Re: [R-pkg-devel] Add reference in Description

2019-09-09 Thread Juhee Lee 
Hi.

Thank you for your reply. The question was solved.

I received another message from CRAN.
I think I can modify it.


Thank you,
Juhee Lee

2019년 9월 9일 (월) 오후 10:13, Uwe Ligges 님이 작성:

>
>
> On 09.09.2019 14:54, Helmut Schütz wrote:
> > Hi Juhee,
> >
> > Juhee Lee wrote on 2019-09-09 12:53:
> >> […] please add these in the Description field
> >> So I added it in the Description field of my DESCRIPTION file like this:
> >>
> >> Description: […]
> >>  Berrington de Gonzalez A, et al.(2012)
> >> ,
> >>  National Research Council(2006, ISBN:978-0-309-09156-5).
> >
> > I would use  instead of 
> > Interesting that CRAN started requesting references a while ago.
> > Note that /nothing/ about it is stated in the 'R-Extensions Manual'.
> >
> >> But, I've gotten the reply like below.
> >>
> >>
> >> Possibly mis-spelled words in DESCRIPTION:
> >> Berrington (32:5)
> >
> > Happens all the time, esp. with names. Sometimes words are common in
> > your particular
> > field but unknown to the spell-checker.
> > It seems that the spell-checker learns or is less strict in later
> > submissions.
> > Nothing to worry about.
> >
> >> Found the following (possibly) invalid DOIs:
> >> DOI: 10.1088/0952-4746/32/3/205
> >> From: DESCRIPTION
> >> Status: Forbidden
> >> Message: 403
> >
> > Strange. Generally you get that only if the document is behind a
> > pay-wall and not
> > even the abstract can be accessed. I could access it.
> > Sometimes an entire site is down for maintenance (as Springer was ~ two
> > weeks ago).
> > Then one gets an HTTP 404.
>
> All true, just le to me add: CRAN sends many requests to these sites a
> day, hence they may reject CRAN traffic, which you can simply ignore.
>
>
> Best,
> Uwe Ligges
>
>
>
> >> How do I modify it?
> >
> > You can't. Be patient. As stated in the note, wait for a member of CRAN
> > to check that.
> > Wetware outperforms silicon-based lifeforms.
> >
> > Cheers,
> > Helmut
> >
>

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Re: [R-pkg-devel] Problems installing dependences of my package

2019-09-09 Thread Travers Ching 
Hi Andrea,

If your code is highly dependent on a specific version, another option is
to include their code directly in your package.  The forecast package is
under GPL-3 license, meaning you can use their code.  You would just need
include the authors as a contributor ([ctb] tag) and make note of it in the
relevant source code files and the Copyright field in the description.

Travers

On Mon, Sep 9, 2019 at 7:57 AM Andrea Vilar Alvarez <
andreavilaralva...@hotmail.com> wrote:

>
>
> Hi,
>
> I am writting because I am doing a package in R and I have some problems
> installing dependences which appear at DESCRIPTION file.
>
> First of all, I am not sure about the difference between Depends and
> Imports, but I only use Depends.
> My problem is that my package is going to be used at different computers
> and for different persons so I want that when other person use my package,
> it can be able to check  if the necesary packages are installed and if they
> are not installed, the package must be able to install  them.
> I supposed that this problem was solved including the necesary packages
> and their versions at “Depends”. And now, I have another problem because
> the versions are usually indicated using “>=”, for example: forecast
> (>=8.7) but I need to use exactly the versión 8.7 because sometimes when
> packages are updated, they lost some functions. But if I use <= or == and
> the package is update to versión 8.8, my package installation fail.
> How can I solve this? If I use R normaly (outside my package), I can
> install older versions of other packages using devtools::install_version()
> so why when I indicate  forecast (<=8.7) at Depends on the DESCRIPTION
> file, R is not able to install an older version if a new one is avaliable?
>
> Thanks in advance for your attention.
>
> Best regards,
>
> Andrea.
>
>
> [[alternative HTML version deleted]]
>
> __
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Re: [R-pkg-devel] Problems installing dependences of my package

2019-09-09 Thread William Dunlap 
> And now, I have another problem because the versions are usually
indicated using “>=”, for example:
> forecast (>=8.7) but I need to use exactly the versión 8.7 because
sometimes when packages are updated,
> they lost some functions. But if I use <= or == and the package is update
to versión 8.8, my package installation fail.

