Re: [Bioc-devel] 'OUTRIDER' Bioconductor package

[Martin Morgan]

I think this is an error in BiocParallel that has been corrected (in v. 1.19.4) 
but not yet propagated through the build system and report.

Martin

On 10/11/19, 7:33 PM, "Bioc-devel on behalf of Christian Mertes" 
 wrote:

Dear Bioc Team,

I noticed already the error and I'm not completely sure why this is 
happening. On appveyor it is going through with no problems. I never 
call the function mcparallel but I did register MulticoreParams() in the 
vignette which could caused the problem. But I'm puzzled why it works on 
appveyor and not on Bioconductor.

I did removed now the MutlicoreParam call. So lets see if it solved the 
problem.

Best,
Christian

Link to appveyor log from the specific commit: 
https://ci.appveyor.com/project/c-mertes/outrider/builds/27915255
This is the error from BioConductor for the same commit:

* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* preparing 'OUTRIDER':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'OUTRIDER.Rnw' using knitr
Warning in MulticoreParam(2) :
   MulticoreParam() not supported on Windows, use SnowParam()
Invalid Parameter - /deVsOutlier-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
   'convert "figure/deVsOutlier-1.png" -trim "figure/deVsOutlier-1.png"' 
execution failed with error code 4
229 genes did not passed the filter due to zero counts. This is 22.9% of 
the genes.
Fri Oct 11 01:01:13 2019: SizeFactor estimation ...
Fri Oct 11 01:01:13 2019: Controlling for confounders ...
Using estimated q with: 23
Fri Oct 11 01:01:13 2019: Using the autoencoder implementation for 
controlling.
Quitting from lines 180-200 (OUTRIDER.Rnw)
Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
'mcparallel' is not an exported object from 'namespace:parallel'
--- failed re-building 'OUTRIDER.Rnw'


Am 10/11/2019 um 7:33 PM schrieb Interdonato, Kayla:
>
> The next Bioconductor release 3.10 is scheduled for October 30^th . 
> The current
>
> Bioc 3.9 release branch will be frozen Tuesday October 15^th . There 
> will be no
>
> opportunities to commit or correct the release 3.9 branch after the 
> freeze.
>
> We like to make an effort to have all Bioconductor packages building and
>
> checking without ERROR or TIMEOUT in both release and devel versions. 
> It seems
>
> your package is producing an ERROR for the Windows builder in the release
>
> version of Bioconductor.
>
> Release build report - 
> https://bioconductor.org/checkResults/3.9/bioc-LATEST/OUTRIDER/
>
> Could you please investigate and make the necessary changes by Tuesday.
>
> If you need any assistance please feel free to ask questions at
>
> bioc-devel@r-project.org .
>
> Thank you,
>
> *Kayla E. Interdonato, MS*
>
> Programmer/Analyst
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> (716)845-1300 x4621
>
>
> 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. 
-- 
*Christian Mertes* | PhD Student / Lab Administrator

*Gagneur Lab* - Computational Genomics
I12 - Department of Informatics
Technical University of Munich
Boltzmannstr. 3, 85748 Garching, Germany

mer...@in.tum.de  | http://gagneurlab.in.tum.de

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Re: [Bioc-devel] 'OUTRIDER' Bioconductor package

[Christian Mertes]

Dear Bioc Team,

I noticed already the error and I'm not completely sure why this is 
happening. On appveyor it is going through with no problems. I never 
call the function mcparallel but I did register MulticoreParams() in the 
vignette which could caused the problem. But I'm puzzled why it works on 
appveyor and not on Bioconductor.

I did removed now the MutlicoreParam call. So lets see if it solved the 
problem.

Best,
Christian

Link to appveyor log from the specific commit: 
https://ci.appveyor.com/project/c-mertes/outrider/builds/27915255
This is the error from BioConductor for the same commit:

* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* preparing 'OUTRIDER':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'OUTRIDER.Rnw' using knitr
Warning in MulticoreParam(2) :
   MulticoreParam() not supported on Windows, use SnowParam()
Invalid Parameter - /deVsOutlier-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
   'convert "figure/deVsOutlier-1.png" -trim "figure/deVsOutlier-1.png"' 
execution failed with error code 4
229 genes did not passed the filter due to zero counts. This is 22.9% of 
the genes.
Fri Oct 11 01:01:13 2019: SizeFactor estimation ...
Fri Oct 11 01:01:13 2019: Controlling for confounders ...
Using estimated q with: 23
Fri Oct 11 01:01:13 2019: Using the autoencoder implementation for 
controlling.
Quitting from lines 180-200 (OUTRIDER.Rnw)
Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
'mcparallel' is not an exported object from 'namespace:parallel'
--- failed re-building 'OUTRIDER.Rnw'


