Re: [R-pkg-devel] r2sundials submission failure

[Serguei Sokol]

Le 15/12/2019 à 17:59, Uwe Ligges a écrit :
Have you tried to write to CRAN@... and ask if thirs party software can 
be installed on CRAN?
No, I didn't. I presumed that CRAN team had other things to do than to 
install any soft that package authors could need. But if this is an 
option, I will try this approach next time. For this one, I integrated a 
subset of sundials soft in the package and it turned out to be far less 
then 20 MB (which is the size I had on my system for the whole set of 
cvodes library and its dependencies). The tarball is only 270 KB and 
compiled libraries on some systems can be up to 7 MB and far less on 
others (e.g. on my linux, compiled without "-g" flag, the whole size of 
$RHOME/library/r2sundial is under 2 MB). Just now, it is pending a 
manual inspection. I hope that library size will not be a problem.


Anyway, I appreciate the hint. Thanks.
Best,
Serguei.



Best,
Uwe Ligges

On 11.12.2019 10:39, Serguei Sokol wrote:

Hi,

I have tried to submit my new package 
https://github.com/sgsokol/r2sundials to CRAN but submission seems to 
be dismissed.
The package needs a third part software 
https://computing.llnl.gov/projects/sundials/cvodes so it cannot be 
built on CRAN automatically. I explained this (and how the package was 
tested by myself) in the submitter's comment (cf. hereafter) and 
second time in the reply to all (as was requested) to automatic 
message from CRAN announcing the building failure but to no avail. The 
submission was done on November 25, more than two weeks later I still 
don't have any response and the package is no more in incoming/ dir on 
cran ftp site. I conclude that this submission is dismissed.


My question is: what can be reasonably done to make a package like 
this (i.e. depending on third part software not available on CRAN) to 
be accepted? Or may be the current policy: all new package must 
automatically build. Period. In my case it can imply ~20 MB additional 
space (source code + libs).


Thanks in advance for any hint.
Serguei.

Submitter's comment: Dear CRAN team,

I submit package r2sundials which
   depends on a third part software
   from
https://computing.llnl.gov/projects/sundials/cvodes
This
   is the reason for which it will not automatically
   build on your test systems. But on my side, I could
   successfully run 'R CMD check --as-cran' on Linux
   (R-3.6.1, gcc8), MacOS Catalina (R-3.6.1, Apple
   clang-1100.0.33.12) and Windows 10 (R-devel r77430,
   gcc-4.9.3). If you wish, I can send you reports from
   these runs. Even if it is improbable, but if you
   decide to run such checks manually by your self,
   installation instructions are available
   on
https://github.com/sgsokol/r2sundials

Moreover,
   winbuilder signals:
Possibly mis-spelled words in
   DESCRIPTION:
   CVODES (3:34)
   Hindmarsh (9:803)
   Rcpp (3:8, 9:285)
   al (9:816)
   cvodes (9:47)
   et (9:813)
   rmumps (9:501)
These all are false
   positives designating software, R packages and
   bibliographic reference.

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] r2sundials submission failure

[Serguei Sokol]

Hi Satya,

Le 16/12/2019 à 14:52, Satyaprakash Nayak a écrit :

Hi Serguei

I apply a similar approach to include the Sundials source code as a part 
of my package (sundialr, on CRAN) which provides an interface for Cvode 
and Cvodes. I didn’t have an issue with the files sizes while submitting 
to CRAN

Good to hear :)


and you can take a look to see if the code would be helpful to you.

https://github.com/sn248/sundialr
I see that you include v4.0.1 of sundials while I included a more recent 
release 5.0.0:

https://github.com/sgsokol/r2sundials

But I think, in the end, the library size must be close to each other.



Although, it would be great if sundials is installed on CRAN machines 
and static libraries for Windows are provided in rtools 4.0
It could be a good thing in general but the end user on other platforms 
will have to install it anyway. Moreover, I see you kept the default 
size for index type:


SUNDIALS_INDEX_TYPE int64_t

while I defined it to int32_t.
It shows that it's hard to satisfy all the tastes in the wild with only 
one library distrubution ;)


Best,
Serguei.