In my experience, it is rare that version<= is required.  What function in
in forecast-8.7 was dropped in -8.8?
I didn't see any, but perhaps I missed something.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Mon, Sep 9, 2019 at 7:58 AM Andrea Vilar Alvarez <
andreavilaralva...@hotmail.com> wrote:

>
>
> Hi,
>
> I am writting because I am doing a package in R and I have some problems
> installing dependences which appear at DESCRIPTION file.
>
> First of all, I am not sure about the difference between Depends and
> Imports, but I only use Depends.
> My problem is that my package is going to be used at different computers
> and for different persons so I want that when other person use my package,
> it can be able to check  if the necesary packages are installed and if they
> are not installed, the package must be able to install  them.
> I supposed that this problem was solved including the necesary packages
> and their versions at “Depends”. And now, I have another problem because
> the versions are usually indicated using “>=”, for example: forecast
> (>=8.7) but I need to use exactly the versión 8.7 because sometimes when
> packages are updated, they lost some functions. But if I use <= or == and
> the package is update to versión 8.8, my package installation fail.
> How can I solve this? If I use R normaly (outside my package), I can
> install older versions of other packages using devtools::install_version()
> so why when I indicate  forecast (<=8.7) at Depends on the DESCRIPTION
> file, R is not able to install an older version if a new one is avaliable?
>
> Thanks in advance for your attention.
>
> Best regards,
>
> Andrea.
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
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>

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Re: [R-pkg-devel] Problems installing dependences of my package

2019-09-09 Thread Michael Dewey 

Dear Andrea

Comments in-line

On 09/09/2019 15:47, Andrea Vilar Alvarez wrote:



Hi,

I am writting because I am doing a package in R and I have some problems 
installing dependences which appear at DESCRIPTION file.

First of all, I am not sure about the difference between Depends and Imports, 
but I only use Depends.
My problem is that my package is going to be used at different computers and 
for different persons so I want that when other person use my package, it can 
be able to check  if the necesary packages are installed and if they are not 
installed, the package must be able to install  them.


If I understand you correctly that is what install.packages() does for 
your users.



I supposed that this problem was solved including the necesary packages and their 
versions at �Depends�. And now, I have another problem because the versions are usually 
indicated using �>=�, for example: forecast (>=8.7) but I need to use exactly the 
versi�n 8.7 because sometimes when packages are updated, they lost some functions. But 
if I use <= or == and the package is update to versi�n 8.8, my package installation 
fail.


As I read the manual. you can specify both and upper and lower bound. It 
is at the bottom of page 9 in the pdf I am reading.



How can I solve this? If I use R normaly (outside my package), I can install older 
versions of other packages using devtools::install_version() so why when I 
indicate  forecast (<=8.7) at Depends on the DESCRIPTION file, R is not able to 
install an older version if a new one is avaliable?

Thanks in advance for your attention.

Best regards,

Andrea.


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Please do not do that as it mangles your post. Please set your mailer o 
post in plain text not HTML






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Re: [R-pkg-devel] Problems installing dependences of my package

2019-09-09 Thread Iñaki Ucar 
On Mon, 9 Sep 2019 at 16:58, Andrea Vilar Alvarez
 wrote:
>
> First of all, I am not sure about the difference between Depends and Imports, 
> but I only use Depends.

Common advice goes the other way around: you should avoid Depends as
much as possible, so that your users' search path doesn't get polluted
with all your dependencies. Rule of thumb: "Depends: pkg1" is like you
are executing "library(pkg1)" in your users' session. You should avoid
that unless it's strictly necessary.

It's important to invest some time to truly understand the difference
between Imports and Depends. Some references:

- 
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies
- http://r-pkgs.had.co.nz/description.html

> My problem is that my package is going to be used at different computers and 
> for different persons so I want that when other person use my package, it can 
> be able to check  if the necesary packages are installed and if they are not 
> installed, the package must be able to install  them.

