Re: [R-pkg-devel] Resubmitting an archived package

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

If you run a spell checker before you submit  then it helps if you put in your 
cran-comments.md file  the list of words flagged and that all of them are 
correct. This makes it just a little easier for CRAN.

-Roy

> On Jun 12, 2024, at 3:35 PM, Ben Bolker  wrote:
> 
>   As far as I know these are all harmless.
> 
>  * the first NOTE is for CRAN consumption
>  * the rest are false positives
> 
> 
> 
> The spell-checking machinery used in package checking is under-documented. 
> There are some useful references here
> 
> https://github.com/r-lib/usethis/issues/1466
> https://ropensci.org/blog/2022/01/21/ropensci-news-digest-january-2022/#to-quote-or-not-to-quote-non-existing-words-in-description
> https://stat.ethz.ch/pipermail/r-package-devel/2016q3/000943.html
> https://stat.ethz.ch/pipermail/r-package-devel/2017q3/001764.html
> 
> I've been meaning to submit a patch to "Writing R Extensions" that would 
> describe this, but so far I haven't. However, I also think that win-builder 
> does *not* pay attention to the .aspell/ stuff documented above ...
> 
> 
> 
> On 2024-06-12 2:12 p.m., Lucas Godoy wrote:
>> Hello everyone,
>> Recently, my R package {smile} was archived due to NOTES. At the time, I
>> was in the final stages of my PhD and unfortunately, I couldn't address the
>> issue in time to prevent the package from being archived.
>> Long story short, I fixed the issues, and now the `R CMD check --as-cran`
>> returns no notes (I'm on a Mac. However, when I submit the package to
>> "win-builder" to get it checked on Windows, I get the following NOTES:
>> "* checking CRAN incoming feasibility ... NOTE
>> Maintainer: 'Lucas da Cunha Godoy '
>> New submission
>> Package was archived on CRAN
>> Possibly misspelled words in DESCRIPTION:
>>   ISSN (17:54)
>>   Moraga (13:60)
>>   al (14:9)
>>   et (13:67)
>> CRAN repository db overrides:
>>   X-CRAN-Comment: Archived on 2024-04-09 as issues were not corrected
>> in time."
>> The "misspelled" words are author names included in the DESCRIPTION file as
>> references. Also, there is a note that the package is being archived.
>> I used GitHub workflows to get the package checked on Linux as well (see
>> here
>> ),
>> and there I got a note about sub-directories with more than 1Mb. To this
>> point, I don't believe I can further shrink those directories.
>> Does anyone have any suggestions on how to fix those issues to get the
>> package on CRAN?
>> My session info is below, just in case.
>> R version 4.3.2 (2023-10-31)
>> Platform: aarch64-apple-darwin20 (64-bit)
>> Running under: macOS Sonoma 14.5
>> Matrix products: default
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;
>>  LAPACK version 3.11.0
>> Thanks a lot,
>> Lucas.
>>  [[alternative HTML version deleted]]
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> -- 
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> (Acting) Graduate chair, Mathematics & Statistics
> > E-mail is sent at my convenience; I don't expect replies outside of working 
> > hours.
> 
> __
> 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] Resubmitting an archived package

[Ben Bolker]

   As far as I know these are all harmless.

  * the first NOTE is for CRAN consumption
  * the rest are false positives



The spell-checking machinery used in package checking is 
under-documented. There are some useful references here


https://github.com/r-lib/usethis/issues/1466
https://ropensci.org/blog/2022/01/21/ropensci-news-digest-january-2022/#to-quote-or-not-to-quote-non-existing-words-in-description
https://stat.ethz.ch/pipermail/r-package-devel/2016q3/000943.html
https://stat.ethz.ch/pipermail/r-package-devel/2017q3/001764.html

 I've been meaning to submit a patch to "Writing R Extensions" that 
would describe this, but so far I haven't. However, I also think that 
win-builder does *not* pay attention to the .aspell/ stuff documented 
above ...




On 2024-06-12 2:12 p.m., Lucas Godoy wrote:

Hello everyone,

Recently, my R package {smile} was archived due to NOTES. At the time, I
was in the final stages of my PhD and unfortunately, I couldn't address the
issue in time to prevent the package from being archived.

