Re: [R-pkg-devel] CRAN nightly tests

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.Will do so,

-Roy

> On Apr 9, 2021, at 4:23 PM, Uwe Ligges  
> wrote:
> 
> 
> 
> On 09.04.2021 21:02, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Just trying to get some information about the CRAN nightly tests.  Are all 
>> the tests for a particular package run a the same time?  
> 
> No.
> 
>> If not,  is there any way to determine when a particular test was last run 
>> (there is a time at the top of the page,  but it may or may not apply to all 
>> of the OSes).  
> 
> No.
> 
> 
> Also can I get the IP address of the the machine that runs the Solaris test?  
> I am befuddled that the Solaris test can not access our server at all.  We 
> did have to block a number of IP addresses recently,  my concerned is that th 
> Solaris test machine may hav been blocked.
> 
> 
> The list does not know. Even the CRAN team does not know the IP address. 
> Professor Ripley runs that machine, so you may ask him via c...@r-project.org.
> 
> Best,
> Uwe Ligges
> 
>> Thanks,
>> -Roy
>> **
>> "The contents of this message do not reflect any position of the U.S. 
>> Government or NOAA."
>> **
>> Roy Mendelssohn
>> Supervisory Operations Research Analyst
>> NOAA/NMFS
>> Environmental Research Division
>> Southwest Fisheries Science Center
>> ***Note new street address***
>> 110 McAllister Way
>> Santa Cruz, CA 95060
>> Phone: (831)-420-3666
>> Fax: (831) 420-3980
>> e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/
>> "Old age and treachery will overcome youth and skill."
>> "From those who have been given much, much will be expected"
>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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Re: [R-pkg-devel] CRAN nightly tests

[Uwe Ligges]

On 09.04.2021 21:02, Roy Mendelssohn - NOAA Federal via R-package-devel 
wrote:
Just trying to get some information about the CRAN nightly tests.  Are all the tests for a particular package run a the same time?  


No.

If not,  is there any way to determine when a particular test was last run (there is a time at the top of the page,  but it may or may not apply to all of the OSes).  


No.


Also can I get the IP address of the the machine that runs the Solaris 
test?  I am befuddled that the Solaris test can not access our server at 
all.  We did have to block a number of IP addresses recently,  my 
concerned is that th Solaris test machine may hav been blocked.



The list does not know. Even the CRAN team does not know the IP address. 
Professor Ripley runs that machine, so you may ask him via 
c...@r-project.org.


Best,
Uwe Ligges


Thanks,

-Roy



**
"The contents of this message do not reflect any position of the U.S. Government or 
NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

__
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[R-pkg-devel] CRAN nightly tests

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Just trying to get some information about the CRAN nightly tests.  Are all the 
tests for a particular package run a the same time?  If not,  is there any way 
to determine when a particular test was last run (there is a time at the top of 
the page,  but it may or may not apply to all of the OSes).  Also can I get the 
IP address of the the machine that runs the Solaris test?  I am befuddled that 
the Solaris test can not access our server at all.  We did have to block a 
number of IP addresses recently,  my concerned is that th Solaris test machine 
may hav been blocked.

Thanks,

-Roy



**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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Re: [R-pkg-devel] Package Vignette depends on Ensembl, server certificate issue?

[Dr. Connie Brett]

Thank you for pointing me to this resource, works like a charm!