That's the whole point of declaring dependencies, and that's how
install.packages() works: I install your package and R figures out
what's needed and installs it for me.

> I supposed that this problem was solved including the necesary packages and 
> their versions at “Depends”.

As noted above, preferably Imports. But yes, that's correct.

> And now, I have another problem because the versions are usually indicated 
> using “>=”, for example: forecast (>=8.7) but I need to use exactly the 
> versión 8.7 because sometimes when packages are updated, they lost some 
> functions. But if I use <= or == and the package is update to versión 8.8, my 
> package installation fail.
> How can I solve this? If I use R normaly (outside my package), I can install 
> older versions of other packages using devtools::install_version() so why 
> when I indicate  forecast (<=8.7) at Depends on the DESCRIPTION file, R is 
> not able to install an older version if a new one is avaliable?

That's another story. R does not support exact versioning. You have
several options to achieve this though [1, 2, 3, 4]. But if you want
to submit your package to CRAN with exact versioning, unfortunately
that's not gonna work; but there are good reasons for that.

[1] https://cran.r-project.org/package=versions
[2] https://cran.r-project.org/package=checkpoint
[3] https://cran.r-project.org/package=rbundler
[4] https://cran.r-project.org/package=packrat

Iñaki

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[R-pkg-devel] Problems installing dependences of my package

2019-09-09 Thread Andrea Vilar Alvarez 


Hi,

I am writting because I am doing a package in R and I have some problems 
installing dependences which appear at DESCRIPTION file.

First of all, I am not sure about the difference between Depends and Imports, 
but I only use Depends.
My problem is that my package is going to be used at different computers and 
for different persons so I want that when other person use my package, it can 
be able to check  if the necesary packages are installed and if they are not 
installed, the package must be able to install  them.
I supposed that this problem was solved including the necesary packages and 
their versions at �Depends�. And now, I have another problem because the 
versions are usually indicated using �>=�, for example: forecast (>=8.7) but I 
need to use exactly the versi�n 8.7 because sometimes when packages are 
updated, they lost some functions. But if I use <= or == and the package is 
update to versi�n 8.8, my package installation fail.
How can I solve this? If I use R normaly (outside my package), I can install 
older versions of other packages using devtools::install_version() so why when 
I indicate  forecast (<=8.7) at Depends on the DESCRIPTION file, R is not able 
to install an older version if a new one is avaliable?

Thanks in advance for your attention.

Best regards,

Andrea.


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Re: [R-pkg-devel] Add reference in Description

2019-09-09 Thread Uwe Ligges 




On 09.09.2019 14:54, Helmut Schütz wrote:

Hi Juhee,

Juhee Lee wrote on 2019-09-09 12:53:

[…] please add these in the Description field
So I added it in the Description field of my DESCRIPTION file like this:

Description: […]
 Berrington de Gonzalez A, et al.(2012) 
,

 National Research Council(2006, ISBN:978-0-309-09156-5).


I would use  instead of 
Interesting that CRAN started requesting references a while ago.
Note that /nothing/ about it is stated in the 'R-Extensions Manual'.


But, I've gotten the reply like below.


Possibly mis-spelled words in DESCRIPTION:
Berrington (32:5)


Happens all the time, esp. with names. Sometimes words are common in 
your particular

field but unknown to the spell-checker.
It seems that the spell-checker learns or is less strict in later 
submissions.

Nothing to worry about.


Found the following (possibly) invalid DOIs:
DOI: 10.1088/0952-4746/32/3/205
From: DESCRIPTION
Status: Forbidden
Message: 403


Strange. Generally you get that only if the document is behind a 
pay-wall and not

even the abstract can be accessed. I could access it.
Sometimes an entire site is down for maintenance (as Springer was ~ two 
weeks ago).

Then one gets an HTTP 404.


All true, just le to me add: CRAN sends many requests to these sites a 
day, hence they may reject CRAN traffic, which you can simply ignore.