Long story short, I fixed the issues, and now the `R CMD check --as-cran`
returns no notes (I'm on a Mac. However, when I submit the package to
"win-builder" to get it checked on Windows, I get the following NOTES:
"* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Lucas da Cunha Godoy '

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
   ISSN (17:54)
   Moraga (13:60)
   al (14:9)
   et (13:67)

CRAN repository db overrides:
   X-CRAN-Comment: Archived on 2024-04-09 as issues were not corrected
 in time."

The "misspelled" words are author names included in the DESCRIPTION file as
references. Also, there is a note that the package is being archived.
I used GitHub workflows to get the package checked on Linux as well (see
here
),
and there I got a note about sub-directories with more than 1Mb. To this
point, I don't believe I can further shrink those directories.

Does anyone have any suggestions on how to fix those issues to get the
package on CRAN?
My session info is below, just in case.

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib

LAPACK:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;
  LAPACK version 3.11.0

Thanks a lot,
Lucas.

[[alternative HTML version deleted]]

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--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of 
working hours.


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Re: [R-pkg-devel] Packages required but not available

[Iris Simmons]

This is actually an issue that was just fixed.

package:vctrs has an error when installing under r86723 because it creates
delayed bindings at package install time that cannot be restored at package
load time.

It may be a small while before the newest R devel version is in use by the
CRAN farm, but after that point package:vctrs will install successfully
again and you can submit your R package.

On Wed, Jun 12, 2024, 14:04 Leonardo Cefalo 
wrote:

> Dear all
>
> I have just submitted a new version of the package SchoolDataIT
> 
>
> On r-devel-linux-x86_64-debian-gcc I got this error
> <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/SchoolDataIT-00check.html>
>
> :
>
> Result: ERROR
>Packages required but not available:
>  'dplyr', 'ggplot2', 'readr', 'readxl', 'rvest', 'stringr', 'tidyr'
>
>Packages suggested but not available for checking: 'testthat',
> 'tidyverse'
>
>See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
>manual.
>
> If I don't get it wrong, this should be a version problem but I cannot
> figure out how to modify the DESCRIPTION in order to avoid this result.
> Also I never noticed such problems with the old package version, though
> no version specification was included either (except for testthat) and
> the DESCRIPTION file had the same Imports and Suggestions fields
>
> I have found this discussion on the posit community
> <
> https://forum.posit.co/t/package-required-but-not-available-error-on-cran/180047>
>
> but I am not sure if it is exactly the same case - also because the same
> platforms did not give any problem with tidyverse packages before.
>
> Could somebody please help me understanding how to fix this?
> Thank you very much in advance
>
> With kindest regards
> LC
>
> 
> Sostieni la formazione e la ricerca universitaria con il tuo 5 per mille
> all'Università di Bari.
> Firma la casella "Finanziamento della ricerca scientifica e della
> Università"
> indicando il codice fiscale 80002170720.
>
> Il tuo contributo può fare la differenza: oggi più che mai!
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[alternative HTML version deleted]]

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[R-pkg-devel] Resubmitting an archived package

[Lucas Godoy]

Hello everyone,

Recently, my R package {smile} was archived due to NOTES. At the time, I
was in the final stages of my PhD and unfortunately, I couldn't address the
issue in time to prevent the package from being archived.

Long story short, I fixed the issues, and now the `R CMD check --as-cran`
returns no notes (I'm on a Mac. However, when I submit the package to
"win-builder" to get it checked on Windows, I get the following NOTES:
"* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Lucas da Cunha Godoy '

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  ISSN (17:54)
  Moraga (13:60)
  al (14:9)
  et (13:67)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-04-09 as issues were not corrected
in time."

The "misspelled" words are author names included in the DESCRIPTION file as
references. Also, there is a note that the package is being archived.
I used GitHub workflows to get the package checked on Linux as well (see
here
),
and there I got a note about sub-directories with more than 1Mb. To this
point, I don't believe I can further shrink those directories.

Does anyone have any suggestions on how to fix those issues to get the
package on CRAN?
My session info is below, just in case.

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib

LAPACK:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;
 LAPACK version 3.11.0

Thanks a lot,
Lucas.

