Re: [Bioc-devel] hg133plus2.db

[Obenchain, Valerie]

I think you're missing a 'u',

> biocLite("hgu133plus2.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development
(unstable)
  (2016-10-22 r71581).
Installing package(s) ‘hgu133plus2.db’
trying URL
'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 2139642 bytes (2.0 MB)
==
downloaded 2.0 MB

Val

On 12/27/2016 02:00 PM, Levi Waldron wrote:
> I don't seem to be able to install hgu133plus2.db in bioc-devel?
>
>> library(BiocInstaller)
> Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
>
>> biocLite("hg133plus2.db")
> BioC_mirror: https://bioconductor.org
>
> Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable)
>
>   (2016-10-26 r71594).
>
> Installing package(s) ‘hg133plus2.db’
>
> Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
>
>   cannot download all files
>
> Warning message:
>
> package ‘hg133plus2.db’ is not available (for R Under development)
>
>> sessionInfo()
> R Under development (unstable) (2016-10-26 r71594)
>
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> Running under: OS X Yosemite 10.10.5
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats graphics  grDevices utils datasets  methods   base
>
>
> other attached packages:
>
> [1] BiocInstaller_1.25.2
>
>
> loaded via a namespace (and not attached):
>
> [1] tools_3.4.0
>
>



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[Bioc-devel] hg133plus2.db

[Levi Waldron]

I don't seem to be able to install hgu133plus2.db in bioc-devel?

> library(BiocInstaller)

Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help

> biocLite("hg133plus2.db")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable)

  (2016-10-26 r71594).

Installing package(s) ‘hg133plus2.db’

Warning: unable to access index for repository
https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:

  cannot download all files

Warning message:

package ‘hg133plus2.db’ is not available (for R Under development)

> sessionInfo()

R Under development (unstable) (2016-10-26 r71594)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X Yosemite 10.10.5


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats graphics  grDevices utils datasets  methods   base


other attached packages:

[1] BiocInstaller_1.25.2


loaded via a namespace (and not attached):

[1] tools_3.4.0

>


-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Rd] colnames for data.frame could be greatly improved

[Jan Gorecki]

Hi there,
Any update on this?
Should I create bugzilla ticket and submit patch?
Regards
Jan Gorecki