Satya


On Mon, 16 Dec 2019 at 03:54, Serguei Sokol > wrote:


Le 15/12/2019 à 17:59, Uwe Ligges a écrit :
 > Have you tried to write to CRAN@... and ask if thirs party
software can
 > be installed on CRAN?
No, I didn't. I presumed that CRAN team had other things to do than to
install any soft that package authors could need. But if this is an
option, I will try this approach next time. For this one, I
integrated a
subset of sundials soft in the package and it turned out to be far less
then 20 MB (which is the size I had on my system for the whole set of
cvodes library and its dependencies). The tarball is only 270 KB and
compiled libraries on some systems can be up to 7 MB and far less on
others (e.g. on my linux, compiled without "-g" flag, the whole size of
$RHOME/library/r2sundial is under 2 MB). Just now, it is pending a
manual inspection. I hope that library size will not be a problem.

Anyway, I appreciate the hint. Thanks.
Best,
Serguei.

 >
 > Best,
 > Uwe Ligges
 >
 > On 11.12.2019 10:39, Serguei Sokol wrote:
 >> Hi,
 >>
 >> I have tried to submit my new package
 >> https://github.com/sgsokol/r2sundials to CRAN but submission
seems to
 >> be dismissed.
 >> The package needs a third part software
 >> https://computing.llnl.gov/projects/sundials/cvodes so it cannot be
 >> built on CRAN automatically. I explained this (and how the
package was
 >> tested by myself) in the submitter's comment (cf. hereafter) and
 >> second time in the reply to all (as was requested) to automatic
 >> message from CRAN announcing the building failure but to no
avail. The
 >> submission was done on November 25, more than two weeks later I
still
 >> don't have any response and the package is no more in incoming/
dir on
 >> cran ftp site. I conclude that this submission is dismissed.
 >>
 >> My question is: what can be reasonably done to make a package like
 >> this (i.e. depending on third part software not available on
CRAN) to
 >> be accepted? Or may be the current policy: all new package must
 >> automatically build. Period. In my case it can imply ~20 MB
additional
 >> space (source code + libs).
 >>
 >> Thanks in advance for any hint.
 >> Serguei.
 >>
 >> Submitter's comment: Dear CRAN team,
 >>
 >> I submit package r2sundials which
 >>    depends on a third part software
 >>    from
 >> https://computing.llnl.gov/projects/sundials/cvodes
 >> This
 >>    is the reason for which it will not automatically
 >>    build on your test systems. But on my side, I could
 >>    successfully run 'R CMD check --as-cran' on Linux
 >>    (R-3.6.1, gcc8), MacOS Catalina (R-3.6.1, Apple
 >>    clang-1100.0.33.12) and Windows 10 (R-devel r77430,
 >>    gcc-4.9.3). If you wish, I can send you reports from
 >>    these runs. Even if it is improbable, but if you
 >>    decide to run such checks manually by your self,
 >>    installation instructions are available
 >>    on
 >> https://github.com/sgsokol/r2sundials
 >>
 >> Moreover,
 >>    winbuilder signals:
 >> Possibly mis-spelled words in
 >>    DESCRIPTION:
 >>    CVODES (3:34)
 >>    Hindmarsh (9:803)
 >>    Rcpp (3:8, 9:285)
 >>    al (9:816)
 >>    cvodes (9:47)
 >>    et (9:813)
 >>    rmumps (9:501)
 >> These all are false
 >>    positives designating software, R packages and
 >>    bibliographic reference.
 >>
 >> __
 >> R-package-devel@r-project.org
 mailing list
 >> https://stat.ethz.ch/mailman/listinfo/r-package-d

[R-pkg-devel] DOI in of package in DESCRIPTION file

[Rainer M Krug]

Hi

UI am preparing my package for CRAN. I have a DOI for my package, and would 
like to add Ito the DESCRIPTION file.

