Re: [R-pkg-devel] Appropriate keyword in help file.

[Rolf Turner]

On 17/04/20 8:41 pm, Uwe Ligges wrote:


keywords are not mandatory.

You can invent your own keywords and use them in

\concept{}
entries.


Thanks Uwe.  This has given me new insight and enlightenment!

cheers,

Rolf

--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

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

Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi Stefano,

Thank you for your share.

Jianhong.

From: Stefano de Pretis 
Date: Friday, April 17, 2020 at 3:18 PM
To: "Jianhong Ou, Ph.D." 
Cc: "bioc-devel@r-project.org" 
Subject: Re: [Bioc-devel] Got timeout for machv2 BUILD

HI,

We solved a similar issue for the INSPEcT package avoiding the parallelization 
in the computation of examples and vignettes. In our case it caused the timeout 
in the Windows environment.

Best,
Stefano

Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. 
mailto:jianhong...@duke.edu>> ha scritto:
Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Got timeout for machv2 BUILD

[Hervé Pagès]

For some reasons the generation of the plots in the vignette is VERY 
slow on machv2. 'R CMD build' actually completed... after 6h! This is 
still under investigation.


Best,
H.


On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:

Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w=



--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Got timeout for machv2 BUILD

[Stefano de Pretis]

HI,

We solved a similar issue for the INSPEcT package avoiding the
parallelization in the computation of examples and vignettes. In our case
it caused the timeout in the Windows environment.

Best,
Stefano

Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. <
jianhong...@duke.edu> ha scritto:

> Hi,
>
> I got timeout for my package motifStack in machv2. But I don't know what
> cuased the issue.
>
> Any help would be greatly appreciated.
>
> Jianhong.
> 
> From: Jianhong Ou, Ph.D.
> Sent: Wednesday, April 15, 2020 7:53 AM
> To: bioc-devel@r-project.org 
> Subject: Got timeout for machv2 BUILD
>
> Hi,
>
> Hope you are doing well.
>
> I got timeout for my package motifStack in machv2. The ellapsedTime is
> 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1
> seconds. I have limited information how to debug.
> Could you share your suggestion? Thank you.
>
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi,

I got timeout for my package motifStack in machv2. But I don't know what cuased 
the issue.

Any help would be greatly appreciated.

Jianhong.

From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org 
Subject: Got timeout for machv2 BUILD

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Nominations for Bioconductor Awards!

[Shepherd, Lori]

Yikes!  Sorry everyone.  That did not format like I thought it would!

Let's recap:


Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of specific criteria.  The deadline for nominations is June 15!
Please see the support site announcement for the links with more information as 
well as the nomination form


https://support.bioconductor.org/p/130094/



Cheers,


Lori Shepherd

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 Shepherd, Lori 

Sent: Friday, April 17, 2020 1:37 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Nominations for Bioconductor Awards!

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of the criteria found at:  
https://secure-web.cisco.com/16tUFz5Y9fiV3wv_pZMAWX8bU4HXzuPOui85-nQ6NxdiPfAd9AGquEUvWb6C-LqP7Yon62aBX8ULdJ8idAqvXqfsS_80ScouEVrCiYdbsjwPmqVEbnGoAIln4gcIdTSltcXdtZqN-SrpDdJ6V6xiB1LzQMUtGkSIQQOK0X37ra7bPWibIkPd2WsBLOzOazj46TnTNdgTH2udZ-EV99vyCBNSU-6hxSFMVD1JaO0xxTHknOWiTg8zKGBRgQfMmGNrGMj9W2UN-O9HYRD-hYd7fveCzPkaRvBnIl3inUB37KohceYdqJ8OfRdo9efhwHjq7MJPEWCxzuPDs4fppgD4R_w/https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I%2Fedit.

Please fill out the nomination form by June 15 : 
https://secure-web.cisco.com/1xiPaCt8pwJs16iKlj7jvaYfJRuP-w9MsvNcZNvld32dl1SpBeEFARwBSlrUJXVOXsfzBL4GIhwPelo-KTR-VUpxPNz9UDtDERtyuf6l1El6gEPTLcOq8K1SF_3MogKWaY6dWWiMfhD43WIzp_VYutvmEhB1vW3JbN9QJkXBkfOC9KUqOPsypOz6Ppj4zSuGJsJt6g2iiPit6j_nrEPTKKHxXHa9zfcfYga9asnMOvYvKeqW4szgu3T-sfVaCWjw2Jl-YIN9jFdGmAmLDc3ki0_x-CCZEyJMLAVFYBpXivjgUUOar5_hewa3T0s6Ift_kLY_qQL5sO2Lia8vQDZ-guw/https%3A%2F%2Fdocs.google.com%2Fforms%2Fd%2Fe%2F1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw%2Fviewform



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/1g37k-69pGF_RmBVN_hfJUIUum16_WvqqMkgsIIQe_Y7t-netnBZMLLRvKVnfy5odntSQzs1q7XcPKYUHF1pxI6n6pzkNyjlZr-8vbYzrj4Pn9sbmsCnBVLgEKsc8P6RI0hKxit_q-XvWb0F7HEo54mKWeMZxSWq5YPAkeQB2GYkDMKI7oLL_jrSaYbL7kyZpkDWmzbsyYnRUnAe4Lfugf77OphRZES3J5U3U6dRRvKSkwmayja3NyByu2m6-ZBXxvMwSYJJUBlmnh8FK_jsJpt4EOBtqX8muETiMzMmOAC8cXJW6FsoQmSiJc1OMQhc3IKyPFFK4tAOCeEVXEdrOzQ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Nominations for Bioconductor Awards!

[Shepherd, Lori]

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project proudly launches the first call for Bioconductor Awards, 
honoring various forms of contributions to the project. Four awardees will be 
selected, each having contributed to the project in an outstanding way based on 
one or more of the criteria found at:  
https://docs.google.com/document/d/1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I/edit.

Please fill out the nomination form by June 15 : 
https://docs.google.com/forms/d/e/1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw/viewform



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] regarding imports github R packages, in new R package's description file

[Krishan Gupta]

Ya so I can include git hub packages, in cran submission policy.
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*




On Fri, Apr 17, 2020 at 10:23 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> This mailing list is for Bioconductor package development and Bioconductor
> submissions not CRAN.
>
> Bioconductor only allows dependencies from CRAN or Bioconductor and does
> not allow github only repositories.
>
> If you indeed meant to submit to CRAN you should check with CRAN's
> submission policies on what they allow:
> https://cran.r-project.org/web/packages/policies.html
>
>
>
> Lori Shepherd
>
> 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
> Krishan Gupta 
> *Sent:* Friday, April 17, 2020 12:45 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] regarding imports github R packages, in new R
> package's description file
>
> I want to build a new package to submit on CRAN, but my package has
> two dependencies harmony and iCTC which are available only on github.
> So now I can import these dependencies in description files.
> Imports:
> BiocManager,
> caret,
> klaR,
> randomForest,
> gbm,
> devtools,
> harmony,
> iCTC
> I did as shown above but I got an error,
> checking package dependencies ... ERROR
> Packages required but not available: 'harmony', 'iCTC'
> How can I resolve the error?
> *Thanks and Regards*
>
> *Krishan Gupta*
>
> *PhD16008PhD Scholar*
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://secure-web.cisco.com/1X7ntaZmDXfDBfzNmUV9Nn9nKY4Jf-6Xxjn3qQBu2ZaTpsT0kOgvP4ECgYOnsCzNJTEnBPotG0xHaX-4V2XjwJaBOvTpG5wRCgo6efcdZ1mNxtE9PBl4bxPEyX0tjV_wd5iBlgj1P5LTngGt_duprz0GJIpx5VXr1WVZ9tWC25wqY0B6cVCRkzDIoYJljiaxEzPncJSy2juwDmrYocyOcyTtydHeUEDV6JIuoKboTe7INnSLdVY0YPID2GCKwLWZ4jbEN8qCBKz1XsEXDeHRkfBaVE_B3svrDfI6VDWRpDC9T3EofkuMVMc64Z3XGuFqBy8WTm3_Qbd66QbJJKicKUw/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] regarding imports github R packages, in new R package's description file

[Shepherd, Lori]

This mailing list is for Bioconductor package development and Bioconductor 
submissions not CRAN.

Bioconductor only allows dependencies from CRAN or Bioconductor and does not 
allow github only repositories.

If you indeed meant to submit to CRAN you should check with CRAN's submission 
policies on what they allow:
https://cran.r-project.org/web/packages/policies.html




Lori Shepherd

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 Krishan Gupta 

Sent: Friday, April 17, 2020 12:45 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] regarding imports github R packages, in new R package's 
description file

I want to build a new package to submit on CRAN, but my package has
two dependencies harmony and iCTC which are available only on github.
So now I can import these dependencies in description files.
Imports:
BiocManager,
caret,
klaR,
randomForest,
gbm,
devtools,
harmony,
iCTC
I did as shown above but I got an error,
checking package dependencies ... ERROR
Packages required but not available: 'harmony', 'iCTC'
How can I resolve the error?
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/1X7ntaZmDXfDBfzNmUV9Nn9nKY4Jf-6Xxjn3qQBu2ZaTpsT0kOgvP4ECgYOnsCzNJTEnBPotG0xHaX-4V2XjwJaBOvTpG5wRCgo6efcdZ1mNxtE9PBl4bxPEyX0tjV_wd5iBlgj1P5LTngGt_duprz0GJIpx5VXr1WVZ9tWC25wqY0B6cVCRkzDIoYJljiaxEzPncJSy2juwDmrYocyOcyTtydHeUEDV6JIuoKboTe7INnSLdVY0YPID2GCKwLWZ4jbEN8qCBKz1XsEXDeHRkfBaVE_B3svrDfI6VDWRpDC9T3EofkuMVMc64Z3XGuFqBy8WTm3_Qbd66QbJJKicKUw/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] regarding imports github R packages, in new R package's description file

[Krishan Gupta]

I want to build a new package to submit on CRAN, but my package has
two dependencies harmony and iCTC which are available only on github.
So now I can import these dependencies in description files.
Imports:
BiocManager,
caret,
klaR,
randomForest,
gbm,
devtools,
harmony,
iCTC
I did as shown above but I got an error,
checking package dependencies ... ERROR
Packages required but not available: 'harmony', 'iCTC'
How can I resolve the error?
*Thanks and Regards*

*Krishan Gupta*

*PhD16008PhD Scholar*

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Question for building error

[Shepherd, Lori]

 The current ERROR
"polygon edge not found"
is  a Bioconductor builder issue having to do with fonts not being found.

We are working on a solution but for now you can ignore.


Lori Shepherd

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 Yang,Peng 

Sent: Friday, April 17, 2020 12:26 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Question for building error

Dear Bioconductor team,

I met a building errors for our package, DeMixT 1.3.6, under Mac OS planform on 
Apr 16th. And it shows failed to create vignettes.

Since R 4.0.0 no longer support OpenMP, I disabled OpenMP under Mac version and 
it passed the building process after I committed the change on Apr 12th.

However, I did not see the specific reason why failed to create vignettes this 
time, may I ask how can I fix this issue?

Thank you so much,
Peng

___
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/12QF5cwOsqhhqNHfZucPE7hNQHMg29DcyIqYCEu8v56LL5qxmnCV9TCVy2j_b-U4OVn3LyOqWCRyTuvFdQj_5QY3w7JUcoJftgLv8G0avlSOrctzdbq2qbVPB12NUDXOcxollfdc_L_zvEq-398S7l8u6ymuRLUdrP7XomQsL1UeNqq00q2Ige7Olc0ocT1Vycv5ZwjMskHW1DGQxNJuemSXFhgyRj2KldZXYOKlSKjg5eO-iIhP8VNOepkmLz2XhKQ_PwKX8SVt2B8b2HTr7x7bRXUpw6mkXgnlA1rsrC7D3LEd_5QtUnYb2iITpdBy6Sf4MhJKGeifbJF1GPbrU2Q/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Question for building error

[Yang,Peng]

Dear Bioconductor team,

I met a building errors for our package, DeMixT 1.3.6, under Mac OS planform on 
Apr 16th. And it shows failed to create vignettes.

Since R 4.0.0 no longer support OpenMP, I disabled OpenMP under Mac version and 
it passed the building process after I committed the change on Apr 12th.

However, I did not see the specific reason why failed to create vignettes this 
time, may I ask how can I fix this issue?

Thank you so much,
Peng

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Rd] Demo for linking native routines between R packages

[Jan Gorecki]

Dirk, Thank you for a comprehensive set of resources on that.

Yet, I think the proposal here make sense.
Packages you mentioned are real-life package. It would be way easier
to learn from a package that is meant to only show this single thing.
For the same reason I think it also make sense to have a "hello world
from C" package linked from WRE. All those native routines
registration, the proper way, is not really that obvious. It would be
much easier to learn from a package that doesn't have any other logic.

Best wishes,
Jan Gorecki

On Fri, Apr 17, 2020 at 3:32 PM Zhang, Jitao David via R-devel
 wrote:
>
> Dear Davis and Dirk,
>
> Thank you very much for the suggestions, which are very valuable and
> helpful.
>
> I will add references to prior examples, document my project with the clear
> step-by-step-style document of Davis's project, and come back again to the
> mailing list.
>
> Best wishes,
> David
>
> On Fri, Apr 17, 2020 at 3:40 PM Dirk Eddelbuettel  wrote:
>
> >
> > Jitao,
> >
> > Thanks for writing this up.
> >
> > You could add a section on 'prior art' and references.  The canonical
> > example
> > always was (c.f. Writing R Extensions)
> >
> >   lme4 <-> Matrix
> >
> > which was followed early by the CRAN packages
> >
> >   zoo <-> xts
> >
> > upon which I built
> >
> >   xts <-> RcppXts
> >
> > with a write-up (from 2013 !!) here:
> > https://gallery.rcpp.org/articles/accessing-xts-api/
> >
> > Via private mail, I helped then-maintainer Vincent connect expm:
> >
> >   expm <-> Matrix
> >
> > and built two packages on CRAN _for the very purpose of exporting API
> > functions to be called_ (which in both cases are from base R as R Core is
> > very careful not get tied into exporting APIs, which is both understandable
> > and a source of added difficulty for us package writers)
> >
> >   RApiDatetime
> >   RApiSerialize
> >
> > The latter one is use by my RcppRedis package, Travers' very nice qs
> > package
> > and Tim's rpg package.
> >
> > To my reading, the R Community is drifting more and more towards collective
> > amnesia where prior work is (pick any one the following)
> >
> >  - ignored altogether
> >  - reinvented by another package
> >  - shadowed by another package
> >
> > rather than extended, improved and/or cited.  That is a collective loss for
> > all of us. It would be nice if you could stear back a little and reference
> > prior related work. My apologies to other packages in this area I have not
> > listed. We really should have a common reference for this.
> >
> > Cheers, Dirk
> >
> > --
> > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> >
>
>
> --
>
> *Dr. Jitao David Zhang | 张继涛 | A Computational Biologist in Drug Discovery*
>
> *Building 93/3.38, **Tel +41 61 688 62 51*
>
> *Roche Pharmaceutical Research and Early Development
> (pRED) | Pharmaceutical Sciences, BiOmics, BEDA (see 
> http://**go.roche.com/BEDA
> **) | Roche Innovation Center Basel | F.
> Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland*
> *Core working hours - No Meetings: Mo/8:30-16:00; Tu/8:30-17:00;
> We/8:30-16:00; Th/9:00-11:30*
> *Available for meetings: Mo/16:00-17:00; We/16:00-17:00**; Th/11:00-17:00;
> Fr/8:00-10:00*
>
> Confidentiality Note: This message is intended only for ...{{dropped:13}}
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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

Re: [Rd] Demo for linking native routines between R packages

[Zhang, Jitao David via R-devel]

Dear Davis and Dirk,

Thank you very much for the suggestions, which are very valuable and
helpful.

I will add references to prior examples, document my project with the clear
step-by-step-style document of Davis's project, and come back again to the
mailing list.

Best wishes,
David

On Fri, Apr 17, 2020 at 3:40 PM Dirk Eddelbuettel  wrote:

>
> Jitao,
>
> Thanks for writing this up.
>
> You could add a section on 'prior art' and references.  The canonical
> example
> always was (c.f. Writing R Extensions)
>
>   lme4 <-> Matrix
>
> which was followed early by the CRAN packages
>
>   zoo <-> xts
>
> upon which I built
>
>   xts <-> RcppXts
>
> with a write-up (from 2013 !!) here:
> https://gallery.rcpp.org/articles/accessing-xts-api/
>
> Via private mail, I helped then-maintainer Vincent connect expm:
>
>   expm <-> Matrix
>
> and built two packages on CRAN _for the very purpose of exporting API
> functions to be called_ (which in both cases are from base R as R Core is
> very careful not get tied into exporting APIs, which is both understandable
> and a source of added difficulty for us package writers)
>
>   RApiDatetime
>   RApiSerialize
>
> The latter one is use by my RcppRedis package, Travers' very nice qs
> package
> and Tim's rpg package.
>
> To my reading, the R Community is drifting more and more towards collective
> amnesia where prior work is (pick any one the following)
>
>  - ignored altogether
>  - reinvented by another package
>  - shadowed by another package
>
> rather than extended, improved and/or cited.  That is a collective loss for
> all of us. It would be nice if you could stear back a little and reference
> prior related work. My apologies to other packages in this area I have not
> listed. We really should have a common reference for this.
>
> Cheers, Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>


-- 

*Dr. Jitao David Zhang | 张继涛 | A Computational Biologist in Drug Discovery*

*Building 93/3.38, **Tel +41 61 688 62 51*

*Roche Pharmaceutical Research and Early Development
(pRED) | Pharmaceutical Sciences, BiOmics, BEDA (see http://**go.roche.com/BEDA
**) | Roche Innovation Center Basel | F.
Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland*
*Core working hours - No Meetings: Mo/8:30-16:00; Tu/8:30-17:00;
We/8:30-16:00; Th/9:00-11:30*
*Available for meetings: Mo/16:00-17:00; We/16:00-17:00**; Th/11:00-17:00;
Fr/8:00-10:00*

Confidentiality Note: This message is intended only for ...{{dropped:13}}

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

Re: [Rd] How to find detritis rejected by "R CMD check" on Debian?

[Ivan Krylov]

This should probably have been addressed to R-pkg-devel, not Rd.

On Fri, 17 Apr 2020 09:14:44 -0500
Spencer Graves  wrote:

> Found the following files/directories:
>    ‘fdaMatlabPath.m’

This is not the "detritus in the temp directory"; the message is related
to the previous line in the log:

>> * checking for non-standard things in the check directory ... NOTE

I searched the repo for the file name in question and got a few hits
[1]. R CMD check runs the \examples{}, including those in
man/fdaMatlabPath.Rd. The function from R/fdaMatlabPath.R, called from
the examples, writes a file in the current directory [2], which
happens to be the check directory during R CMD check. In order to
conform to the CRAN policy, the function should receive the target file
name as a parameter instead, and the example should pass a file path
somewhere in tempdir().

-- 
Best regards,
Ivan

[1] https://github.com/JamesRamsay5/fda/search?q=fdaMatlabPath.m

[2]
https://github.com/JamesRamsay5/fda/blob/ca077f87f69efcfc434eeea39f4fff6136fcfaeb/R/fdaMatlabPath.R#L33

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

Re: [Rd] How to find detritis rejected by "R CMD check" on Debian?

[Duncan Murdoch]

On 17/04/2020 10:14 a.m., Spencer Graves wrote:

Hello:


    How can someone help me find and fix the following, contained in
00check.log on Debian for "https://github.com/JamesRamsay5/fda":


NOTE
Found the following files/directories:
    ‘fdaMatlabPath.m’
* checking for detritus in the temp directory ... OK


    See:



That would have resulted from running the example in ?fdaMatlabPath.

You could stop that from happening in a test by using

if (interactive())
  fdaMatlabPath()

but it still potentially wipes out a user's file.  Can't you ask the 
user for the filename to write to, and have the example write to 
tempdir() instead of the current directory?


Duncan Murdoch

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

Re: [Rd] How to find detritis rejected by "R CMD check" on Debian?

[Dirk Eddelbuettel]

Spencer,

On 17 April 2020 at 09:14, Spencer Graves wrote:
|    How can someone help me find and fix the following, contained in 
| 00check.log on Debian for "https://github.com/JamesRamsay5/fda":
| 
| NOTE
| Found the following files/directories:
|    ‘fdaMatlabPath.m’
| * checking for detritus in the temp directory ... OK

Obviously from your package, so you could use a tool like 'grep' locally.

We can just turn to Gabor's handy CRAN mirror at GitHub, open the
repo at github.com/cran/fda and enter the filename in the search.
Second hit is

  writeLines(d2a, 'fdaMatlabPath.m')

which is obviously a file _you write_ and not not delete just as
the package checking diagnostic suggests. As frequently suggested here or on
r-package-devel (where this belonged), prefix paths by `tempdir()` or change
there first.

Dirk



-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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

[Rd] How to find detritis rejected by "R CMD check" on Debian?

[Spencer Graves]

Hello:


  How can someone help me find and fix the following, contained in 
00check.log on Debian for "https://github.com/JamesRamsay5/fda":



NOTE
Found the following files/directories:
  ‘fdaMatlabPath.m’
* checking for detritus in the temp directory ... OK


  See:


https://win-builder.r-project.org/incoming_pretest/fda_5.1.3_20200416_225207/Debian/00check.log


  Thanks,
  Spencer Graves

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

Re: [Rd] Demo for linking native routines between R packages

[Davis Vaughan]

I tried to do this a little. I mentioned xts along with:
bdsmatrix https://github.com/cran/bdsmatrix
cleancall https://github.com/r-lib/cleancall/

On Fri, Apr 17, 2020 at 9:40 AM Dirk Eddelbuettel  wrote:

>
> Jitao,
>
> Thanks for writing this up.
>
> You could add a section on 'prior art' and references.  The canonical
> example
> always was (c.f. Writing R Extensions)
>
>   lme4 <-> Matrix
>
> which was followed early by the CRAN packages
>
>   zoo <-> xts
>
> upon which I built
>
>   xts <-> RcppXts
>
> with a write-up (from 2013 !!) here:
> https://gallery.rcpp.org/articles/accessing-xts-api/
>
> Via private mail, I helped then-maintainer Vincent connect expm:
>
>   expm <-> Matrix
>
> and built two packages on CRAN _for the very purpose of exporting API
> functions to be called_ (which in both cases are from base R as R Core is
> very careful not get tied into exporting APIs, which is both understandable
> and a source of added difficulty for us package writers)
>
>   RApiDatetime
>   RApiSerialize
>
> The latter one is use by my RcppRedis package, Travers' very nice qs
> package
> and Tim's rpg package.
>
> To my reading, the R Community is drifting more and more towards collective
> amnesia where prior work is (pick any one the following)
>
>  - ignored altogether
>  - reinvented by another package
>  - shadowed by another package
>
> rather than extended, improved and/or cited.  That is a collective loss for
> all of us. It would be nice if you could stear back a little and reference
> prior related work. My apologies to other packages in this area I have not
> listed. We really should have a common reference for this.
>
> Cheers, Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

[[alternative HTML version deleted]]

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

Re: [Rd] Demo for linking native routines between R packages

[Dirk Eddelbuettel]

Jitao,

Thanks for writing this up.

You could add a section on 'prior art' and references.  The canonical example
always was (c.f. Writing R Extensions)

  lme4 <-> Matrix

which was followed early by the CRAN packages

  zoo <-> xts
  
upon which I built

  xts <-> RcppXts
  
with a write-up (from 2013 !!) here: 
https://gallery.rcpp.org/articles/accessing-xts-api/

Via private mail, I helped then-maintainer Vincent connect expm:

  expm <-> Matrix

and built two packages on CRAN _for the very purpose of exporting API
functions to be called_ (which in both cases are from base R as R Core is
very careful not get tied into exporting APIs, which is both understandable
and a source of added difficulty for us package writers)

  RApiDatetime
  RApiSerialize

The latter one is use by my RcppRedis package, Travers' very nice qs package
and Tim's rpg package.

To my reading, the R Community is drifting more and more towards collective
amnesia where prior work is (pick any one the following)

 - ignored altogether
 - reinvented by another package
 - shadowed by another package
 
rather than extended, improved and/or cited.  That is a collective loss for
all of us. It would be nice if you could stear back a little and reference
prior related work. My apologies to other packages in this area I have not
listed. We really should have a common reference for this.

Cheers, Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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

Re: [Rd] Demo for linking native routines between R packages

[Zhang, Jitao David via R-devel]

Dear Davis,

Thank you a lot for sharing this, and I am happy that I was not the only
one who need to do it once to learn:)

I proposed to add my repo to the manual. I think it makes sense to add both
of ours, if possible, or we could merge them together and add that to the
manual.

Long-term URL stability is apparently an issue, but I think we may find a
solution there.

Anyway, thanks a lot for sharing!

Best wishes,
David

On Fri, Apr 17, 2020 at 3:12 PM Davis Vaughan  wrote:

> Nice David! I also wrote up something similar a little while back
> https://github.com/DavisVaughan/cexport
>
> -Davis
>
> On Fri, Apr 17, 2020 at 7:09 AM Zhang, Jitao David via R-devel <
> r-devel@r-project.org> wrote:
>
>> Dear R developers,
>>
>> I want to advertise a small project for the educational purpose to show
>> people how to link native routines.
>>
>> In R programming, we need to link to native routines in C, C++, or Fortran
>> from the R environment. In most cases, the linking works within one
>> package, namely the R code in a package calls the native code in the same
>> package.
>>
>> This is not necessarily always the case. Sometimes, a piece of C or R code
>> in a package needs to link to native routines in another R package.
>> The *Writing
>> R Extensions manual describes *how to do this in the section *Linking to
>> native routines in other packages*. However, some details were not clear
>> to
>> me, and I could find no demo dedicated to this purpose.
>>
>> Therefore, I decided to build a demo that is available at my Github
>> repository Accio/demo-linking-native
>> . Besides implementing the
>> linking of native routines between R packages, the project also documents
>> issues that I met and how I solved them.
>>
>> In case you find the demo useful or you have suggestions on how to improve
>> it, please let me know. I wonder whether you think it is a good idea to
>> suggest to the core team to add the project to the manual so that other
>> people can understand the process better with the demo.
>>
>> In case of questions, let me know.
>>
>> Best wishes,
>> David
>>
>> --
>>
>> *Dr. Jitao David Zhang | 张继涛 | A Computational Biologist in Drug
>> Discovery*
>>
>> *Building 93/3.38, **Tel +41 61 688 62 51*
>>
>> *Roche Pharmaceutical Research and Early Development
>> (pRED) | Pharmaceutical Sciences, BiOmics, BEDA (see http://**
>> go.roche.com/BEDA
>> **) | Roche Innovation Center Basel | F.
>> Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland*
>> *Core working hours - No Meetings: Mo/8:30-16:00; Tu/8:30-17:00;
>> We/8:30-16:00; Th/9:00-11:30*
>> *Available for meetings: Mo/16:00-17:00; We/16:00-17:00**; Th/11:00-17:00;
>> Fr/8:00-10:00*
>>
>> Confidentiality Note: This message is intended only for ...{{dropped:13}}
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>

-- 

*Dr. Jitao David Zhang | 张继涛 | A Computational Biologist in Drug Discovery*

*Building 93/3.38, **Tel +41 61 688 62 51*

*Roche Pharmaceutical Research and Early Development
(pRED) | Pharmaceutical Sciences, BiOmics, BEDA (see http://**go.roche.com/BEDA
**) | Roche Innovation Center Basel | F.
Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland*
*Core working hours - No Meetings: Mo/8:30-16:00; Tu/8:30-17:00;
We/8:30-16:00; Th/9:00-11:30*
*Available for meetings: Mo/16:00-17:00; We/16:00-17:00**; Th/11:00-17:00;
Fr/8:00-10:00*

Confidentiality Note: This message is intended only for ...{{dropped:13}}

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

Re: [Rd] Demo for linking native routines between R packages

[Davis Vaughan]

Nice David! I also wrote up something similar a little while back
https://github.com/DavisVaughan/cexport

-Davis

On Fri, Apr 17, 2020 at 7:09 AM Zhang, Jitao David via R-devel <
r-devel@r-project.org> wrote:

> Dear R developers,
>
> I want to advertise a small project for the educational purpose to show
> people how to link native routines.
>
> In R programming, we need to link to native routines in C, C++, or Fortran
> from the R environment. In most cases, the linking works within one
> package, namely the R code in a package calls the native code in the same
> package.
>
> This is not necessarily always the case. Sometimes, a piece of C or R code
> in a package needs to link to native routines in another R package.
> The *Writing
> R Extensions manual describes *how to do this in the section *Linking to
> native routines in other packages*. However, some details were not clear to
> me, and I could find no demo dedicated to this purpose.
>
> Therefore, I decided to build a demo that is available at my Github
> repository Accio/demo-linking-native
> . Besides implementing the
> linking of native routines between R packages, the project also documents
> issues that I met and how I solved them.
>
> In case you find the demo useful or you have suggestions on how to improve
> it, please let me know. I wonder whether you think it is a good idea to
> suggest to the core team to add the project to the manual so that other
> people can understand the process better with the demo.
>
> In case of questions, let me know.
>
> Best wishes,
> David
>
> --
>
> *Dr. Jitao David Zhang | 张继涛 | A Computational Biologist in Drug Discovery*
>
> *Building 93/3.38, **Tel +41 61 688 62 51*
>
> *Roche Pharmaceutical Research and Early Development
> (pRED) | Pharmaceutical Sciences, BiOmics, BEDA (see http://**
> go.roche.com/BEDA
> **) | Roche Innovation Center Basel | F.
> Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland*
> *Core working hours - No Meetings: Mo/8:30-16:00; Tu/8:30-17:00;
> We/8:30-16:00; Th/9:00-11:30*
> *Available for meetings: Mo/16:00-17:00; We/16:00-17:00**; Th/11:00-17:00;
> Fr/8:00-10:00*
>
> Confidentiality Note: This message is intended only for ...{{dropped:13}}
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

[[alternative HTML version deleted]]

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

Re: [Bioc-devel] Transfer Maintainership of a Package ClusterJudge

[Turaga, Nitesh]

Hi Adrian, 

You have to first activate your BiocCredentials account 
https://git.bioconductor.org/BiocCredentials/. 

Once you activate your account, you should be able to log in and add some SSH 
keys. You'll be given access to the system once you add your SSH keys. 

Also, please change the email address in the DESCRIPTION file of the package.

Should you have any questions on how to manage your repository, please check 
http://bioconductor.org/developers/how-to/git/.

Best,

Nitesh 

On 4/16/20, 3:03 PM, "Bioc-devel on behalf of Adrian Pasculescu" 
 wrote:

Hi ,

I am the original maintainer of the ClusterJudge but my original email
address (pascule...@lunenfeld.ca) is no longer valid.
I need to continue maintaining the package under the new email address:
a.pascule...@gmail.com
I created a new github repo: 
https://secure-web.cisco.com/1sCaxjhRuZo99ozJCU75a7QnU1lswB29hIn0hqXYOOmXbgcoUdfMsNaSCUiaujM5gog_RQ1pJYSpkT1uMQwp2ppyjUcoAnd-TAc0JmPaR1paAqVX01mx7JBimm5taYpBaOmJlELUk-gs13gE29icKPvpzVOG6ZQ6jcIA-G7rT6roMO_qrZXfjG2EuoDcW9aIFYgp2X6ph7MZCB1Hyp8SumsT197WMNa_qGUFJ4QmPekX14fj8gNH1_1xx-yp-tkHQe8Ts2E88-EBYJdxwIoT3DLxRWbfe4E4UO1FDW6KbNsuxBIZi6_PHm0h8YJxO3hSkZxgfa2jnmufgid_z9eFTTg/https%3A%2F%2Fgithub.com%2Fapasculescu%2FClusterJudge
However I cannot update the package as I am not recognized by bioconductor.

I cannot re-register to bioconductor under the new email address since the
original DESCRIPTION of the ClusterJudge (and the bioconductor database of
maintainers) contains my old and inactive email address.

Can you please help and indicate what are my next steps,
Many thanks,
Adrian Pasculescu
(see also some previous email related to the subject)

-- Forwarded message -
De : Hervé Pagès 
Date: mer. 15 avr. 2020 à 22:29
Subject: Re: ClusterJudge bioconductor package
To: Adrian Pasculescu 
Cc: Frederick Roth 


Hi Adrian,

You're looking at the wrong place. The web hook is for triggering builds
during the package submission process. We're way past this ;-)

One the package is accepted and added to git.bioconductor.org, you need
to push your changes to git.bioconductor.org in addition to pushing them
to your GitHub repo. See our documentation here

https://secure-web.cisco.com/1tt0anS6Ry8ADw1Qx4iLhGwW5C4oOroYjPEnwi2d1gnYurIieI1wDpHup0lBDQc29xE01gZkqZl-WQ9xtpjd7cdNCK5gpkHtaYP_bBgnj8OyWa_awl1BVqfjLcScn4RhijJWETu4IKRofCH4WTJaCTOjcfXjxfou1U-2BxPLfbWGNo_-Si-rL1Yyw3M5zeqPQWqTAbJRtC5sgcprXigibqGvWmSGJ6TgY2cPIgLxIhGsFW12GgdRTH-d43qQOkw4bFxl9PYen_QWzTbDoYgmMoNlpevupHksXGkIq4-WUcWow2d15W1yZWnfK5BlVVK1FDAANkkochiV6fwV-936lRl-_mvFAoSiUPr8DD32TLdk/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2F
 for the details.

Any further question related to how to maintain/update your package
should be asked on the bioc-devel mailing list.

Thanks,
H.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list

https://secure-web.cisco.com/1FSR8Sz3lcAlO_CfKTJFpuqDBQgMxOAyE-rlHnmBLnwgDSIzEiS0zwUCmVA5xJJGwe5r1OxxE4W82H8QCyCPYJSnL2-GO0bjkE2FqfqwuT5X-w_61mhxovIOoBH5kr0epla_QPVQdWUKRj3tZy0FJ0CZt4EVOac7VsPWx_FYlJFblGE-UgU1SnSRFgJDF1k6QkLt5t9A-E10t9P305Q0TOsWE6YMPtJ-4U29-LTPg87U5Y4te9nbz3vkSAGaouKtJ6UkY6R8M2v1uhewAbdhbGjd8OiY09QfNG_L5iTn81xfpI28ubbNPDdL1LhU-E97DmxpILZh8ioIZ1jlfrK8vKQ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel




This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

[Shepherd, Lori]

Firstly,  macv2 is R devel so to accurately test  you should be using R 4.0.0  
with Bioc 3.11 packages.

However, this ERROR is  a Bioconductor builder issue having to do with fonts 
not being found.  We are working on a solution but for now you can ignore.


Lori Shepherd

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 Koustav Pal 

Sent: Friday, April 17, 2020 8:18 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

Hi,

My package, HiCBricks is showing failed builds on the Mac builder macv2.

I have checked the packaged on my Mac running Catalina 10.15 and R 3.6.1. The 
build is ok.

Also, GitHub travis-ci build reports are fine.

The error message is �polygon edge not found�

Any help is much appreciated.

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu




[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/1IrFIOKst3BtpIPzK9DHMF2B1Ca1D6I6tx12OEbHO6gtNrqssIKqv-Rgi7XH2v7Md6Z7jMPA5gfYg-jeAeZ_Qdz2Z1IyoTgpnC20212TvsgthdsqnPfud4RjywPFsAtlf-w9CzoWaMl2JYCWssGnAYsglVJppHPlT3hIOPnYWFziQ79PTXylPvziRrANN-XRg7-mDVGTtRReyGS0laO47qDhUye1ClpI6VzW18tOnv9n_3XxUZR1ebpr5cI1hPAjFeqY02bhFfuBE6r9mjMqJKdbnaDsHLu0LHeRiYR9uL4ZHNLwQkv_QV7k6iB3PHHuR0zMfa8rX3QqO00nK1pRpRw/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

[Koustav Pal]

Hi,

My package, HiCBricks is showing failed builds on the Mac builder macv2.

I have checked the packaged on my Mac running Catalina 10.15 and R 3.6.1. The 
build is ok.

Also, GitHub travis-ci build reports are fine. 

The error message is “polygon edge not found”

Any help is much appreciated.

Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu




[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Rd] Demo for linking native routines between R packages

[Zhang, Jitao David via R-devel]

Dear R developers,

I want to advertise a small project for the educational purpose to show
people how to link native routines.

In R programming, we need to link to native routines in C, C++, or Fortran
from the R environment. In most cases, the linking works within one
package, namely the R code in a package calls the native code in the same
package.

This is not necessarily always the case. Sometimes, a piece of C or R code
in a package needs to link to native routines in another R package.
The *Writing
R Extensions manual describes *how to do this in the section *Linking to
native routines in other packages*. However, some details were not clear to
me, and I could find no demo dedicated to this purpose.

Therefore, I decided to build a demo that is available at my Github
repository Accio/demo-linking-native
. Besides implementing the
linking of native routines between R packages, the project also documents
issues that I met and how I solved them.

In case you find the demo useful or you have suggestions on how to improve
it, please let me know. I wonder whether you think it is a good idea to
suggest to the core team to add the project to the manual so that other
people can understand the process better with the demo.

In case of questions, let me know.

Best wishes,
David

-- 

*Dr. Jitao David Zhang | 张继涛 | A Computational Biologist in Drug Discovery*

*Building 93/3.38, **Tel +41 61 688 62 51*

*Roche Pharmaceutical Research and Early Development
(pRED) | Pharmaceutical Sciences, BiOmics, BEDA (see http://**go.roche.com/BEDA
**) | Roche Innovation Center Basel | F.
Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland*
*Core working hours - No Meetings: Mo/8:30-16:00; Tu/8:30-17:00;
We/8:30-16:00; Th/9:00-11:30*
*Available for meetings: Mo/16:00-17:00; We/16:00-17:00**; Th/11:00-17:00;
Fr/8:00-10:00*

Confidentiality Note: This message is intended only for ...{{dropped:13}}

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

Re: [R-pkg-devel] Appropriate keyword in help file.

[Uwe Ligges]

keywords are not mandatory.

You can invent your own keywords and use them in

\concept{}
entries.

Best,
Uwe Ligges



On 17.04.2020 02:57, Jeff Newmiller wrote:

You can get away with a lot if you are not distributing your package. But I 
usually try to satisfy R CMD check at least.

On April 16, 2020 5:50:04 PM PDT, Rolf Turner  wrote:


On 17/04/20 12:14 pm, Duncan Murdoch wrote:


On 16/04/2020 8:12 p.m., Rolf Turner wrote:


I'm writing a package (just for my own use, for the time being at

least)

that contains a function for estimating the parameters of a
distribution.  The function is essentially a wrapper for fitdistr()

from

the MASS package.

When I looked at RShowDoc("KEYWORDS"), I could not find an

appropriate

keyword to use in the help file for this function.  There's "htest &
Statistical Inference", but that's not right, since this function is
about estimation, not hypothesis testing.  I'd hoped that there'd be

a

keyword "estimation" (or "point estimation") or something like that,

but

there isn't.

I guess I can use "utilities" (???) or "misc", but these seem a bit
unsatisfactory.

Can anyone suggest a better idea?


Don't use any keyword. When was the last time you searched on one?



I have *never* in my life searched on a keyword! :-)

I just thought that it was an Immutable Law of the Universe that a help

file had to have at least one keyword, and that the R Gods would rain
fire and brimstone down upon one's head if no keyword was supplied.

In a similar vein:  would the R Gods allow me to make up my own keyword

rather than choosing from those listed by RShowDoc("KEYWORDS")?

Thanks.

cheers,

Rolf




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

Re: [Rd] suggestion: "." in [lsv]apply()

[Sokol Serguei]

Thanks Simon,

Now, I see better your argument.

Le 16/04/2020 à 22:48, Simon Urbanek a écrit :
... I'm not arguing against the principle, I'm arguing about your 
particular proposal as it is inconsistent and not general.
This sounds promising for me. May be in a (new?) future, R core will 
come with a correct proposal for this principle?
Meanwhile, to avoid substitute(), I'll look on the side of formula 
syntax deviation as your example x ~> i + x suggested.


Best,
Serguei.

Personally, I find the current syntax much clearer and readable 
(defining anything by convention like . being the function variable 
seems arbitrary and "dirty" to me), but if you wanted to define a 
shorter syntax, you could use something like x ~> i + x. That said, I 
really don't see the value of not using function(x) [especially these 
days when people are arguing for long variable names with the 
justification that IDEs do all the work anyway], but as I said, my 
argument was against the actual proposal, not general ideas about 
syntax improvement. Cheers, Simon
On 17/04/2020, at 3:53 AM, Sokol Serguei  
wrote: Simon, Thanks for replying. In what follows I won't try to 
argue (I understood that you find this a bad idea) but I would like 
to make clearer some of your point for me (and may be for others). Le 
16/04/2020 à 16:48, Simon Urbanek a écrit :

Serguei,
On 17/04/2020, at 2:24 AM, Sokol Serguei  
wrote: Hi, I would like to make a suggestion for a small syntactic 
modification of FUN argument in the family of functions 
[lsv]apply(). The idea is to allow one-liner expressions without 
typing "function(item) {...}" to surround them. The argument to the 
anonymous function is simply referred as ".". Let take an example. 
With this new feature, the following call sapply(split(mtcars, 
mtcars$cyl), function(d) summary(lm(mpg ~ wt, d))$r.squared) # 4 6 
8 #0.5086326 0.4645102 0.4229655 could be rewritten as 
sapply(split(mtcars, mtcars$cyl), summary(lm(mpg ~ wt, 
.))$r.squared) "Not a big saving in typing" you can say but 
multiplied by the number of [lsv]apply usage and a neater look, I 
think, the idea merits to be considered. 
It's not in any way "neater", not only is it less readable, it's 
just plain wrong. What if the expression returned a function? 
do you mean like in l=sapply(1:3, function(i) function(x) i+x) 
l[[1]](3) # 4 l[[2]](3) # 5 This is indeed a corner case but a pair 
of () or {} can keep wsapply() in course: l=wsapply(1:3, (function(x) 
.+x)) l[[1]](3) # 4 l[[2]](3) # 5
How do you know that you don't want to apply the result of the call? 
A small example (if it is significantly different from the one above) 
would be very helpful for me to understand this point.
For the same reason the implementation below won't work - very often 
you just pass a symbol that evaluates to a function and always en 
expression that returns a function and there is no way to 
distinguish that from your new proposed syntax. 

Even with () or {} around such "dotted" expression? Best, Serguei.
When you feel compelled to use substitute() you should hear alarm 
bells that something is wrong ;). You can certainly write a new 
function that uses a different syntax (and I'm sure someone has 
already done that in the package space), but what you propose is 
incompatible with *apply in R (and very much not R syntax). Cheers, 
Simon
To illustrate a possible implementation, I propose a wrapper 
example for sapply(): wsapply=function(l, fun, ...) { 
s=substitute(fun) if (is.name(s) || is.call(s) && 
s[[1]]==as.name("function")) { sapply(l, fun, ...) # legacy call } 
else { sapply(l, function(d) eval(s, list(.=d)), ...) } } Now, we 
can do: wsapply(split(mtcars, mtcars$cyl), summary(lm(mpg ~ wt, 
.))$r.squared) or, traditional way: wsapply(split(mtcars, 
mtcars$cyl), function(d) summary(lm(mpg ~ wt, d))$r.squared) the 
both work. How do you feel about that? Best, Serguei. 
__ 
R-devel@r-project.org mailing list 
https://stat.ethz.ch/mailman/listinfo/r-devel 




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