Best,
Uwe Ligges




How do I modify it?


You can't. Be patient. As stated in the note, wait for a member of CRAN 
to check that.

Wetware outperforms silicon-based lifeforms.

Cheers,
Helmut



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Re: [R-pkg-devel] Add reference in Description

2019-09-09 Thread Helmut Schütz 

Hi Juhee,

Juhee Lee wrote on 2019-09-09 12:53:

[…] please add these in the Description field
So I added it in the Description field of my DESCRIPTION file like this:

Description: […]
 Berrington de Gonzalez A, et al.(2012) ,
 National Research Council(2006, ISBN:978-0-309-09156-5).


I would use  instead of 
Interesting that CRAN started requesting references a while ago.
Note that /nothing/ about it is stated in the 'R-Extensions Manual'.


But, I've gotten the reply like below.


Possibly mis-spelled words in DESCRIPTION:
Berrington (32:5)


Happens all the time, esp. with names. Sometimes words are common in 
your particular

field but unknown to the spell-checker.
It seems that the spell-checker learns or is less strict in later 
submissions.

Nothing to worry about.


Found the following (possibly) invalid DOIs:
DOI: 10.1088/0952-4746/32/3/205
From: DESCRIPTION
Status: Forbidden
Message: 403


Strange. Generally you get that only if the document is behind a 
pay-wall and not

even the abstract can be accessed. I could access it.
Sometimes an entire site is down for maintenance (as Springer was ~ two 
weeks ago).

Then one gets an HTTP 404.


How do I modify it?


You can't. Be patient. As stated in the note, wait for a member of CRAN 
to check that.

Wetware outperforms silicon-based lifeforms.

Cheers,
Helmut

--
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BEBAC – Consultancy Services for
Bioequivalence and Bioavailability Studies
Neubaugasse 36/11
1070 Vienna, Austria
W https://bebac.at/
F https://forum.bebac.at/

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[R-pkg-devel] Add reference in Description

2019-09-09 Thread Juhee Lee 
Hello, I submitted my package to CRAN and received this mail.


On 03.09.2019 23:33, CRAN submission wrote:
> [This was generated from CRAN.R-project.org/submit.html
]
>
> The following package was uploaded to CRAN:
> ===
>
> Package Information:
> Package: LARisk
> Version: 0.1.1
> Title: Estimate of Lifetime Attributable Cancer Risk
> Author(s): Young-Min Kim [aut, cre], YeongWoo Park [aut], Jinkyoung Yoo
> [aut], Taesung Shin [aut], DeokKi An [aut], Juhee Lee [aut],
> YuJeong An [aut], Songwon Seo [ctb], WonJin Lee [ctb], EunShil
> Cha [ctb], Seulki Ko [ctb], KyoungAe Kong [ctb]
> Maintainer: Young-Min Kim
> Suggests: R.rsp
> Description: The 'LARisk' to compute lifetime attributable risk of
> radiation-induced cancer reveals that it can be helpful with
> enhancement of the flexibility in research with fast
> calculation and various options.

Thanks, if there are references describing the (theoretical background
of) methods in your package, please add these in the Description field
of your DESCRIPTION file in the form
authors (year)
authors (year)
authors (year, ISBN:...)
with no space after 'doi:', 'arXiv:' and angle brackets for auto-linking.


So I added it in the Description field of my DESCRIPTION file like this:

Description: The 'LARisk' to compute lifetime attributable risk of
radiation-induced cancer reveals that it can be helpful with
enhancement of the flexibility in research with fast calculation
and various options. Important reference papers include
Berrington de Gonzalez A, et al.(2012) ,
National Research Council(2006, ISBN:978-0-309-09156-5).



But, I've gotten the reply like below.


Dear maintainer,

package LARisk_0.1.1.tar.gz has been auto-processed and is pending a manual
inspection. A CRAN team member will typically respond to you within the
next 5 working days. For technical reasons you may receive a second copy of
this message when a team member triggers a new check.

Log dir:
The files will be removed after roughly 7 days.
Installation time in seconds: 19
Check time in seconds: 111
R Under development (unstable) (2019-09-02 r77130)

Pretests results:
Windows:
Status: 1 NOTE
Debian:
Status: 1 NOTE



No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service

--

Flavor: r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Young-Min Kim '

New submission

Possibly mis-spelled words in DESCRIPTION:
Berrington (32:5)
al (32:34)
de (32:16)

Flavor: r-devel-linux-x86_64-debian-gcc
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Young-Min Kim '

New submission

Possibly mis-spelled words in DESCRIPTION:
Berrington (32:5)
al (32:34)
de (32:16)

Found the following (possibly) invalid DOIs:
DOI: 10.1088/0952-4746/32/3/205
From: DESCRIPTION
Status: Forbidden
Message: 403


How do I modify it?


Best regards,

Juhee Lee.

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

2019-09-09 Thread Tomas Kalibera 
Please refer to BLAS_LIBS, LAPACK_LIBS in Writing R Extensions. For an 
example package that uses BLAS/LAPACK, see e.g. "stats" or "Matrix". The 
package will then use the BLAS/LAPACK implementation as chosen by the 
user/system administrator at dynamic linking time (see R Installation 
and Administration Manual for the defailts) - be it say reference BLAS, 
OpenBLAS, MKL or other; as a package author, one does not have to care 
which one it is.


Best
Tomas

On 9/8/19 2:22 PM, Sameh M. Abdulah wrote:

Brian,

This is the code I am using to linking with BLAS using MKL or OpenBLAS

#MKL
if [ -n "$MKLROOT" ] && [ -d "$MKLROOT" ]; then
 echo "mkl_dir directory exists!"
 echo "Great... continue set-up"
 source ${MKLROOT}/bin/mklvars.sh intel64
 DEFINE_BLAS_LIBS_CMAKE="-DBLAS_LIBRARIES='-L${MKLROOT}/lib 
-Wl,-rpath,${MKLROOT}/lib -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm 
-ldl'"
 #DEFINE_BLAS_LIBS_CMAKE="-DBLAS_LIBRARIES='-L${MKLROOT}/lib\ 
-Wl,-rpath,${MKLROOT}/lib\ -lmkl_intel_lp64\ -lmkl_sequential\ -lmkl_core\ -lpthread\ 
-lm\ -ldl'"
 XFLAG="-DBLA_VENDOR=Intel"
else
 echo "MKL not found, trying to compile and use OpenBLAS"
 XFLAG="-DBLA_VENDOR=Open"
 USE_OPENBLAS='true'
fi

# openblas
if [ "true" == "$USE_OPENBLAS" ]
then
 if pkg-config --exists openblas
 then
 _LOCATION=`pkg-config --variable=libdir openblas`
 echo "OpenBLAS FOUND in [$_LOCATION]"
 else
 if [ "$BUILD_DEPENDENCIES" == "true" ]
 then
 echo "Building OpenBLAS..."
 cd $TMPDIR
 wget https://github.com/xianyi/OpenBLAS/archive/v0.3.3.tar.gz -O - 
| tar -zx
 cd OpenBLAS-0.3.3
 $MAKE -j  >/dev/null|| $MAKE || { echo 'OpenBLAS installation 
failed' ; exit 1; }
 $MAKE install PREFIX=$PREFIX
 export CPATH=$CPATH:$PREFIX/include
 else
 echo ""
 echo "OpenBLAS NOT FOUND"
 echo "Please download it from: 
https://github.com/xianyi/OpenBLAS/releases;
 echo "After installing it, set the proper PKG_CONFIG_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 wrote:
 > 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.
 
 It isn't entirely clear what your question is, but shouldn't you just

 be linking to the BLAS and leave the choice of BLAS to the individual
 installation?  In most cases you should probably not be statically
 linking to the BLAS.
 
 Here is an old paper by Dirk with more information that might help you

 sort it out.
 
 https://cran.r-project.org/web/packages/gcbd/vignettes/gcbd.pdf
 
 Regards,
 
 Brian
 
 --

 Brian G. Peterson
 ph: +1.773.459.4973
 im: bgpbraverock
 
 


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