Am 10/11/2019 um 7:33 PM schrieb Interdonato, Kayla:
>
> The next Bioconductor release 3.10 is scheduled for October 30^th . 
> The current
>
> Bioc 3.9 release branch will be frozen Tuesday October 15^th . There 
> will be no
>
> opportunities to commit or correct the release 3.9 branch after the 
> freeze.
>
> We like to make an effort to have all Bioconductor packages building and
>
> checking without ERROR or TIMEOUT in both release and devel versions. 
> It seems
>
> your package is producing an ERROR for the Windows builder in the release
>
> version of Bioconductor.
>
> Release build report - 
> https://bioconductor.org/checkResults/3.9/bioc-LATEST/OUTRIDER/
>
> Could you please investigate and make the necessary changes by Tuesday.
>
> If you need any assistance please feel free to ask questions at
>
> bioc-devel@r-project.org .
>
> Thank you,
>
> *Kayla E. Interdonato, MS*
>
> Programmer/Analyst
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> (716)845-1300 x4621
>
>
> 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. 
-- 
*Christian Mertes* | PhD Student / Lab Administrator

*Gagneur Lab* - Computational Genomics
I12 - Department of Informatics
Technical University of Munich
Boltzmannstr. 3, 85748 Garching, Germany

mer...@in.tum.de  | http://gagneurlab.in.tum.de

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Re: [Rd] New matrix function

[Gabor Grothendieck]

The link you posted used the same inputs as in my example. If that is
not what you meant maybe
a different example is needed.
Regards.

On Fri, Oct 11, 2019 at 2:39 PM Pages, Herve  wrote:
>
> Has someone looked into the image processing area for this? That sounds
> a little bit too high-level for base R to me (and I would be surprised
> if any mainstream programming language had this kind of functionality
> built-in).
>
> H.
>
> On 10/11/19 03:44, Morgan Morgan wrote:
> > Hi All,
> >
> > I was looking for a function to find a small matrix inside a larger matrix
> > in R similar to the one described in the following link:
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mathworks.com_matlabcentral_answers_194708-2Dindex-2Da-2Dsmall-2Dmatrix-2Din-2Da-2Dlarger-2Dmatrix=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=v96tqHMO3CLNBS7KTmdshM371i6W_v8_2H5bdVy_KHo=9Eu0WySIEzrWuYXFhwhHETpZQzi6hHLd84DZsbZsXYY=
> >
> > I couldn't find anything.
> >
> > The above function can be seen as a "generalisation" of the "which"
> > function as well as the function described in the following post:
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__coolbutuseless.github.io_2018_04_03_finding-2Da-2Dlength-2Dn-2Dneedle-2Din-2Da-2Dhaystack_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=v96tqHMO3CLNBS7KTmdshM371i6W_v8_2H5bdVy_KHo=qZ3SJ8t8zEDA-em4WT7gBmN66qvvCKKKXRJunoF6P3k=
> >
> > Would be possible to add such a function to base R?
> >
> > I am happy to work with someone from the R core team (if you wish) and
> > suggest an implementation in C.
> >
> > Thank you
> > Best regards,
> > Morgan
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=v96tqHMO3CLNBS7KTmdshM371i6W_v8_2H5bdVy_KHo=tyVSs9EYVBd_dmVm1LSC23GhUzbBv8ULvtsveo-COoU=
> >
>
> --
> 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
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
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tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

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[Bioc-devel] Bioconductor 3.10 db0s are available

[Interdonato, Kayla]

The newest db0 packages for the upcoming Bioconductor 3.10 release are up and 
should propagate within a day or so. The deadline for submitting contributed 
annotations will be Wednesday October 23rd.

The new db0 packages are:

anopheles.db0_3.10.0.tar.gz
arabidopsis.db0_3.10.0.tar.gz
bovine.db0_3.10.0.tar.gz
canine.db0_3.10.0.tar.gz
chicken.db0_3.10.0.tar.gz
chimp.db0_3.10.0.tar.gz
ecoliK12.db0_3.10.0.tar.gz
ecoliSakai.db0_3.10.0.tar.gz
fly.db0_3.10.0.tar.gz
human.db0_3.10.0.tar.gz
malaria.db0_3.10.0.tar.gz
mouse.db0_3.10.0.tar.gz
pig.db0_3.10.0.tar.gz
rat.db0_3.10.0.tar.gz
rhesus.db0_3.10.0.tar.gz
worm.db0_3.10.0.tar.gz
xenopus.db0_3.10.0.tar.gz
yeast.db0_3.10.0.tar.gz
zebrafish.db0_3.10.0.tar.gz

Thank you and happy Friday!

Kayla E. Interdonato, MS
Programmer/Analyst
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
(716)845-1300 x4621


This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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Re: [Rd] New matrix function

[Pages, Herve]

Has someone looked into the image processing area for this? That sounds 
a little bit too high-level for base R to me (and I would be surprised 
if any mainstream programming language had this kind of functionality 
built-in).