[[alternative HTML version deleted]]

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[R-pkg-devel] Packages required but not available

[Leonardo Cefalo]

Dear all

I have just submitted a new version of the package SchoolDataIT 



On r-devel-linux-x86_64-debian-gcc I got this error 
 
:


Result: ERROR
  Packages required but not available:
'dplyr', 'ggplot2', 'readr', 'readxl', 'rvest', 'stringr', 'tidyr'

  Packages suggested but not available for checking: 'testthat', 
'tidyverse'


  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

If I don't get it wrong, this should be a version problem but I cannot 
figure out how to modify the DESCRIPTION in order to avoid this result.
Also I never noticed such problems with the old package version, though 
no version specification was included either (except for testthat) and 
the DESCRIPTION file had the same Imports and Suggestions fields


I have found this discussion on the posit community 
 
but I am not sure if it is exactly the same case - also because the same 
platforms did not give any problem with tidyverse packages before.


Could somebody please help me understanding how to fix this?
Thank you very much in advance

With kindest regards
LC

Sostieni la formazione e la ricerca universitaria con il tuo 5 per mille 
all'Università di Bari.
Firma la casella "Finanziamento della ricerca scientifica e della 
Università"

indicando il codice fiscale 80002170720.

Il tuo contributo può fare la differenza: oggi più che mai!

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Re: [Rd] Fields used by available.packages

[Kurt Hornik]

> Lluís Revilla writes:

> Yes, I think that would be enough. 

Thanks.  And of course add documentation ...

Will try to get this in in the next few days.

Best
-k

> Thank you, Kurt!


> Lluís

> On Wed, 12 Jun 2024 at 16:35, Kurt Hornik  wrote:

>> Lluís Revilla writes:
   
> Lluis,
   
> So in available.packages() I could replace
   
>     if (is.null(fields))
>         fields <- requiredFields
>     else {
>         stopifnot(is.character(fields))
>         fields <- unique(c(requiredFields, fields))
>     }
   
> by someting like
   
>     if(is.null(fields))
>         fields <- getOption("available_packages_fields")
>     if(is.null(fields))
>         fields <- requiredFields
>     else {
>         stopifnot(is.character(fields))
>         fields <- unique(c(requiredFields, fields))
>     }
   
> ?
   
> Best
> -k

>> Hi all,
>> I have recently been researching how available.packages and
>> install.packages filter packages from repositories with additional
> fields
>> in their PACKAGES file.
   
>> Currently there are some default filters, but users (and R admins) can
> set
>> up their own filters by passing a list to the fields argument or adding
>> them to the "available_packages_filters" option.
>> But if the fields used by the filters are not read by default, then
> users
>> must manually add the required fields to each call to
> available.packages.
   
>> This makes it difficult to use new fields and to control what is
> installed
>> in highly regulated systems which want to use more fields to select
> what is
>> installed.
   
>> Current workarounds considered are:
>>   1) The filtering function requiring new fields intercepts the call to
>> available.packages and adds the desired fields via eval in
>> parent.environment and then adds the filters again.
>>   2) Import new data (remote or local) when filtering packages, merge
> them
>> and filter accordingly.
>>   3) Suggestions?
   
>> The first solution is complicated, while the second doesn't use the R
>> machinery of tools::write_PACKAGES to set up the repository with all
> the
>> fields (although how to add more fields to the repository file is a
>> different issue).
   
>> Would it be possible to add a new option to add fields to be read by
>> available.packages, similar to filters?
>> The same approach for fields as for filters would avoid the two
> workarounds
>> mentioned. To match it, the new option could be named
>> "available_packages_fields".
   
>> I look forward to hearing from you,
   
>> Lluís
   
>>        [[alternative HTML version deleted]]
   
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] Fields used by available.packages

[Lluís Revilla]

Yes, I think that would be enough.
Thank you, Kurt!