At the moment, I am adding

DOI: https://zenodo.org/record/3229615

To the DESCRIPTION file. This raises not an error during check, but tells me, 
that DOI is a unknown field.

Is there a recommended way, of adding the DOI of a package to the DESCRIPTION 
file? I did not find anything when googling.

Thanks,

Rainer



--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] DOI in of package in DESCRIPTION file

[Robert M. Flight]

Are you wanting to provide the DOI for citation purposes? Then I would
recommend making sure you have a valid citation file
https://r-pkgs.org/inst.html#inst-citation (which should be fine having a
DOI field), and add it to the README as well.

-Robert

Robert M Flight, PhD
Bioinformatics Research Associate
Puller of Rabbits from Hats
Research Parasite
Resource Center for Stable Isotope Resolved Metabolomics
Manager, Systems Biology and Omics Integration Journal Club
Markey Cancer Center
CC434 Roach Building
University of Kentucky
Lexington, KY

Twitter: @rmflight
Web: rmflight.github.io
ORCID: http://orcid.org/-0001-8141-7788
EM rfligh...@gmail.com
PH 502-509-1827 <(502)%20509-1827>

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. - Ronald Fisher

On Mon, Dec 16, 2019 at 9:43 AM Rainer M Krug  wrote:

> Hi
>
> UI am preparing my package for CRAN. I have a DOI for my package, and
> would like to add Ito the DESCRIPTION file.
>
> At the moment, I am adding
>
> DOI: https://zenodo.org/record/3229615
>
> To the DESCRIPTION file. This raises not an error during check, but tells
> me, that DOI is a unknown field.
>
> Is there a recommended way, of adding the DOI of a package to the
> DESCRIPTION file? I did not find anything when googling.
>
> Thanks,
>
> Rainer
>
>
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
>
> Orcid ID: -0002-7490-0066
>
> Department of Evolutionary Biology and Environmental Studies
> University of Zürich
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 Zürich
> Switzerland
>
> Office: +41 (0)44 635 47 64
> Cell:   +41 (0)78 630 66 57
> email:  rainer.k...@uzh.ch
> rai...@krugs.de
> Skype: RMkrug
>
> PGP: 0x0F52F982
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[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] DOI in of package in DESCRIPTION file

[Georgi Boshnakov]

Something like the following should do:  

 

Note that https://zenodo.org/record/3229615 is an URL. Not doi.


Georgi Boshnakov

-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Rainer M Krug
Sent: 16 December 2019 14:35
To: List r-package-devel
Subject: [R-pkg-devel] DOI in of package in DESCRIPTION file

Hi

UI am preparing my package for CRAN. I have a DOI for my package, and would 
like to add Ito the DESCRIPTION file.

At the moment, I am adding

DOI: https://zenodo.org/record/3229615

To the DESCRIPTION file. This raises not an error during check, but tells me, 
that DOI is a unknown field.

Is there a recommended way, of adding the DOI of a package to the DESCRIPTION 
file? I did not find anything when googling.

Thanks,

Rainer



--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] DOI in of package in DESCRIPTION file

[Rainer M Krug]

Thanks Uwe, I will do so.

Rainer


> On 16 Dec 2019, at 15:56, Uwe Ligges  wrote:
> 
> 
> 
> On 16.12.2019 15:34, Rainer M Krug wrote:
>> Hi
>> UI am preparing my package for CRAN. I have a DOI for my package, and would 
>> like to add Ito the DESCRIPTION file.
>> At the moment, I am adding
>>  DOI: https://zenodo.org/record/3229615
> 
> This is not a DOI, the DOI is actually
> 
> 10.5281/zenodo.3229615
> 
> and we do not have a field fo it, but you can cite it within the Description 
> field and link to it via a sentence and DOI such as:
> 
> "See R.M. Krug and O. Petchey (2019) ."
> 
> Best,
> Uwe Ligges
> 
> 
>> To the DESCRIPTION file. This raises not an error during check, but tells 
>> me, that DOI is a unknown field.
>> Is there a recommended way, of adding the DOI of a package to the 
>> DESCRIPTION file? I did not find anything when googling.
>> Thanks,
>> Rainer
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
>> UCT), Dipl. Phys. (Germany)
>> Orcid ID: -0002-7490-0066
>> Department of Evolutionary Biology and Environmental Studies
>> University of Zürich
>> Office Y34-J-74
>> Winterthurerstrasse 190
>> 8075 Zürich
>> Switzerland
>> Office:  +41 (0)44 635 47 64
>> Cell:+41 (0)78 630 66 57
>> email:  rainer.k...@uzh.ch
>>  rai...@krugs.de
>> Skype: RMkrug
>> PGP: 0x0F52F982
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982




