date:20210816

[R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

2021-08-16 Thread David Norris

Whereas Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have 
equivalents in Latin-1 encoding, and I have used these without difficulty in 
strings, neither U+2206 (INCREMENT) nor U+0394 (Greek Delta) does:
https://en.wikipedia.org/wiki/ISO/IEC_8859-1
Consequently, my attempt to use a parameter named '\u2206t' as in the following

> attr(path_list,'performance') <- self$report(J = length(path_list)
>, t1 = round(t1)
>, t2 = round(t2)
>, "\u2206t" = round(t2 - 
> t1)
>  )

generates the following WARNING on Windows R-CMD-check:

> checking R files for syntax errors ... WARNING
  Warning in file 'R/cpe.R':
unable to translate 't' to native encoding

>From this article by Tomas Kalibera
https://developer.r-project.org/Blog/public/2020/05/02/utf-8-support-on-windows/,
I gather that quite often problems such as these won't actually bubble up to 
the user experience.
Is this one such case? Or would this WARNING be fatal to a CRAN submission?


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Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

2021-08-16 Thread Ivan Krylov

On Mon, 16 Aug 2021 09:05:54 +
David Norris  wrote:

> Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have
> equivalents in Latin-1 encoding, and I have used these without
> difficulty in strings, neither U+2206 (INCREMENT) nor U+0394 (Greek
> Delta) does

But not in some other locale encodings on Windows (e.g. CP-1251), nor
in some single-byte locale encodings on *nix-like systems (e.g.
ru_RU.KOI8-R), which are admittedly used much rarer nowadays than on
Windows. Unless I'm mistaken, the "\u2206t" in your example needs to
become a symbol, and symbols are always translated into the locale
encoding [1] [2].

I would expect this warning to be a problem for CRAN, but I'm just
another package developer, so I could be wrong.

-- 
Best regards,
Ivan

[1]
https://github.com/r-devel/r-svn/blob/9b13376f5e630f584a68d3815da004dc79c059a3/src/main/sysutils.c#L1046-L1052

[2]
https://github.com/r-devel/r-svn/blob/9b13376f5e630f584a68d3815da004dc79c059a3/src/main/sysutils.c#L842

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Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

2021-08-16 Thread Tomas Kalibera




On 8/16/21 12:42 PM, Ivan Krylov wrote:

On Mon, 16 Aug 2021 09:05:54 +
David Norris  wrote:


Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have
equivalents in Latin-1 encoding, and I have used these without
difficulty in strings, neither U+2206 (INCREMENT) nor U+0394 (Greek
Delta) does

But not in some other locale encodings on Windows (e.g. CP-1251), nor
in some single-byte locale encodings on *nix-like systems (e.g.
ru_RU.KOI8-R), which are admittedly used much rarer nowadays than on
Windows. Unless I'm mistaken, the "\u2206t" in your example needs to
become a symbol, and symbols are always translated into the locale
encoding [1] [2].

I would expect this warning to be a problem for CRAN, but I'm just
another package developer, so I could be wrong.

Yes, this is a problem. Only ASCII characters should be used in symbol 
names (in R packages), as they can be represented in every (supported) 
locale.


Some characters would be best-fitted by Windows (replaced by other 
similar characters) during translation to native encoding, if they are 
not representable directly, but that can produce surprising results and 
should not be relied on, definitely not in packages.


Best
Tomas

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[R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

2021-08-16 Thread Pooja Gangras via R-package-devel

Hi all,

PFA the pre-check results for my package surfaltr from CRAN. I am having 
troubles with a package dependency on Debian that I am not able to fix. 2 
functions in my package require a Bioconductor package msa 
(https://bioconductor.org/packages/release/bioc/html/msa.html). To deal with 
this error, I tried the following solution of adding a call to BiocManager and 
also including a code for msa installation but it did not help:

#' @importFrom BiocManager install
#' @import msa
.
.
.
Foo() {
if (!requireNamespace("msa", quietly = TRUE)){
BiocManager::install("msa")}
}

How do I solve the problem so that I don't generate this error with Debian?

Thank you,
Pooja


Pooja Gangras, Ph.D.
Postdoctoral Research Scientist - RNA Therapeutics
Eli Lilly and Company
Lilly Corporate Center, Indianapolis IN 46285 U.S.A.
Office phone number: (317) 651-0589
Cellphone number: (614) 906-0940
gangras_po...@lilly.com | www.lilly.com


CONFIDENTIALITY NOTICE: This email message (including all attachments) is for 
the sole use of the intended recipient(s) and may contain confidential 
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the sender by reply email and destroy all copies of the original message.

-Original Message-
From: lig...@statistik.tu-dortmund.de  
Sent: Monday, August 16, 2021 10:32 AM
To: Pooja Gangras 
Cc: cran-submissi...@r-project.org
Subject: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Dear maintainer,
 
package surfaltr_1.0.0.9000.tar.gz does not pass the incoming checks 
automatically, please see the following pre-tests:
Windows: 

Status: 1 NOTE
Debian: 

Status: 1 ERROR, 1 NOTE
 

 
Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.
 
More details are given in the directory:

The files will be removed after roughly 7 days.
 
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: 'Pooja Gangras '
  
  New submission
  
  Version contains large components (1.0.0.9000)
  
  Possibly misspelled words in DESCRIPTION:
APPRIS (25:78)
Isoform (3:44)
Phobius (22:29, 26:81)
SurfaltR (24:68)
TMHMM (22:19, 26:72)
Topologies (3:61)
bioinformatic (22:71)
customizable (27:19)
druggable (17:65)
isoform (28:42)
isoforms (19:41, 23:48, 25:12)
oligonucleotide (18:51)
proteome (17:75)
subcellular (19:85)
surfaltR (4:17, 27:59)
surfaltrbib (29:143)
topologies (24:3, 26:55)
transmembrane (20:29)

Flavor: r-devel-linux-x86_64-debian-gcc
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'Pooja Gangras '
  
  New submission
  
  Version contains large components (1.0.0.9000)
  
  Possibly misspelled words in DESCRIPTION:
APPRIS (25:78)
Isoform (3:44)
Phobius (22:29, 26:81)
SurfaltR (24:68)
TMHMM (22:19, 26:72)
Topologies (3:61)
bioinformatic (22:71)
customizable (27:19)
druggable (17:65)
isoform (28:42)
isoforms (19:41, 23:48, 25:12)
proteome (17:75)
subcellular (19:85)
surfaltR (4:17, 27:59)
surfaltrbib (29:143)
topologies (24:3, 26:55)
transmembrane (20:29)

Flavor: r-devel-linux-x86_64-debian-gcc
Check: package dependencies, Result: ERROR
  Package required but not available: 'msa'
  
  See section 'The DESCRIPTION file' in the 'Writing R Extensions'
  manual.
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Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

2021-08-16 Thread David Norris

Thanks to you both, Ivan and Tomas. Capital D it is, then.
-David

From: Tomas Kalibera 
Date: Monday, August 16, 2021 at 8:48 AM
To: Ivan Krylov , David Norris 

Cc: "r-package-devel@r-project.org" 
Subject: Re: [R-pkg-devel] UX for "WARNING unable to translate to native 
encoding"?

On 8/16/21 12:42 PM, Ivan Krylov wrote:
On Mon, 16 Aug 2021 09:05:54 +
David Norris  wrote:

Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have
equivalents in Latin-1 encoding, and I have used these without
difficulty in strings, neither U+2206 (INCREMENT) nor U+0394 (Greek
Delta) does
But not in some other locale encodings on Windows (e.g. CP-1251), nor
in some single-byte locale encodings on *nix-like systems (e.g.
ru_RU.KOI8-R), which are admittedly used much rarer nowadays than on
Windows. Unless I'm mistaken, the "\u2206t" in your example needs to
become a symbol, and symbols are always translated into the locale
encoding [1] [2].

I would expect this warning to be a problem for CRAN, but I'm just
another package developer, so I could be wrong.

Yes, this is a problem. Only ASCII characters should be used in symbol 
names (in R packages), as they can be represented in every (supported) 
locale.

Some characters would be best-fitted by Windows (replaced by other 
similar characters) during translation to native encoding, if they are 
not representable directly, but that can produce surprising results and 
should not be relied on, definitely not in packages.

Best
Tomas

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Re: [R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

2021-08-16 Thread Sebastian Meyer

Packages on CRAN can depend on released packages from both CRAN and 
Bioconductor.


I don't know why "msa" is missing on the Debian check machine. The check 
results of another CRAN package that suggests "msa" indicate that this 
package is currently unavailable on all Linux, Solaris and macOS 
machines of the CRAN check farm: 
https://cran.r-project.org/web/checks/check_results_bio3d.html


Maybe this is a temporary problem? You could try resubmitting in a few days.

I think you should remove the automatic package installation from your 
functions; they should not write to the user's home filespace without 
consent.

You should probably also avoid this NOTE when submitting to CRAN:

> Version contains large components (1.0.0.9000)

Best regards,

Sebastian Meyer


Am 16.08.21 um 17:37 schrieb Pooja Gangras via R-package-devel:

Hi all,

PFA the pre-check results for my package surfaltr from CRAN. I am having 
troubles with a package dependency on Debian that I am not able to fix. 2 
functions in my package require a Bioconductor package msa 
(https://bioconductor.org/packages/release/bioc/html/msa.html). To deal with 
this error, I tried the following solution of adding a call to BiocManager and 
also including a code for msa installation but it did not help:

#' @importFrom BiocManager install
#' @import msa
.
.
.
Foo() {
if (!requireNamespace("msa", quietly = TRUE)){
 BiocManager::install("msa")}
}

How do I solve the problem so that I don't generate this error with Debian?

Thank you,
Pooja


Pooja Gangras, Ph.D.
Postdoctoral Research Scientist - RNA Therapeutics
Eli Lilly and Company
Lilly Corporate Center, Indianapolis IN 46285 U.S.A.
Office phone number: (317) 651-0589
Cellphone number: (614) 906-0940
gangras_po...@lilly.com | www.lilly.com


CONFIDENTIALITY NOTICE: This email message (including all attachments) is for 
the sole use of the intended recipient(s) and may contain confidential 
information. Any unauthorized review, use, disclosure, copying or distribution 
is strictly prohibited. If you are not the intended recipient, please contact 
the sender by reply email and destroy all copies of the original message.

-Original Message-
From: lig...@statistik.tu-dortmund.de 
Sent: Monday, August 16, 2021 10:32 AM
To: Pooja Gangras 
Cc: cran-submissi...@r-project.org
Subject: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Dear maintainer,
  
package surfaltr_1.0.0.9000.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:

Windows: 

Status: 1 NOTE
Debian: 

Status: 1 ERROR, 1 NOTE
  

  
Please fix all problems and resubmit a fixed version via the webform.

If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.
  
More details are given in the directory:


The files will be removed after roughly 7 days.
  
No strong reverse dependencies to be checked.
  
Best regards,

CRAN teams' auto-check service


__
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Re: [R-pkg-devel] [EXTERNAL] Re: FW: [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

2021-08-16 Thread Pooja Gangras via R-package-devel

Thank you so much Sebastian!
Pooja

Pooja Gangras, Ph.D.
Postdoctoral Research Scientist - RNA Therapeutics
Eli Lilly and Company
Lilly Corporate Center, Indianapolis IN 46285 U.S.A.
Office phone number: (317) 651-0589
Cellphone number: (614) 906-0940
gangras_po...@lilly.com | www.lilly.com


CONFIDENTIALITY NOTICE: This email message (including all attachments) is for 
the sole use of the intended recipient(s) and may contain confidential 
information. Any unauthorized review, use, disclosure, copying or distribution 
is strictly prohibited. If you are not the intended recipient, please contact 
the sender by reply email and destroy all copies of the original message.

-Original Message-
From: Sebastian Meyer  
Sent: Monday, August 16, 2021 2:49 PM
To: Pooja Gangras ; r-package-devel@r-project.org
Subject: [EXTERNAL] Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN 
submission surfaltr 1.0.0.9000

EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Packages on CRAN can depend on released packages from both CRAN and 
Bioconductor.

I don't know why "msa" is missing on the Debian check machine. The check 
results of another CRAN package that suggests "msa" indicate that this package 
is currently unavailable on all Linux, Solaris and macOS machines of the CRAN 
check farm: 
https://cran.r-project.org/web/checks/check_results_bio3d.html

Maybe this is a temporary problem? You could try resubmitting in a few days.

I think you should remove the automatic package installation from your 
functions; they should not write to the user's home filespace without consent.
You should probably also avoid this NOTE when submitting to CRAN:

 > Version contains large components (1.0.0.9000)

Best regards,

Sebastian Meyer


Am 16.08.21 um 17:37 schrieb Pooja Gangras via R-package-devel:
> Hi all,
> 
> PFA the pre-check results for my package surfaltr from CRAN. I am having 
> troubles with a package dependency on Debian that I am not able to fix. 2 
> functions in my package require a Bioconductor package msa 
> (https://bioconductor.org/packages/release/bioc/html/msa.html). To deal with 
> this error, I tried the following solution of adding a call to BiocManager 
> and also including a code for msa installation but it did not help:
> 
> #' @importFrom BiocManager install
> #' @import msa
> .
> .
> .
> Foo() {
> if (!requireNamespace("msa", quietly = TRUE)){
>  BiocManager::install("msa")}
> }
> 
> How do I solve the problem so that I don't generate this error with Debian?
> 
> Thank you,
> Pooja
> 
> 
> Pooja Gangras, Ph.D.
> Postdoctoral Research Scientist - RNA Therapeutics Eli Lilly and 
> Company Lilly Corporate Center, Indianapolis IN 46285 U.S.A.
> Office phone number: (317) 651-0589
> Cellphone number: (614) 906-0940
> gangras_po...@lilly.com | www.lilly.com
> 
> 
> CONFIDENTIALITY NOTICE: This email message (including all attachments) is for 
> the sole use of the intended recipient(s) and may contain confidential 
> information. Any unauthorized review, use, disclosure, copying or 
> distribution is strictly prohibited. If you are not the intended recipient, 
> please contact the sender by reply email and destroy all copies of the 
> original message.
> 
> -Original Message-
> From: lig...@statistik.tu-dortmund.de 
> 
> Sent: Monday, August 16, 2021 10:32 AM
> To: Pooja Gangras 
> Cc: cran-submissi...@r-project.org
> Subject: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 
> 1.0.0.9000
> 
> EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
> attachments.
> 
> Dear maintainer,
>   
> package surfaltr_1.0.0.9000.tar.gz does not pass the incoming checks 
> automatically, please see the following pre-tests:
> Windows: 
>  0_20210816_162209/Windows/00check.log>
> Status: 1 NOTE
> Debian: 
>  0_20210816_162209/Debian/00check.log>
> Status: 1 ERROR, 1 NOTE
>   
> 
>   
> Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help on the 
> R-package-devel mailing list:
> 
> If you are fairly certain the rejection is a false positive, please reply-all 
> to this message and explain.
>   
> More details are given in the directory:
>  0_20210816_162209/> The files will be removed after roughly 7 days.
>   
> No strong reverse dependencies to be checked.
>   
> Best regards,
> CRAN teams' auto-check service
> 
> 
> __
> R-package-devel@r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 

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Re: [R-pkg-devel] WinBuilder error: dependency version not available

2021-08-16 Thread Carrie Tribble

Dear Berry,

Thanks for your reply! I was away from my computer until now. We also
submitted to CRAN, but the dependency version is still causing an error:

package RevGadgets_1.0.0.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
> Windows: <
> https://win-builder.r-project.org/incoming_pretest/RevGadgets_1.0.0_20210805_041017/Windows/00check.log
> >
> Status: 1 ERROR, 1 NOTE
> Debian: <
> https://win-builder.r-project.org/incoming_pretest/RevGadgets_1.0.0_20210805_041017/Debian/00check.log
> >
> Status: 1 NOTE

Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help on
> the R-package-devel mailing list:
> 
> If you are fairly certain the rejection is a false positive, please
> reply-all to this message and explain.

More details are given in the directory:
> <
> https://win-builder.r-project.org/incoming_pretest/RevGadgets_1.0.0_20210805_041017/
> >
> The files will be removed after roughly 7 days.


The ERROR referenced is the same ggtree version error, and the Note is
simply that this is a first time CRAN submission. Is there any way that a
bioconductor package could be manually installed on WinBuilder? If so,
perhaps we could ask the dependency's maintainer to help us out and upload
the new version themselves. Other ideas would be very welcome --- we have a
deadline for getting the package on CRAN so waiting for the dependency to
be updated is not an ideal solution for us!

Thanks again for your help and suggestions!
Carrie

---
Carrie M. Tribble, PhD 
Postdoctoral Researcher in the Zenil-Ferguson Lab

University of Hawaiʻi at Mānoa



On Mon, Aug 9, 2021 at 1:20 PM Berry Boessenkool <
berryboessenk...@hotmail.com> wrote:

>
> If it works on all other testing platforms, I'd just submit to CRAN and
> see if it works.
> You may also just wait out until ggtree works on winbuilder...
>
> Regards,
> Berry
>
>
>
> --
> *From:* R-package-devel  on behalf
> of Carrie Tribble 
> *Sent:* Friday, August 6, 2021 22:34
> *To:* r-package-devel@r-project.org 
> *Subject:* [R-pkg-devel] WinBuilder error: dependency version not
> available
>
> I am in the final stages of preparing an R package
>  to submit to CRAN.
> The package passes devtools::check() locally, GitHub Actions on multiple
> systems (including windows), devtools::check_rhub() remotely, and
> rhub::check_on_windows(check_args = "--force-multiarch"). However, it fails
> on WinBuilder.
>
> I'd appreciate any advice or suggestions. More details below:
>
> You can see the full WinBuilder log here:
>  https://win-builder.r-project.org/kTnuoY4Kqo8B/00check.log
> 
>
> * checking CRAN incoming feasibility ... NOTE
> > Maintainer: 'Carrie Tribble ' New submission
> Possibly
> > misspelled words in DESCRIPTION:
> > RevBayes (3:45, 22:92)
> > * checking package namespace information ... OK
> > * checking package dependencies ... ERROR
> > Package required and available but unsuitable version: 'ggtree' See
> > section 'The DESCRIPTION file' in the 'Writing R Extensions'
> > manual.
> > * DONE
> > Status: 1 ERROR, 1 NOTE
>
>
> We require the latest version of ggtree, a bioconductor package.
> Unfortunately, this latest version is necessary for our package to
> function. What's the best way to get access to that version of ggtree on
> WinBuilder?
>
> You can see the log for the successful rhub check_on_windows run here:
>
> https://builder.r-hub.io/status/RevGadgets_1.0.0.tar.gz-8367c3a164ad47379c8bd89c81347ceb
> ,
> and find the package on GitHub here:
> https://github.com/cmt2/RevGadgets/tree/development.
>
> Thank you!
>
> ---
> Carrie M. Tribble, PhD 
> Postdoctoral Researcher in the Zenil-Ferguson Lab
> 
> University of Hawaiʻi at Mānoa
>
> [[alternative HTML version deleted]]
>
> __
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>

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[R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

[R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

Re: [R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

Re: [R-pkg-devel] [EXTERNAL] Re: FW: [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

Re: [R-pkg-devel] WinBuilder error: dependency version not available

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