> On Apr 9, 2021, at 12:14 AM, Jeff Newmiller  wrote:
> 
> Maybe use r.rsp?
> 
> https://blog.r-hub.io/2020/06/03/vignettes/
> How to include my pre-print / cheatsheet as a PDF vignette?
> 
> 
> 
> On April 8, 2021 12:39:20 PM PDT, "Dr. Connie Brett" 
>  wrote:
>> Hello,
>> I have a package (DGEobj) that depends on the Ensembl service to look
>> up information used to build the vignette.  My builds work fine on
>> Travis, locally and on R-hub.  Occasionally I have seen blips with
>> regard to internet-based resources not being available, and my vignette
>> depends on a number of internet resources to get example datasets. 
>> However when I submitted my package to CRAN today the failures Windows
>> and Debian were that the server certificate verification failed ( SSL
>> certificate problem: unable to get local issuer certificate).
>> I’m not sure if there is something I can do about this or if this is
>> considered a "false positive" per the email - it seems like a "wait and
>> retry" issue.  I don’t want to be rude uploading the package again
>> without a change or erroneously emailing in response to the rejection. 
>> How should this be handled properly now and into the future?  It isn’t
>> feasible to not use Ensembl for this vignette.
>> Thanks for your insight and feedback!
>> 
>> Flavor: r-devel-windows-ix86+x86_64
>> Check: re-building of vignette outputs, Result: WARNING
>> Error(s) in re-building vignettes:
>> --- re-building 'DGEobj_Overview.Rmd' using rmarkdown
>> 
>> Ensembl site unresponsive, trying asia mirror
>> Quitting from lines 259-280 (DGEobj_Overview.Rmd) 
>> Error: processing vignette 'DGEobj_Overview.Rmd' failed with
>> diagnostics:
>> SSL certificate problem: unable to get local issuer certificate
>> --- failed re-building 'DGEobj_Overview.Rmd'
>> 
>> SUMMARY: processing the following file failed:
>>  'DGEobj_Overview.Rmd'
>> 
>> Error: Vignette re-building failed.
>> Execution halted
>> 
>> 
>> Flavor: r-devel-linux-x86_64-debian-gcc
>> Check: re-building of vignette outputs, Result: WARNING
>> Error(s) in re-building vignettes:
>> --- re-building 'DGEobj_Overview.Rmd' using rmarkdown
>> 
>> Ensembl site unresponsive, trying asia mirror
>> Quitting from lines 235-256 (DGEobj_Overview.Rmd) 
>> Error: processing vignette 'DGEobj_Overview.Rmd' failed with
>> diagnostics:
>> server certificate verification failed. CAfile: none CRLfile: none
>> --- failed re-building 'DGEobj_Overview.Rmd'
>> 
>> SUMMARY: processing the following file failed:
>>  'DGEobj_Overview.Rmd'
>> 
>> Error: Vignette re-building failed.
>> Execution halted
>>  [[alternative HTML version deleted]]
>> 
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> -- 
> Sent from my phone. Please excuse my brevity.

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[R-pkg-devel] Problem with building with libcurl on Windows

[Janssen-10, R.R.E. (Roel)]

Dear all,


The package I've tried to submit uses HTSlib, which in turn uses libcurl.  From 
the build logs, I think there is a version mismatch, or configuration problem 
with libcurl:

https://win-builder.r-project.org/incoming_pretest/USCDtools_0.0.1_20210409_093124/Windows/00install.out

The problem seems to boil down to:


undefined reference to `_imp__CertEnumCertificatesInStore@8'

Can I do anything about it in my package?

Kind regards,
Roel Janssen


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Re: [R-pkg-devel] Debugging M1mac problems [solved]

[Ivan Krylov]

On Sat, 27 Mar 2021 17:26:16 +0300
Ivan Krylov  wrote:

> I'm probably doing something stupid with the file names that usually
> works but isn't guaranteed to work in all cases, but I cannot figure
> it out.

Long story short, the problem turned out to be that I called basename()
and dirname() on paths not guaranteed to exist. Thanks to Tomas
Kalibera for pointing me in the right direction!

I'd wager a guess that I would have reproduced the same issue on an
Intel macOS machine with Big Sur installed (this being the other main
difference between Intel/High Sierra machines where all tests passed
and the M1/Big Sur machine where they failed). The "package check
results" page now shows all "OK" for the updated version, so I must
have fixed it.

I guess the moral of the story is that sometimes, it's easier to fix a
problem than reproduce it for oneself.

-- 
Best,
Ivan

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Re: [R-pkg-devel] Package Vignette depends on Ensembl, server certificate issue?

[Jeff Newmiller]

Maybe use r.rsp?

https://blog.r-hub.io/2020/06/03/vignettes/
How to include my pre-print / cheatsheet as a PDF vignette?



On April 8, 2021 12:39:20 PM PDT, "Dr. Connie Brett" 
 wrote:
>Hello,
>I have a package (DGEobj) that depends on the Ensembl service to look
>up information used to build the vignette.  My builds work fine on
>Travis, locally and on R-hub.  Occasionally I have seen blips with
>regard to internet-based resources not being available, and my vignette
>depends on a number of internet resources to get example datasets. 
>However when I submitted my package to CRAN today the failures Windows
>and Debian were that the server certificate verification failed ( SSL
>certificate problem: unable to get local issuer certificate).
>I’m not sure if there is something I can do about this or if this is
>considered a "false positive" per the email - it seems like a "wait and
>retry" issue.  I don’t want to be rude uploading the package again
>without a change or erroneously emailing in response to the rejection. 
>How should this be handled properly now and into the future?  It isn’t
>feasible to not use Ensembl for this vignette.
>Thanks for your insight and feedback!
>
>Flavor: r-devel-windows-ix86+x86_64
>Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> --- re-building 'DGEobj_Overview.Rmd' using rmarkdown
>
> Ensembl site unresponsive, trying asia mirror
> Quitting from lines 259-280 (DGEobj_Overview.Rmd) 
>Error: processing vignette 'DGEobj_Overview.Rmd' failed with
>diagnostics:
> SSL certificate problem: unable to get local issuer certificate
> --- failed re-building 'DGEobj_Overview.Rmd'
>
> SUMMARY: processing the following file failed:
>   'DGEobj_Overview.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>
>
>Flavor: r-devel-linux-x86_64-debian-gcc
>Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> --- re-building 'DGEobj_Overview.Rmd' using rmarkdown
>
> Ensembl site unresponsive, trying asia mirror
> Quitting from lines 235-256 (DGEobj_Overview.Rmd) 
>Error: processing vignette 'DGEobj_Overview.Rmd' failed with
>diagnostics:
> server certificate verification failed. CAfile: none CRLfile: none
> --- failed re-building 'DGEobj_Overview.Rmd'
>
> SUMMARY: processing the following file failed:
>   'DGEobj_Overview.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>   [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
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[R-pkg-devel] Package Vignette depends on Ensembl, server certificate issue?

[Dr. Connie Brett]

Hello,
I have a package (DGEobj) that depends on the Ensembl service to look up 
information used to build the vignette.  My builds work fine on Travis, locally 
and on R-hub.  Occasionally I have seen blips with regard to internet-based 
resources not being available, and my vignette depends on a number of internet 
resources to get example datasets.  However when I submitted my package to CRAN 
today the failures Windows and Debian were that the server certificate 
verification failed ( SSL certificate problem: unable to get local issuer 
certificate).
I’m not sure if there is something I can do about this or if this is considered 
a "false positive" per the email - it seems like a "wait and retry" issue.  I 
don’t want to be rude uploading the package again without a change or 
erroneously emailing in response to the rejection. 
How should this be handled properly now and into the future?  It isn’t feasible 
to not use Ensembl for this vignette.
Thanks for your insight and feedback!

Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
 Error(s) in re-building vignettes:
 --- re-building 'DGEobj_Overview.Rmd' using rmarkdown

 Ensembl site unresponsive, trying asia mirror
 Quitting from lines 259-280 (DGEobj_Overview.Rmd) 
 Error: processing vignette 'DGEobj_Overview.Rmd' failed with diagnostics:
 SSL certificate problem: unable to get local issuer certificate
 --- failed re-building 'DGEobj_Overview.Rmd'

 SUMMARY: processing the following file failed:
   'DGEobj_Overview.Rmd'

 Error: Vignette re-building failed.
 Execution halted


Flavor: r-devel-linux-x86_64-debian-gcc
Check: re-building of vignette outputs, Result: WARNING
 Error(s) in re-building vignettes:
 --- re-building 'DGEobj_Overview.Rmd' using rmarkdown

 Ensembl site unresponsive, trying asia mirror
 Quitting from lines 235-256 (DGEobj_Overview.Rmd) 
 Error: processing vignette 'DGEobj_Overview.Rmd' failed with diagnostics:
 server certificate verification failed. CAfile: none CRLfile: none
 --- failed re-building 'DGEobj_Overview.Rmd'

 SUMMARY: processing the following file failed:
   'DGEobj_Overview.Rmd'

 Error: Vignette re-building failed.
 Execution halted
[[alternative HTML version deleted]]

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