[[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] DOI in of package in DESCRIPTION file

[Rainer M Krug]

Thanks Robert,

I will add this as well as in the Description field.

Rainer


> On 16 Dec 2019, at 15:52, Robert M. Flight  wrote:
> 
> Are you wanting to provide the DOI for citation purposes? Then I would 
> recommend making sure you have a valid citation file 
> https://r-pkgs.org/inst.html#inst-citation 
>  (which should be fine having a 
> DOI field), and add it to the README as well.
> 
> -Robert
> 
> Robert M Flight, PhD
> Bioinformatics Research Associate
> Puller of Rabbits from Hats
> Research Parasite
> Resource Center for Stable Isotope Resolved Metabolomics
> Manager, Systems Biology and Omics Integration Journal Club
> Markey Cancer Center
> CC434 Roach Building
> University of Kentucky
> Lexington, KY
> 
> Twitter: @rmflight
> Web: rmflight.github.io 
> ORCID: http://orcid.org/-0001-8141-7788 
> 
> EM rfligh...@gmail.com 
> PH 502-509-1827 
> 
> To call in the statistician after the experiment is done may be no more than 
> asking him to perform a post-mortem examination: he may be able to say what 
> the experiment died of. - Ronald Fisher
> 
> On Mon, Dec 16, 2019 at 9:43 AM Rainer M Krug  > wrote:
> Hi
> 
> UI am preparing my package for CRAN. I have a DOI for my package, and would 
> like to add Ito the DESCRIPTION file.
> 
> At the moment, I am adding
> 
> DOI: https://zenodo.org/record/3229615 
> 
> 
> To the DESCRIPTION file. This raises not an error during check, but tells me, 
> that DOI is a unknown field.
> 
> Is there a recommended way, of adding the DOI of a package to the DESCRIPTION 
> file? I did not find anything when googling.
> 
> Thanks,
> 
> Rainer
> 
> 
> 
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> UCT), Dipl. Phys. (Germany)
> 
> Orcid ID: -0002-7490-0066
> 
> Department of Evolutionary Biology and Environmental Studies
> University of Zürich
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 Zürich
> Switzerland
> 
> Office: +41 (0)44 635 47 64
> Cell:   +41 (0)78 630 66 57
> email:  rainer.k...@uzh.ch 
> rai...@krugs.de 
> Skype: RMkrug
> 
> PGP: 0x0F52F982
> 
> __
> R-package-devel@r-project.org  mailing 
> list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel 
> 

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982




[[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] DOI in of package in DESCRIPTION file

[Uwe Ligges]

On 16.12.2019 15:34, Rainer M Krug wrote:

Hi

UI am preparing my package for CRAN. I have a DOI for my package, and would 
like to add Ito the DESCRIPTION file.

At the moment, I am adding

DOI: https://zenodo.org/record/3229615


This is not a DOI, the DOI is actually

10.5281/zenodo.3229615

and we do not have a field fo it, but you can cite it within the 
Description field and link to it via a sentence and DOI such as:


"See R.M. Krug and O. Petchey (2019) ."

Best,
Uwe Ligges




To the DESCRIPTION file. This raises not an error during check, but tells me, 
that DOI is a unknown field.

Is there a recommended way, of adding the DOI of a package to the DESCRIPTION 
file? I did not find anything when googling.

Thanks,

Rainer



--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel