Re: [Rd] Is NULL a vector?

2018-07-23 Thread Hadley Wickham 
On Mon, Jul 23, 2018 at 2:17 PM, Duncan Murdoch
 wrote:
> On 23/07/2018 3:03 PM, Hadley Wickham wrote:
>>
>> Hi all,
>>
>> Would you generally consider NULL to be a vector?
>
>
> According to the language definition (in the doc directory), it is not:
> "Vectors can be thought of as contiguous cells containing data. Cells are
> accessed through indexing operations such as x[5]. More details are given in
> Indexing.
>
> R has six basic (‘atomic’) vector types: logical, integer, real, complex,
> string (or character) and raw. The modes and storage modes for the different
> vector types are listed in the following table."
>
> and later
>
> "There is a special object called NULL. It is used whenever there is a need
> to indicate or specify that an object is absent. It should not be confused
> with a vector or list of zero length."

Perfect, thanks!

Also available online at
https://cran.r-project.org/doc/manuals/r-release/R-lang.html#Vector-objects

Hadley

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Re: [Bioc-devel] Synching version numbers went wrong

2018-07-23 Thread White, Shana (vandersm) 
Hi Mike,


My colleague and I have spent a few hours attempting to fix this problem; we 
can only propogate changes with version numbers 1.5x and cannot do 1.6x or 1.7x 
on the devel branch - it seems like the  Bioconductor automatic checks are 
preventing us from updating the files and at this point we believe the version 
number can only be fixed from within Bioconductor.  Does the Bioconductor team 
need to manually change the version number or should we try to force push the 
changes ourselves? Please let me know if you need any additional details.


Best,



Shana White
Ph. D Candidate  - Biostatistics + 
Bioinformatics
Predoctoral Fellow - MECEH
Room 318 Kettering Labs
vande...@mail.uc.edu
937-657-8289



From: Mike Smith 
Sent: Thursday, July 12, 2018 4:57:55 AM
To: White, Shana (vandersm)
Cc: bioc-devel
Subject: Re: [Bioc-devel] Synching version numbers went wrong

Hi Shana,

It looks like the release version of KEGGlincs is 1.6.x and the devel version 
should be 1.7.x.When you're committing to the master branch of 
git.bioconductor.org this equates to the devel 
version and there's a check in place to prevent even version numbers being 
committed here.  My recommendation is to make sure that your DESCRIPTION file 
for that commit has a version number of 1.7.x which should put things back on 
track.

If you also need to add your changes to the release version (I guess the 
current build error means you do) then you can see the instructions at 
https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ 
Step 4 details incorporating changes from one branch to another, and then you 
need to manually make sure the DESCRIPTION file for committing to the 
RELEASE_3_7 branch contains a 1.6.x version number.

Mike

On Wed, 11 Jul 2018 at 18:19, White, Shana (vandersm) 
mailto:vande...@mail.uc.edu>> wrote:
Hello, when attempting to fix a bug [introduced into my package] and propagate 
the changes I somehow managed to roll back the middle version number on one of 
my branches and ended up with the following error message when attempting to 
correct my mistake:



Error message:


shanas-macbook:KEGGlincs shanabanana$ git push upstream master

Counting objects: 3, done.

Delta compression using up to 4 threads.

Compressing objects: 100% (3/3), done.

Writing objects: 100% (3/3), 298 bytes | 0 bytes/s, done.

Total 3 (delta 2), reused 0 (delta 0)

remote: Error: Illegal version bump from '1.5.1' to '1.6.1'. Check

remote: http://bioconductor.org/developers/how-to/version-numbering/

remote: for details


Many thanks,


Shana White
Ph. D Candidate  - Biostatistics + 
Bioinformatics
Predoctoral Fellow - MECEH
Room 318 Kettering Labs
vande...@mail.uc.edu
937-657-8289


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Re: [Rd] Is NULL a vector?

2018-07-23 Thread Duncan Murdoch 

On 23/07/2018 3:03 PM, Hadley Wickham wrote:

Hi all,

Would you generally consider NULL to be a vector? 


According to the language definition (in the doc directory), it is not: 
"Vectors can be thought of as contiguous cells containing data. Cells 
are accessed through indexing operations such as x[5]. More details are 
given in Indexing.


R has six basic (‘atomic’) vector types: logical, integer, real, 
complex, string (or character) and raw. The modes and storage modes for 
the different vector types are listed in the following table."


and later

"There is a special object called NULL. It is used whenever there is a 
need to indicate or specify that an object is absent. It should not be 
confused with a vector or list of zero length."


Duncan Murdoch

Base R functions are

a little inconsistent:

## In favour

``` r
identical(as.vector(NULL), NULL)
#> [1] TRUE

identical(as(NULL, "vector"), NULL)
#> [1] TRUE

# supports key vector vector generics
length(NULL)
#> [1] 0
NULL[c(3, 4, 5)]
#> NULL
NULL[[1]]
#> NULL
```

## Against

``` r
is.vector(NULL)
#> [1] FALSE

is(NULL, "vector")
#> [1] FALSE
```

## Abstentions

``` r
is.atomic(NULL)
#> [1] TRUE
# documentation states "returns NULL if x is of an atomic type (or NULL)"
# is "or" exclusive or inclusive?
```

Hadley



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[Rd] Is NULL a vector?

2018-07-23 Thread Hadley Wickham 
Hi all,

Would you generally consider NULL to be a vector? Base R functions are
a little inconsistent:

## In favour

``` r
identical(as.vector(NULL), NULL)
#> [1] TRUE

identical(as(NULL, "vector"), NULL)
#> [1] TRUE

# supports key vector vector generics
length(NULL)
#> [1] 0
NULL[c(3, 4, 5)]
#> NULL
NULL[[1]]
#> NULL
```

## Against

``` r
is.vector(NULL)
#> [1] FALSE

is(NULL, "vector")
#> [1] FALSE
```

## Abstentions

``` r
is.atomic(NULL)
#> [1] TRUE
# documentation states "returns NULL if x is of an atomic type (or NULL)"
# is "or" exclusive or inclusive?
```

Hadley

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Re: [Bioc-devel] EXTERNAL: MetID accepted, release?

2018-07-23 Thread Shepherd, Lori 
The package has been accepted and added to the devel branch of Bioconductor and 
can be found
http://bioconductor.org/packages/3.8/bioc/html/MetID.html

The bioconductor releases happen twice a year; generally in spring (apr/may) 
and fall (oct/nov). We do not have an exact date for the fall release but it 
will most likely be late October. Your package will be in this bioconductor 3.8 
release. 

Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Bioc-devel  on behalf of 
zzric...@gmail.com 
Sent: Monday, July 23, 2018 12:05:12 PM
To: bioc-devel@r-project.org
Subject: EXTERNAL: [Bioc-devel] MetID accepted, release?

Hi There,

I am the author of MetID, the package is accepted. I am just wondering when
it will be released in full version? Is there any necessary step need to
take?

Thanks
Zhenzhi Li

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[Rd] Suggestion for updating `p.adjust` with new method (BKY 2006)

2018-07-23 Thread Xiaoqing Claire Rong-Mullins 
Dear R contributors,

I suggest adding a new method to `p.adjust` ("Adjust P-values for Multiple
Comparisons",
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html).

This new method is published in Benjamini, Krieger, Yekutieli 2016 Adaptive
linear step-up procedures that control the false discovery rate
(Biometrika). https://doi.org/10.1093/biomet/93.3.491

This paper described multiple methods for adjusting p-values, where the "TST"
method (Definition 6) performed the best when test statistics are
positively correlated, per my interpretation. This method can be labeled as
"BKY", for the three authors Benjamini, Krieger, Yekutieli.

I apologize if this is a duplication.


Best,
Claire

Xiaoqing Claire Rong-Mullins
Bioinformatic Specialist
Division of Biostatistics
College of Public Health
The Ohio State University

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[Bioc-devel] MetID accepted, release?

2018-07-23 Thread zzrickli 
Hi There,

I am the author of MetID, the package is accepted. I am just wondering when
it will be released in full version? Is there any necessary step need to
take?

Thanks
Zhenzhi Li

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Re: [Bioc-devel] tokay2 internet connectivity

2018-07-23 Thread Obenchain, Valerie 
Hi Klara,

Unfortunately I still don't have an solution for this. For some reason, 
Internet Explorer on our Windows build machines cannot access the 
https://omabrowser.org/ web site. The problem can be reproduced independent of 
your package simply by opening IE and trying to access the site - this returns 
a 'page cannot be displayed' error.

I've looked extensively into the settings for IE, cipher suites and any known 
security issues. None of these has led to a solution. I don't have a problem 
accessing other web sites from IE on the Windows builders. However, I also 
don't have a problem accessing omabrowser.org from other browsers or other 
combinations of Windows/IE. The problem appears to be unique to the combination 
of the omabrowser.org site and some setting in Windows Server 2012R/ IE 11 on 
the builders.

If anyone in the community has experienced a similar problem with IE I'd 
welcome help troubleshooting - feel free to contact me off-list at 
valerie.obench...@roswellpark.org.

I've contacted the OMA browser people to ask if anything has changed with their 
web interface in the recent months. For the time being please ignore the 
Windows error for OmaDB.

Thanks.
Valerie




On 07/06/2018 10:38 AM, Obenchain, Valerie wrote:

Thanks for your patience on this. I belive it's related to the Internet 
Explorer settings on the builders. Hope to have this resolved soon.

Valerie



On 07/05/2018 10:35 AM, Obenchain, Valerie wrote:
Thanks for the report. I'll look into it.

Valerie

On 07/02/2018 06:00 AM, Klara Kaleb wrote:

Hi Bioc team,

I am one of the maintainers for the OmaDB package, now in 3.7 release. The 
package is passing build and check on both mac and linux, however I am still 
experiencing an error on windows (tokay2) which I reported earlier and was 
suggested it might be due to connectivity problems by Martin. We have increased 
the robustness of the error handling in the package since (more useful error 
message, sending the request again 3 times at increasing intervals if it does 
fail etc) which has shown that the error is indeed due to transient internet 
connection of the server.

To alleviate this in the vignettes, instead of sending requests to the API I 
have included some lightweight example objects with the package. However, the 
error still occurs in tests and some function examples. As the package is an 
API wrapper and so internet connection dependant, I am not sure what is the 
best way to address this error. Would you kindly be able to provide some 
guidance on this?

Many thanks in advance,

Klara
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[Rd] oddity in transform

2018-07-23 Thread Gabor Grothendieck 
Note the inconsistency in the names in these two examples.  X.Time in
the first case and Time.1 in the second case.

  > transform(BOD, X = BOD[1:2] * seq(6))
Time demand X.Time X.demand
  118.3  1  8.3
  22   10.3  4 20.6
  33   19.0  9 57.0
  44   16.0 16 64.0
  55   15.6 25 78.0
  67   19.8 42118.8

  > transform(BOD, X = BOD[1] * seq(6))
Time demand Time.1
  118.3  1
  22   10.3  4
  33   19.0  9
  44   16.0 16
  55   15.6 25
  67   19.8 42

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[Rd] CRAN: R 3.5.0 Not Available

2018-07-23 Thread Juan Telleria Ruiz de Aguirre 
In CRAN, R 3.5.0 is not available for download on "Previous Releases
of R for Windows". ¿Could it be added?

https://cran.r-project.org/

Thanks.

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