Lluís

On Wed, 12 Jun 2024 at 16:35, Kurt Hornik  wrote:

> > Lluís Revilla writes:
>
> Lluis,
>
> So in available.packages() I could replace
>
> if (is.null(fields))
> fields <- requiredFields
> else {
> stopifnot(is.character(fields))
> fields <- unique(c(requiredFields, fields))
> }
>
> by someting like
>
> if(is.null(fields))
> fields <- getOption("available_packages_fields")
> if(is.null(fields))
> fields <- requiredFields
> else {
> stopifnot(is.character(fields))
> fields <- unique(c(requiredFields, fields))
> }
>
> ?
>
> Best
> -k
>
>
>
> > Hi all,
> > I have recently been researching how available.packages and
> > install.packages filter packages from repositories with additional fields
> > in their PACKAGES file.
>
> > Currently there are some default filters, but users (and R admins) can
> set
> > up their own filters by passing a list to the fields argument or adding
> > them to the "available_packages_filters" option.
> > But if the fields used by the filters are not read by default, then users
> > must manually add the required fields to each call to available.packages.
>
> > This makes it difficult to use new fields and to control what is
> installed
> > in highly regulated systems which want to use more fields to select what
> is
> > installed.
>
> > Current workarounds considered are:
> >  1) The filtering function requiring new fields intercepts the call to
> > available.packages and adds the desired fields via eval in
> > parent.environment and then adds the filters again.
> >  2) Import new data (remote or local) when filtering packages, merge them
> > and filter accordingly.
> >  3) Suggestions?
>
> > The first solution is complicated, while the second doesn't use the R
> > machinery of tools::write_PACKAGES to set up the repository with all the
> > fields (although how to add more fields to the repository file is a
> > different issue).
>
> > Would it be possible to add a new option to add fields to be read by
> > available.packages, similar to filters?
> > The same approach for fields as for filters would avoid the two
> workarounds
> > mentioned. To match it, the new option could be named
> > "available_packages_fields".
>
> > I look forward to hearing from you,
>
> > Lluís
>
> >   [[alternative HTML version deleted]]
>
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>

[[alternative HTML version deleted]]

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Re: [Rd] Fields used by available.packages

[Kurt Hornik]

> Lluís Revilla writes:

Lluis,

So in available.packages() I could replace

if (is.null(fields))
fields <- requiredFields
else {
stopifnot(is.character(fields))
fields <- unique(c(requiredFields, fields))
}

by someting like

if(is.null(fields))
fields <- getOption("available_packages_fields")
if(is.null(fields))
fields <- requiredFields
else {
stopifnot(is.character(fields))
fields <- unique(c(requiredFields, fields))
}

?

Best
-k



> Hi all,
> I have recently been researching how available.packages and
> install.packages filter packages from repositories with additional fields
> in their PACKAGES file.

> Currently there are some default filters, but users (and R admins) can set
> up their own filters by passing a list to the fields argument or adding
> them to the "available_packages_filters" option.
> But if the fields used by the filters are not read by default, then users
> must manually add the required fields to each call to available.packages.

> This makes it difficult to use new fields and to control what is installed
> in highly regulated systems which want to use more fields to select what is
> installed.

> Current workarounds considered are:
>  1) The filtering function requiring new fields intercepts the call to
> available.packages and adds the desired fields via eval in
> parent.environment and then adds the filters again.
>  2) Import new data (remote or local) when filtering packages, merge them
> and filter accordingly.
>  3) Suggestions?

> The first solution is complicated, while the second doesn't use the R
> machinery of tools::write_PACKAGES to set up the repository with all the
> fields (although how to add more fields to the repository file is a
> different issue).

> Would it be possible to add a new option to add fields to be read by
> available.packages, similar to filters?
> The same approach for fields as for filters would avoid the two workarounds
> mentioned. To match it, the new option could be named
> "available_packages_fields".

> I look forward to hearing from you,

> Lluís

>   [[alternative HTML version deleted]]

> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Bioc-devel] [EXTERNAL] Re: Deeptarget package

[Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel]

Dear Kristian,

This is very important question. Thanks for checking in. The manuscript is 
under review, and I believe that we already agreed and followed to Depmap’s 
policies. The input data we used in this package here contains only a subset of 
the data we used in the manuscript, and it is for demonstration how the package 
works. In addition to this, Deeptarget does have a function to pull out the 
data from Depmap and it is called Depmap2DeepTarget. I think this is where your 
concern is coming from.  This function we incorporated the Depmap package from 
@Laurent Gatto which allows users to 
download data from depmap.org.  Therefore, I would love to leave this for  
@Laurent Gatto to chime in to address your 
concern.