H.

On 10/11/19 03:44, Morgan Morgan wrote:
> Hi All,
> 
> I was looking for a function to find a small matrix inside a larger matrix
> in R similar to the one described in the following link:
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mathworks.com_matlabcentral_answers_194708-2Dindex-2Da-2Dsmall-2Dmatrix-2Din-2Da-2Dlarger-2Dmatrix=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=v96tqHMO3CLNBS7KTmdshM371i6W_v8_2H5bdVy_KHo=9Eu0WySIEzrWuYXFhwhHETpZQzi6hHLd84DZsbZsXYY=
> 
> I couldn't find anything.
> 
> The above function can be seen as a "generalisation" of the "which"
> function as well as the function described in the following post:
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__coolbutuseless.github.io_2018_04_03_finding-2Da-2Dlength-2Dn-2Dneedle-2Din-2Da-2Dhaystack_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=v96tqHMO3CLNBS7KTmdshM371i6W_v8_2H5bdVy_KHo=qZ3SJ8t8zEDA-em4WT7gBmN66qvvCKKKXRJunoF6P3k=
> 
> Would be possible to add such a function to base R?
> 
> I am happy to work with someone from the R core team (if you wish) and
> suggest an implementation in C.
> 
> Thank you
> Best regards,
> Morgan
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=v96tqHMO3CLNBS7KTmdshM371i6W_v8_2H5bdVy_KHo=tyVSs9EYVBd_dmVm1LSC23GhUzbBv8ULvtsveo-COoU=
> 

-- 
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
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[Bioc-devel] check fails on arch 'i386'

[Toth, Reka]

Dear BioC developers,

The most recent build of methrix fails on Tokay1 server:
https://bioconductor.org/spb_reports/methrix_buildreport_20191009174210.html
The error message is the following:

** running examples for arch 'i386' ... ERROR
Running examples in 'methrix-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_region_summary
> ### Title: Extract and summarize methylation or coverage info by regions of
> ###   interest
> ### Aliases: get_region_summary
>
> ### ** Examples
>
> data("methrix_data")
> get_region_summary(m = methrix_data, regions = data.table(chr = "chr21", 
> start = 27867971, end =  27868103), type = "M", how = "mean")
-Checking for overlaps..
Error: cannot allocate vector of size 1.4 Gb
Execution halted

I am a bit puzzled what the reasons could be, since it passed this step during 
the previous builds and I didn’t change any of the functions in my last commit.
When I run the check on our local Windows, I don’t get any error. We use a very 
small dataset as example, it definitely should not use a vector of size 1.4 Gb.

I would appreciate every input or idea on how to tackle this error.
Thanks a lot!

Best,
Reka

Dr. Reka Toth
Computational Epigenomics Group
Division of Epigenomics and Cancer Risk Factors /C010
Postdoctoral Fellow

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany

r.t...@dkfz-heidelberg.de
www.dkfz.de

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Re: [Rd] New matrix function

[Gabor Grothendieck]

I pressed return too soon.

If we had such a multiply then

   which(embed(A, x) %==.&% reverse(x))

On Fri, Oct 11, 2019 at 10:57 AM Gabor Grothendieck
 wrote:
>
> Also note that the functionality discussed could be regarded as a 
> generalization
> of matrix multiplication where *  and + are general functions and in this case
> we have * replaced by == and + replaced by &.
>
> On Fri, Oct 11, 2019 at 10:46 AM Gabor Grothendieck
>  wrote:
> >
> > Using the example in the link here are two one-liners:
> >
> >   A <- c(2,3,4,1,2,3,4,1,1,2)
> >   x <- c(1,2)
> >
> >   # 1 - zoo
> >   library(zoo)
> >   which( rollapply(A, length(x), identical, x, fill = FALSE, align = 
> > "left") )
> >   ## [1] 4 9
> >
> >   # 2 - Base R using conversion to character
> >   gregexpr(paste(x, collapse = ""), paste(A, collapse = ""))[[1]]
> >   ## [1] 4 9
> >   ...snip ...
> >
> > On Fri, Oct 11, 2019 at 3:45 AM Morgan Morgan  
> > wrote:
> > >
> > > Hi All,
> > >
> > > I was looking for a function to find a small matrix inside a larger matrix
> > > in R similar to the one described in the following link:
> > >
> > > https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
> > >
> > > I couldn't find anything.
> > >
> > > The above function can be seen as a "generalisation" of the "which"
> > > function as well as the function described in the following post:
> > >
> > > https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
> > >
> > > Would be possible to add such a function to base R?
> > >
> > > I am happy to work with someone from the R core team (if you wish) and
> > > suggest an implementation in C.
> > >
> > > Thank you
> > > Best regards,
> > > Morgan
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
> >
> > --
> > Statistics & Software Consulting
> > GKX Group, GKX Associates Inc.
> > tel: 1-877-GKX-GROUP
> > email: ggrothendieck at gmail.com
>
>
>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com



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[Bioc-devel] Big repo problem & consequences: all commits duplicated

[Cuklina Jelena]

Dear all,

while trying to fix the WARNING of “too big files” for my repo proBatch, I used 
BFG, and ALL my commits (or at least many-many dozens of them) are duplicated 
(some up to 5-10 copies). I guess this is because of my pull-push efforts, 
which I naively “resolved” with git pull origin master 
--allow-unrelated-histories.

