested its streams on hyperthreaded CPUs and clusters. -- Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
4 days later
Hi Avinash, So the argument for the importance of reproducible research *definitely* resonates with us here as it is a major goal of ours. However while the decision to use the same library as your paper helps to make the immediate work more reproducible, it simultaneously hampers others from benefiting from that because of the engineering problems that it creates for end users. Ultimately, this project has a longstanding commitment to try and provide not only a way for your previous work to be validated, but also a way for others to build upon and eventually extend that previous work. And both of these goals are crucial if your package is to be valuable to the greater scientific community over the long term. Anyhow I will try and work with you on our issue tracker to see if we can find a way to resolve this with you. Thanks for contributing! Marc
On 01/26/2015 08:14 AM, avinash sahu wrote:
Hi Dan, Now I have included source code of the rsampl.h in the GOAL package. Although, rlecuyer is good candidate for random number generator, I currently avoid using it because I wanted results of our submitted manuscript to be completely reproducible. I can reproduce the results using ransampl library by setting seed that I have stored. Changing to other random generator libraries will imply that I have recheck results of the manuscript are reproducible and possibly change some of them which is not possible at this stage. I will reserve that inclusion for the future. I have resubmitted the GOAL package. thanks avi On Fri, Jan 23, 2015 at 9:37 PM, Levi Waldron <levi.waldron at hunter.cuny.edu> wrote:
On Fri, Jan 23, 2015 at 1:58 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
However, you should consider using Rlecuyer as it has no external
dependencies (see Levi's post to this thread). Then your package should build on windows. I think so too - it's also a standard solution in R, implemented natively in r-core's parallel library and suggested by the snow library. I used it in my pensim library before transitioning to parallel, and have tested its streams on hyperthreaded CPUs and clusters. -- Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org
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