Thanks,

Trinh

From: Kristian Ullrich 
Date: Wednesday, June 12, 2024 at 2:42 AM
To: Nguyen, Trinh (NIH/NCI) [C] 
Cc: Kern, Lori , bioc-devel@r-project.org 

Subject: [EXTERNAL] Re: [Bioc-devel] Deeptarget package
Dear Nguyen,

I have a question related to the data that you use and I just bring it up here 
since I would also like to ask the bioconductor developers, how this can be 
handled properly.

The depmap.org portal has a clear "Terms and Condition" 
statement that you need to agree on if one uses any of the data that is 
provided by the portal. (See below) So one need to click a "I agree" button to 
stick to their policies.

How have you managed that a user of your package first send this agreement to 
the depmap.org portal once the user uses data from the 
portal?

Thank you in anticipation

Best regards

Kristian

Here is their policy:

"
Terms and Conditions
By using this site, you agree to our terms and conditions below.
Overview of Terms
These Terms of Use reflect the Broad Institute’s commitment to Open Science 
through its mission to provide freely available online services, databases and 
software relating to data contributed from life science experiments to the 
largest possible community. They impose no additional constraints on the use of 
the contributed data than those provided by the original data owners.
The data made available on this website were generated for research purposes 
and are not intended for clinical use.
The original data may be subject to rights claimed by third parties, including 
but not limited to, patent, copyright, other intellectual property rights, 
biodiversity-related access and benefit-sharing rights. It is the 
responsibility of users of Broad Institute services to ensure that their 
exploitation of the data does not infringe any of the rights of such third 
parties.
The information and materials ("Data") made available on this web site 
including the database of genomic profiles, mutations, genetic and 
pharmacologic screening data (referred to collectively herein as the 
"Database") are made available to you (and your employing entity, where the 
download or use is within the scope of your employment by such entity- 
collectively "You").
Any questions or comments concerning these Terms of Use can be addressed to: 
Cancer Dependency Map, Broad Institute, 415 Main Street, Cambridge, MA 02142, 
USA
By accessing and viewing this Database, You agree to the following terms and 
conditions:
Attribution
You agree to acknowledge the Broad Institute (e.g., in publications, services 
or products) for any of its online services, databases or software in 
accordance with good scientific practice. You agree to use the acknowledgment 
wording provided for the relevant Data (provided by the original data owners) 
as indicated on the appropriate web page.
Confidentiality
In the case of cell lines in the Database, many of which are established and 
have been in the public domain for years, You agree to preserve, at all times, 
the confidentiality of Data pertaining to identifiable Data Subjects. In 
particular, You shall undertake not to use, or attempt to use the Data to 
deliberately compromise or otherwise infringe the confidentiality of 
information on Data Subjects and their right to privacy.
Updating the Terms of Use
While we will retain our commitment to Open Science, we reserve the right to 
update these Terms of Use at any time. When alterations are inevitable, we will 
attempt to give reasonable notice of any changes by placing a notice on our 
website, but you may wish to check each time you use the website. The date of 
the most recent revision will appear on this, the 
‘DepMap.org Terms of Use’ page. If you do not agree to 
these changes, please do not continue to use our online services. We will also 
make available an archived copy of the previous Terms of Use for comparison.
Indemnification and Disclaimer of Warranties
You are using this Database at Your own risk, and You hereby agree to hold 
Broad and its contributors and their trustees, directors, officers, employees, 
and affiliated investigators 

Re: [Bioc-devel] Error in methylclockData package

[Kern, Lori via Bioc-devel]

I can't reproduce either of these and when I check the resources on the 
builders they load successfully so doesn't appear to be a caching issue.  I 
would expect them to clear up on the next run of the builders.   Let's see what 
happens on the next run and if they continue to error I can look further into 
it.




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Morgan, 
Michael via Bioc-devel 
Sent: Wednesday, June 12, 2024 4:02 AM
To: Dolors Pelegrí ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Error in methylclockData package

Dear BioC Team,
I am receiving a similar error from the MouseThymusAgeing package:
> smart.data <- MouseSMARTseqData(samples = "day1")
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for 
documentation
loading from cache
field not found in version - adding
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for 
documentation
loading from cache
Error: failed to load resource
  name: EH4592
  title: SMARTseq processed counts (day 1)
  reason: unknown input format
Execution halted

Which is subsequently propagating through to errors in miloR on nebbiolo1 only 
(Windows and Mac build servers are unaffected).