What can I do now (because my repo is now massive exactly because everything is 
in many-many copies).

Best regards,
Jelena Čuklina.

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Re: [Rd] New matrix function

[Joris Meys]

As a package is a collection of functions, and as "base" is not used to
refer to the base package but to all packages that form "base R" (so utils,
graphics, stats, methods, parallel, ...), the functions in the parallel
package are one example of functions incorporated in "base R" from a
package. Actually two, because the functions in parallel are based on both
snow and multicore.

This has no relation to changes in implementation (which often don't happen
due to back-compatibility issues in edge cases).

Kind regards
Joris

On Fri, Oct 11, 2019 at 4:42 PM Morgan Morgan 
wrote:

> I think you are confusing package and function here. Plus some of the R
> Core packages, that you mention, contain functions that should probably be
> replaced by functions with better implementation from packages on CRAN.
>
> Best regards
> Morgan
>
> On Fri, 11 Oct 2019 15:22 Joris Meys,  wrote:
>
>>
>>
>> On Fri, Oct 11, 2019 at 3:55 PM Morgan Morgan 
>> wrote:
>>
>>> How do you prove usefulness of a feature?
>>> Do you have an example of a feature that has been added after proving to
>>> be
>>> useful in the package space first?
>>>
>>> Thank you,
>>> Morgan
>>>
>>
>> The parallel package (a base package like utils, stats, ...) was added as
>> a drop-in replacement of the packages snow and multicore for parallel
>> computing. That's one example, but sure there's more.
>>
>> Kind regards
>> Joris
>>
>> --
>> Joris Meys
>> Statistical consultant
>>
>> Department of Data Analysis and Mathematical Modelling
>> Ghent University
>> Coupure Links 653, B-9000 Gent (Belgium)
>>
>> 
>>
>> ---
>> Biowiskundedagen 2018-2019
>> http://www.biowiskundedagen.ugent.be/
>>
>> ---
>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>
>

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


---
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http://www.biowiskundedagen.ugent.be/

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Re: [Rd] New matrix function

[Morgan Morgan]

Your answer makes much more sense to me.
I will probably end up adding the function to a package.
Some processes and decisions on how R is developed seems to be obscure to
me.

Thank you
Morgan

On Fri, 11 Oct 2019 15:30 Avraham Adler,  wrote:

> It’s rather difficult. For example, the base R Kendall tau is written with
> the naive O(n^2). The much faster O(n log n) implementation was programmed
> and is in the pcaPP package. When I say much faster, I mean that my
> implementation in Excel VBA was faster than R for 10,000 or so pairs.
> R-Core decided not to implement that code, and instead made a note about
> the faster implementation living in pcaPP in the help for “cor”. See [1]
> for the 2012 discussion. My point is it’s really really difficult to get
> something in Base R. Develop it well, put it in a package, and you have
> basically the same result.
>
> Avi
>
> [1] https://stat.ethz.ch/pipermail/r-devel/2012-June/064351.html
>
> On Fri, Oct 11, 2019 at 9:55 AM Morgan Morgan 
> wrote:
>
>> How do you prove usefulness of a feature?
>> Do you have an example of a feature that has been added after proving to
>> be
>> useful in the package space first?
>>
>> Thank you,
>> Morgan
>>
>> On Fri, 11 Oct 2019 13:53 Michael Lawrence, 
>> wrote:
>>
>> > Thanks for this interesting suggestion, Morgan. While there is no strict
>> > criteria for base R inclusion, one criterion relevant in this case is
>> that
>> > the usefulness of a feature be proven in the package space first.
>> >
>> > Michael
>> >
>> >
>> > On Fri, Oct 11, 2019 at 5:19 AM Morgan Morgan <
>> morgan.email...@gmail.com>
>> > wrote:
>> >
>> >> On Fri, 11 Oct 2019 10:45 Duncan Murdoch, 
>> >> wrote:
>> >>
>> >> > On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
>> >> > > Hi All,
>> >> > >
>> >> > > I was looking for a function to find a small matrix inside a larger
>> >> > matrix
>> >> > > in R similar to the one described in the following link:
>> >> > >
>> >> > >
>> >> >
>> >>
>> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
>> >> > >
>> >> > > I couldn't find anything.
>> >> > >
>> >> > > The above function can be seen as a "generalisation" of the "which"
>> >> > > function as well as the function described in the following post:
>> >> > >
>> >> > >
>> >> >
>> >>
>> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
>> >> > >
>> >> > > Would be possible to add such a function to base R?
>> >> > >
>> >> > > I am happy to work with someone from the R core team (if you wish)
>> and
>> >> > > suggest an implementation in C.
>> >> >
>> >> > That seems like it would sometimes be a useful function, and maybe
>> >> > someone will point out a package that already contains it.  But if
>> not,
>> >> > why would it belong in base R?
>> >> >
>> >>
>> >> If someone already implemented it, that would great indeed. I think it
>> is
>> >> a
>> >> very general and basic function, hence base R could be a good place for
>> >> it?
>> >>
>> >> But this is probably not a good reason; maybe someone from the R core
>> team
>> >> can shed some light on how they decide whether or not to include a
>> >> function
>> >> in base R?
>> >>
>> >>
>> >> > Duncan Murdoch
>> >> >
>> >>
>> >> [[alternative HTML version deleted]]
>> >>
>> >> __
>> >> R-devel@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>> >>
>> >
>> >
>> > --
>> > Michael Lawrence
>> > Scientist, Bioinformatics and Computational Biology
>> > Genentech, A Member of the Roche Group
>> > Office +1 (650) 225-7760
>> > micha...@gene.com
>> >
>> > Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> --
> Sent from Gmail Mobile
>