Quitting from lines 47-50 [unnamed-chunk-2] (milo_contrasts.Rmd)
Error: processing vignette 'milo_contrasts.Rmd' failed with diagnostics:
failed to load resource
  name: EH4592
  title: SMARTseq processed counts (day 1)
  reason: unknown input format

Is this an issue with caching files?

Regards
Mike Morgan

Pronouns: He/Him
Lecturer
6.17, Institute of Medical Sciences
School of Medicine, Medical Sciences & Nutrition
University of Aberdeen
Foresterhill
Aberdeen
AB25 2ZD
Tel: 01224 437397
Web: 
https://secure-web.cisco.com/1hyURm21NrL7byNpOrxiBZ9a9xz4cDF-n4OMT-AQOSyvTN6cZdOnzmiFftAyFY5_TAfAkcznKKXRhwg85OL8y5rTVUKTkZSnDz8K1qM5AhGqj9NmlSQSagK-Xvbs3-g07pGXOD2gEPTnCTeTPc53ZksF4dO9MmSdZjlGCu2TMh37if3Jzrbadn797r2zkwFjHAb1XIV-kRHSlk_d5FL_yBIo6k0WSmFlmQezPZgEfBkiImWwjod9aUmYieRzOyscrGS3B8YfOlgfumnOan_MpOvkru2IDDo_v1ROoiPGv1j9XNfHnAtahG2q5OgwELJbw/https%3A%2F%2Fwww.abdn.ac.uk%2Fims%2Fresearch%2Fprofiles%2Fmichael.morgan%23research



From: Bioc-devel  on behalf of Dolors 
Pelegr�dolors.pele...@isglobal.org>
Date: Wednesday, 12 June 2024 at 08:38
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Error in methylclockData package
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Dear Bioconductor team,

I have seen that the methylclockData package gives an error when loading
the EH6082 resource, the error is:

get_TestDataset()
see ?methylclockData and browseVignettes('methylclockData') for
documentation
loading from cache
Warning in grepl("RD[ABX][2-9]\n", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\n", magic) : input string 1 is invalid
Warning in grepl("RD[ABX][2-9]\r", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\r", magic) : input string 1 is invalid
Warning in gsub("[\n\r]*", "", magic) :
 unable to translate '<89>HDF
' to a wide string
Error: failed to load resource
 name: EH6082
 title: Test Dataset
 reason: error in evaluating the argument 'x' in selecting a method for
function 'get': input string 1 is invalid
Execution halted


Full Bioconductor Checks:
https://bioconductor.org/checkResults/3.19/data-experiment-LATEST/methylclockData/nebbiolo1-checksrc.html

I don't know the reason or how I could solve it, I've searched the
distribution list and I haven't found any similar error. Could you please
give me some guidance to solve the error?


Best,

--

Dolors Pelegr�is�ioinformatics

*IS**Global*

Barcelona Institute for Global Health

Barcelona Biomedical Research Park (PRBB)

Doctor Aiguader 88

E-08003 Barcelona, 

Re: [Bioc-devel] Error in methylclockData package

[Morgan, Michael via Bioc-devel]

Dear BioC Team,
I am receiving a similar error from the MouseThymusAgeing package:
> smart.data <- MouseSMARTseqData(samples = "day1")
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for 
documentation
loading from cache
field not found in version - adding
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for 
documentation
loading from cache
Error: failed to load resource
  name: EH4592
  title: SMARTseq processed counts (day 1)
  reason: unknown input format
Execution halted

Which is subsequently propagating through to errors in miloR on nebbiolo1 only 
(Windows and Mac build servers are unaffected).

Quitting from lines 47-50 [unnamed-chunk-2] (milo_contrasts.Rmd)
Error: processing vignette 'milo_contrasts.Rmd' failed with diagnostics:
failed to load resource
  name: EH4592
  title: SMARTseq processed counts (day 1)
  reason: unknown input format

Is this an issue with caching files?

Regards
Mike Morgan

Pronouns: He/Him
Lecturer
6.17, Institute of Medical Sciences
School of Medicine, Medical Sciences & Nutrition
University of Aberdeen
Foresterhill
Aberdeen
AB25 2ZD
Tel: 01224 437397
Web: https://www.abdn.ac.uk/ims/research/profiles/michael.morgan#research



From: Bioc-devel  on behalf of Dolors Pelegr� 

Date: Wednesday, 12 June 2024 at 08:38
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Error in methylclockData package
[You don't often get email from dolors.pele...@isglobal.org. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

CAUTION: External email. Ensure this message is from a trusted source and 
exercise caution before clicking links/opening attachments.


Dear Bioconductor team,

I have seen that the methylclockData package gives an error when loading
the EH6082 resource, the error is:

get_TestDataset()
see ?methylclockData and browseVignettes('methylclockData') for
documentation
loading from cache
Warning in grepl("RD[ABX][2-9]\n", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\n", magic) : input string 1 is invalid
Warning in grepl("RD[ABX][2-9]\r", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\r", magic) : input string 1 is invalid
Warning in gsub("[\n\r]*", "", magic) :
 unable to translate '<89>HDF
' to a wide string
Error: failed to load resource
 name: EH6082
 title: Test Dataset
 reason: error in evaluating the argument 'x' in selecting a method for
function 'get': input string 1 is invalid
Execution halted


Full Bioconductor Checks:
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fdata-experiment-LATEST%2FmethylclockData%2Fnebbiolo1-checksrc.html=05%7C02%7Cmichael.morgan%40abdn.ac.uk%7C7cf59c23897b4cdaac7c08dc8ab294ec%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C638537746815147182%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=5xNgHAP7fBa8znh5OFWkf0q1hcDu4L2CRvbgwNDPtFE%3D=0

I don't know the reason or how I could solve it, I've searched the
distribution list and I haven't found any similar error. Could you please
give me some guidance to solve the error?


Best,

--

Dolors Pelegr� Sis�

Bioinformatics

*IS**Global*

Barcelona Institute for Global Health

Barcelona Biomedical Research Park (PRBB)

Doctor Aiguader 88

E-08003 Barcelona, Spain

Tel. +34 93 2147351

dolors.pele...@isglobal.org 

https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.isglobal.org%2F=05%7C02%7Cmichael.morgan%40abdn.ac.uk%7C7cf59c23897b4cdaac7c08dc8ab294ec%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C638537746815163555%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=EaYBHQus6IhhRz7qHzQMzhiU9RpFjyAQhLbyWZ0bK4w%3D=0

--


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[Bioc-devel] Error in methylclockData package

[Dolors Pelegrí]

Dear Bioconductor team,

I have seen that the methylclockData package gives an error when loading
the EH6082 resource, the error is:

get_TestDataset()
see ?methylclockData and browseVignettes('methylclockData') for
documentation
loading from cache
Warning in grepl("RD[ABX][2-9]\n", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\n", magic) : input string 1 is invalid
Warning in grepl("RD[ABX][2-9]\r", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\r", magic) : input string 1 is invalid
Warning in gsub("[\n\r]*", "", magic) :
 unable to translate '<89>HDF
' to a wide string
Error: failed to load resource
 name: EH6082
 title: Test Dataset
 reason: error in evaluating the argument 'x' in selecting a method for
function 'get': input string 1 is invalid
Execution halted


Full Bioconductor Checks:
https://bioconductor.org/checkResults/3.19/data-experiment-LATEST/methylclockData/nebbiolo1-checksrc.html

I don't know the reason or how I could solve it, I've searched the
distribution list and I haven't found any similar error. Could you please
give me some guidance to solve the error?


Best,

-- 

Dolors Pelegrí Sisó

Bioinformatics

*IS**Global*

Barcelona Institute for Global Health

Barcelona Biomedical Research Park (PRBB)

Doctor Aiguader 88

E-08003 Barcelona, Spain

Tel. +34 93 2147351

dolors.pele...@isglobal.org 

www.isglobal.org

-- 


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Re: [Bioc-devel] Deeptarget package

[Kristian Ullrich]

Dear Nguyen,

I have a question related to the data that you use and I just bring it up here 
since I would also like to ask the bioconductor developers, how this can be 
handled properly.

The depmap.org  portal has a clear "Terms and Condition" 
statement that you need to agree on if one uses any of the data that is 
provided by the portal. (See below) So one need to click a "I agree" button to 
stick to their policies.

How have you managed that a user of your package first send this agreement to 
the depmap.org  portal once the user uses data from the 
portal?

Thank you in anticipation

Best regards

Kristian

Here is their policy:

"
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