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Re: [Rd] New matrix function

[Gabor Grothendieck]

Also note that the functionality discussed could be regarded as a generalization
of matrix multiplication where *  and + are general functions and in this case
we have * replaced by == and + replaced by &.

On Fri, Oct 11, 2019 at 10:46 AM Gabor Grothendieck
 wrote:
>
> Using the example in the link here are two one-liners:
>
>   A <- c(2,3,4,1,2,3,4,1,1,2)
>   x <- c(1,2)
>
>   # 1 - zoo
>   library(zoo)
>   which( rollapply(A, length(x), identical, x, fill = FALSE, align = "left") )
>   ## [1] 4 9
>
>   # 2 - Base R using conversion to character
>   gregexpr(paste(x, collapse = ""), paste(A, collapse = ""))[[1]]
>   ## [1] 4 9
>   ...snip ...
>
> On Fri, Oct 11, 2019 at 3:45 AM Morgan Morgan  
> wrote:
> >
> > Hi All,
> >
> > I was looking for a function to find a small matrix inside a larger matrix
> > in R similar to the one described in the following link:
> >
> > https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
> >
> > I couldn't find anything.
> >
> > The above function can be seen as a "generalisation" of the "which"
> > function as well as the function described in the following post:
> >
> > https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
> >
> > Would be possible to add such a function to base R?
> >
> > I am happy to work with someone from the R core team (if you wish) and
> > suggest an implementation in C.
> >
> > Thank you
> > Best regards,
> > Morgan
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com



-- 
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Re: [Rd] New matrix function

[Gabor Grothendieck]

Using the example in the link here are two one-liners:

  A <- c(2,3,4,1,2,3,4,1,1,2)
  x <- c(1,2)

  # 1 - zoo
  library(zoo)
  which( rollapply(A, length(x), identical, x, fill = FALSE, align = "left") )
  ## [1] 4 9

  # 2 - Base R using conversion to character
  gregexpr(paste(x, collapse = ""), paste(A, collapse = ""))[[1]]
  ## [1] 4 9
  ...snip ...

On Fri, Oct 11, 2019 at 3:45 AM Morgan Morgan  wrote:
>
> Hi All,
>
> I was looking for a function to find a small matrix inside a larger matrix
> in R similar to the one described in the following link:
>
> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
>
> I couldn't find anything.
>
> The above function can be seen as a "generalisation" of the "which"
> function as well as the function described in the following post:
>
> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
>
> Would be possible to add such a function to base R?
>
> I am happy to work with someone from the R core team (if you wish) and
> suggest an implementation in C.
>
> Thank you
> Best regards,
> Morgan
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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Re: [Rd] New matrix function

[Avraham Adler]

Perhaps. But aren’t you looking to implementation a function which finds a
submatrix? If I’m confused, please accept my apologies.

Avi

On Fri, Oct 11, 2019 at 10:43 AM Morgan Morgan 
wrote:

> I think you are confusing package and function here. Plus some of the R
> Core packages, that you mention, contain functions that should probably be
> replaced by functions with better implementation from packages on CRAN.
>
> Best regards
> Morgan
>
> On Fri, 11 Oct 2019 15:22 Joris Meys,  wrote:
>
> >
> >
> > On Fri, Oct 11, 2019 at 3:55 PM Morgan Morgan  >
> > wrote:
> >
> >> How do you prove usefulness of a feature?
> >> Do you have an example of a feature that has been added after proving to
> >> be
> >> useful in the package space first?
> >>
> >> Thank you,
> >> Morgan
> >>
> >
> > The parallel package (a base package like utils, stats, ...) was added as
> > a drop-in replacement of the packages snow and multicore for parallel
> > computing. That's one example, but sure there's more.
> >
> > Kind regards
> > Joris
> >
> > --
> > Joris Meys
> > Statistical consultant
> >
> > Department of Data Analysis and Mathematical Modelling
> > Ghent University
> > Coupure Links 653, B-9000 Gent (Belgium)
> >
> > <
> https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g
> >
> >
> > ---
> > Biowiskundedagen 2018-2019
> > http://www.biowiskundedagen.ugent.be/
> >
> > ---
> > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] New matrix function

[Morgan Morgan]

I think you are confusing package and function here. Plus some of the R
Core packages, that you mention, contain functions that should probably be
replaced by functions with better implementation from packages on CRAN.

Best regards
Morgan

On Fri, 11 Oct 2019 15:22 Joris Meys,  wrote:

>
>
> On Fri, Oct 11, 2019 at 3:55 PM Morgan Morgan 
> wrote:
>
>> How do you prove usefulness of a feature?
>> Do you have an example of a feature that has been added after proving to
>> be
>> useful in the package space first?
>>
>> Thank you,
>> Morgan
>>
>
> The parallel package (a base package like utils, stats, ...) was added as
> a drop-in replacement of the packages snow and multicore for parallel
> computing. That's one example, but sure there's more.
>
> Kind regards
> Joris
>
> --
> Joris Meys
> Statistical consultant
>
> Department of Data Analysis and Mathematical Modelling
> Ghent University
> Coupure Links 653, B-9000 Gent (Belgium)
>
> 
>
> ---
> Biowiskundedagen 2018-2019
> http://www.biowiskundedagen.ugent.be/
>
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>

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Re: [Rd] New matrix function

[Avraham Adler]

It’s rather difficult. For example, the base R Kendall tau is written with
the naive O(n^2). The much faster O(n log n) implementation was programmed
and is in the pcaPP package. When I say much faster, I mean that my
implementation in Excel VBA was faster than R for 10,000 or so pairs.
R-Core decided not to implement that code, and instead made a note about
the faster implementation living in pcaPP in the help for “cor”. See [1]
for the 2012 discussion. My point is it’s really really difficult to get
something in Base R. Develop it well, put it in a package, and you have
basically the same result.

Avi

[1] https://stat.ethz.ch/pipermail/r-devel/2012-June/064351.html

On Fri, Oct 11, 2019 at 9:55 AM Morgan Morgan 
wrote:

> How do you prove usefulness of a feature?
> Do you have an example of a feature that has been added after proving to be
> useful in the package space first?
>
> Thank you,
> Morgan
>
> On Fri, 11 Oct 2019 13:53 Michael Lawrence, 
> wrote:
>
> > Thanks for this interesting suggestion, Morgan. While there is no strict
> > criteria for base R inclusion, one criterion relevant in this case is
> that
> > the usefulness of a feature be proven in the package space first.
> >
> > Michael
> >
> >
> > On Fri, Oct 11, 2019 at 5:19 AM Morgan Morgan  >
> > wrote:
> >
> >> On Fri, 11 Oct 2019 10:45 Duncan Murdoch, 
> >> wrote:
> >>
> >> > On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
> >> > > Hi All,
> >> > >
> >> > > I was looking for a function to find a small matrix inside a larger
> >> > matrix
> >> > > in R similar to the one described in the following link:
> >> > >
> >> > >
> >> >
> >>
> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
> >> > >
> >> > > I couldn't find anything.
> >> > >
> >> > > The above function can be seen as a "generalisation" of the "which"
> >> > > function as well as the function described in the following post:
> >> > >
> >> > >
> >> >
> >>
> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
> >> > >
> >> > > Would be possible to add such a function to base R?
> >> > >
> >> > > I am happy to work with someone from the R core team (if you wish)
> and
> >> > > suggest an implementation in C.
> >> >
> >> > That seems like it would sometimes be a useful function, and maybe
> >> > someone will point out a package that already contains it.  But if
> not,
> >> > why would it belong in base R?
> >> >
> >>
> >> If someone already implemented it, that would great indeed. I think it
> is
> >> a
> >> very general and basic function, hence base R could be a good place for
> >> it?
> >>
> >> But this is probably not a good reason; maybe someone from the R core
> team
> >> can shed some light on how they decide whether or not to include a
> >> function
> >> in base R?
> >>
> >>
> >> > Duncan Murdoch
> >> >
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> __
> >> R-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >
> >
> > --
> > Michael Lawrence
> > Scientist, Bioinformatics and Computational Biology
> > Genentech, A Member of the Roche Group
> > Office +1 (650) 225-7760
> > micha...@gene.com
> >
> > Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
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Re: [Rd] New matrix function

[Morgan Morgan]

How do you prove usefulness of a feature?
Do you have an example of a feature that has been added after proving to be
useful in the package space first?

Thank you,
Morgan

On Fri, 11 Oct 2019 13:53 Michael Lawrence, 
wrote:

> Thanks for this interesting suggestion, Morgan. While there is no strict
> criteria for base R inclusion, one criterion relevant in this case is that
> the usefulness of a feature be proven in the package space first.
>
> Michael
>
>
> On Fri, Oct 11, 2019 at 5:19 AM Morgan Morgan 
> wrote:
>
>> On Fri, 11 Oct 2019 10:45 Duncan Murdoch, 
>> wrote:
>>
>> > On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
>> > > Hi All,
>> > >
>> > > I was looking for a function to find a small matrix inside a larger
>> > matrix
>> > > in R similar to the one described in the following link:
>> > >
>> > >
>> >
>> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
>> > >
>> > > I couldn't find anything.
>> > >
>> > > The above function can be seen as a "generalisation" of the "which"
>> > > function as well as the function described in the following post:
>> > >
>> > >
>> >
>> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
>> > >
>> > > Would be possible to add such a function to base R?
>> > >
>> > > I am happy to work with someone from the R core team (if you wish) and
>> > > suggest an implementation in C.
>> >
>> > That seems like it would sometimes be a useful function, and maybe
>> > someone will point out a package that already contains it.  But if not,
>> > why would it belong in base R?
>> >
>>
>> If someone already implemented it, that would great indeed. I think it is
>> a
>> very general and basic function, hence base R could be a good place for
>> it?
>>
>> But this is probably not a good reason; maybe someone from the R core team
>> can shed some light on how they decide whether or not to include a
>> function
>> in base R?
>>
>>
>> > Duncan Murdoch
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
> --
> Michael Lawrence
> Scientist, Bioinformatics and Computational Biology
> Genentech, A Member of the Roche Group
> Office +1 (650) 225-7760
> micha...@gene.com
>
> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>

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Re: [Rd] New matrix function

[Michael Lawrence via R-devel]

Thanks for this interesting suggestion, Morgan. While there is no strict
criteria for base R inclusion, one criterion relevant in this case is that
the usefulness of a feature be proven in the package space first.

Michael


On Fri, Oct 11, 2019 at 5:19 AM Morgan Morgan 
wrote:

> On Fri, 11 Oct 2019 10:45 Duncan Murdoch, 
> wrote:
>
> > On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
> > > Hi All,
> > >
> > > I was looking for a function to find a small matrix inside a larger
> > matrix
> > > in R similar to the one described in the following link:
> > >
> > >
> >
> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
> > >
> > > I couldn't find anything.
> > >
> > > The above function can be seen as a "generalisation" of the "which"
> > > function as well as the function described in the following post:
> > >
> > >
> >
> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
> > >
> > > Would be possible to add such a function to base R?
> > >
> > > I am happy to work with someone from the R core team (if you wish) and
> > > suggest an implementation in C.
> >
> > That seems like it would sometimes be a useful function, and maybe
> > someone will point out a package that already contains it.  But if not,
> > why would it belong in base R?
> >
>
> If someone already implemented it, that would great indeed. I think it is a
> very general and basic function, hence base R could be a good place for it?
>
> But this is probably not a good reason; maybe someone from the R core team
> can shed some light on how they decide whether or not to include a function
> in base R?
>
>
> > Duncan Murdoch
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
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Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha...@gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

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Re: [Rd] New matrix function

[Wang Jiefei]

Hi Morgan,

I think there is a discussion on how developers include a function in base
R in another thread:

https://stat.ethz.ch/pipermail/r-devel/2019-October/078551.html


Best,
Jiefei

On Fri, Oct 11, 2019 at 8:19 AM Morgan Morgan 
wrote:

> On Fri, 11 Oct 2019 10:45 Duncan Murdoch, 
> wrote:
>
> > On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
> > > Hi All,
> > >
> > > I was looking for a function to find a small matrix inside a larger
> > matrix
> > > in R similar to the one described in the following link:
> > >
> > >
> >
> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
> > >
> > > I couldn't find anything.
> > >
> > > The above function can be seen as a "generalisation" of the "which"
> > > function as well as the function described in the following post:
> > >
> > >
> >
> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
> > >
> > > Would be possible to add such a function to base R?
> > >
> > > I am happy to work with someone from the R core team (if you wish) and
> > > suggest an implementation in C.
> >
> > That seems like it would sometimes be a useful function, and maybe
> > someone will point out a package that already contains it.  But if not,
> > why would it belong in base R?
> >
>
> If someone already implemented it, that would great indeed. I think it is a
> very general and basic function, hence base R could be a good place for it?
>
> But this is probably not a good reason; maybe someone from the R core team
> can shed some light on how they decide whether or not to include a function
> in base R?
>
>
> > Duncan Murdoch
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Bioc-devel] RELEASE_3_9 Branch freeze

[Shepherd, Lori]

In preparation for the Bioconductor 3.10 release on October 30th we will be 
freezing the current release 3.9 branch on Tuesday October 15th . There will be 
no opportunities to commit or correct the release 3.9 branch after the freeze. 
We encourage everyone to push fixes as soon as possible and wanted to send out 
a general reminder that this is the last weekend for changes to RELEASE_3_9 
branch on Bioconductor.




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, 
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Re: [Rd] New matrix function

[Morgan Morgan]

On Fri, 11 Oct 2019 10:45 Duncan Murdoch,  wrote:

> On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
> > Hi All,
> >
> > I was looking for a function to find a small matrix inside a larger
> matrix
> > in R similar to the one described in the following link:
> >
> >
> https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix
> >
> > I couldn't find anything.
> >
> > The above function can be seen as a "generalisation" of the "which"
> > function as well as the function described in the following post:
> >
> >
> https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/
> >
> > Would be possible to add such a function to base R?
> >
> > I am happy to work with someone from the R core team (if you wish) and
> > suggest an implementation in C.
>
> That seems like it would sometimes be a useful function, and maybe
> someone will point out a package that already contains it.  But if not,
> why would it belong in base R?
>

If someone already implemented it, that would great indeed. I think it is a
very general and basic function, hence base R could be a good place for it?

But this is probably not a good reason; maybe someone from the R core team
can shed some light on how they decide whether or not to include a function
in base R?


> Duncan Murdoch
>

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Re: [Rd] New matrix function

[Spencer Graves]

On 2019-10-11 04:45, Duncan Murdoch wrote:

On 11/10/2019 6:44 a.m., Morgan Morgan wrote:

Hi All,

I was looking for a function to find a small matrix inside a larger 
matrix

in R similar to the one described in the following link:

https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix 



I couldn't find anything.

The above function can be seen as a "generalisation" of the "which"
function as well as the function described in the following post:

https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/ 



Would be possible to add such a function to base R?

I am happy to work with someone from the R core team (if you wish) and
suggest an implementation in C.


That seems like it would sometimes be a useful function, and maybe 
someone will point out a package that already contains it.  But if 
not, why would it belong in base R?



  The natural thing could be to add it to another existing package.


  A list of different search tools appear in the Wikiversity 
article on "Searching R packages".[1]  I especially like the "sos" 
package, which includes a vignette, [2] but I also use RDocumentation 
and occasionally Rseek.  Google Advanced Search[3] is also very good;  
I've used that for other things, but not searching for R packages.



  I've had modest luck suggesting additions to other packages if I 
write the function and documentation with good examples that tend to 
ensure quality.  Some maintainers reject my suggestions;  other have 
accepted them.



  Spencer Graves


[1]
https://en.wikiversity.org/wiki/Searching_R_Packages


[2] Caveat:  I wrote both that Wikiversity article and the "sos" 
package, so I'm biased.



[3]
https://www.google.com/advanced_search



Duncan Murdoch

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Re: [Rd] New matrix function

[Duncan Murdoch]

On 11/10/2019 6:44 a.m., Morgan Morgan wrote:

Hi All,

I was looking for a function to find a small matrix inside a larger matrix
in R similar to the one described in the following link:

https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix

I couldn't find anything.

The above function can be seen as a "generalisation" of the "which"
function as well as the function described in the following post:

https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/

Would be possible to add such a function to base R?

I am happy to work with someone from the R core team (if you wish) and
suggest an implementation in C.


That seems like it would sometimes be a useful function, and maybe 
someone will point out a package that already contains it.  But if not, 
why would it belong in base R?


Duncan Murdoch

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[Rd] New matrix function

[Morgan Morgan]

Hi All,

I was looking for a function to find a small matrix inside a larger matrix
in R similar to the one described in the following link:

https://www.mathworks.com/matlabcentral/answers/194708-index-a-small-matrix-in-a-larger-matrix

I couldn't find anything.

The above function can be seen as a "generalisation" of the "which"
function as well as the function described in the following post:

https://coolbutuseless.github.io/2018/04/03/finding-a-length-n-needle-in-a-haystack/

Would be possible to add such a function to base R?

I am happy to work with someone from the R core team (if you wish) and
suggest an implementation in C.

Thank you
Best regards,
Morgan

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