On 20 December 2016 at 01:27, Jan Gorecki  wrote:
> Hello,
>
> colnames seems to be not optimized well for data.frame. It escapes
> processing for data.frame in
>
>   if (is.data.frame(x) && do.NULL)
> return(names(x))
>
> but only when do.NULL true. This makes huge difference when do.NULL
> false. Minimal edit to `colnames`:
>
> if (is.data.frame(x)) {
> nm <- names(x)
> if (do.NULL || !is.null(nm))
> return(nm)
> else
> return(paste0(prefix, seq_along(x)))
> }
>
> Script and timings:
>
> N=1e7; K=100
> set.seed(1)
> DF <- data.frame(
> id1 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> id2 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> id3 = sample(sprintf("id%010d",1:(N/K)), N, TRUE), # small groups (char)
> id4 = sample(K, N, TRUE),  # large groups (int)
> id5 = sample(K, N, TRUE),  # large groups (int)
> id6 = sample(N/K, N, TRUE),# small groups (int)
> v1 =  sample(5, N, TRUE),  # int in range [1,5]
> v2 =  sample(5, N, TRUE),  # int in range [1,5]
> v3 =  sample(round(runif(100,max=100),4), N, TRUE) # numeric e.g. 23.5749
> )
> cat("GB =", round(sum(gc()[,2])/1024, 3), "\n")
> #GB = 0.397
> colnames(DF) = NULL
> system.time(nm1<-colnames(DF, FALSE))
> #   user  system elapsed
> # 22.158   0.299  22.498
> print(nm1)
> #[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
>
> ### restart R
>
> colnames <- function (x, do.NULL = TRUE, prefix = "col")
> {
> if (is.data.frame(x)) {
> nm <- names(x)
> if (do.NULL || !is.null(nm))
> return(nm)
> else
> return(paste0(prefix, seq_along(x)))
> }
> dn <- dimnames(x)
> if (!is.null(dn[[2L]]))
> dn[[2L]]
> else {
> nc <- NCOL(x)
> if (do.NULL)
> NULL
> else if (nc > 0L)
> paste0(prefix, seq_len(nc))
> else character()
> }
> }
> N=1e7; K=100
> set.seed(1)
> DF <- data.frame(
> id1 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> id2 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> id3 = sample(sprintf("id%010d",1:(N/K)), N, TRUE), # small groups (char)
> id4 = sample(K, N, TRUE),  # large groups (int)
> id5 = sample(K, N, TRUE),  # large groups (int)
> id6 = sample(N/K, N, TRUE),# small groups (int)
> v1 =  sample(5, N, TRUE),  # int in range [1,5]
> v2 =  sample(5, N, TRUE),  # int in range [1,5]
> v3 =  sample(round(runif(100,max=100),4), N, TRUE) # numeric e.g. 23.5749
> )
> cat("GB =", round(sum(gc()[,2])/1024, 3), "\n")
> #GB = 0.397
> colnames(DF) = NULL
> system.time(nm1<-colnames(DF, FALSE))
> #   user  system elapsed
> #  0.001   0.000   0.000
> print(nm1)
> #[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
>
> sessionInfo()
> #R Under development (unstable) (2016-12-19 r71815)
> #Platform: x86_64-pc-linux-gnu (64-bit)
> #Running under: Debian GNU/Linux stretch/sid
> #
> #locale:
> # [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> # [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> # [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> # [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> # [9] LC_ADDRESS=C   LC_TELEPHONE=C
> #[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> #
> #attached base packages:
> #[1] stats graphics  grDevices utils datasets  methods   base  #
> #
> #loaded via a namespace (and not attached):
> #[1] compiler_3.4.0

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Re: [Bioc-devel] adding a package maintainer

[Obenchain, Valerie]

Hi Stephanie,

You can modify the maintainer name/email in the DESCRIPTION file
yourself by checking out of svn, make the change and then commit.

## release
svn co
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/packageName

## devel
svn co
https://hedgehog.fhcrc.org/biocondcutor/trunk/madman/Rpacks/packageName

Martin or Herve will have to give the new maintainer access to the
package repo. Do they already have an svn user name and password? What
package repo should they be added to?

Valerie







On 12/27/2016 09:00 AM, Stephanie M. Gogarten wrote:
> Which core team member should we contact to add a new maintainer to an 
> existing package?
>
> thanks,
> Stephanie
>
> ___
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>



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[Rd] Proper attribution in Authors@R for the d3.js library by Mike Bostock

[Bryan Hanson]

I have a couple of packages that use the d3.js library developed (and 
copyrighted) by Mike Bostock.  One package uses it extensively, another only 
for one function.  I use R to piece together parts files containing JavaScript 
that I have written, which use d3.js functions and eventually the d3 library is 
called from a temporary web page.

To date, I have pointed to Bostock's library in the Rd files.  However, there 
are a growing number of packages that use d3.js now, and the habit (standard?) 
now seems to be to put Bostock in Authors@R, but they do so in different ways.  
Here are a few examples:

D3partitionR:  Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, 
http://d3js.org. The partitionChart, sunburst, the treemap, the zoomable 
circlePacking, the collapsible indented tree and the collapsible tree are all 
derived from his works.)

scatterD3:  Mike Bostock [aut, cph] (d3.js library, http://d3js.org)

qrage:  Michael Bostock [ctb, cph] (D3.js library)

And there are others.

?person offers the following options that seem relevant:

"aut"
(Author) Use for full authors who have made substantial contributions to the 
package and should show up in the package citation.

"com"
(Compiler) Use for persons who collected code (potentially in other languages) 
but did not make further substantial contributions to the package.

"ctb"
(Contributor) Use for authors who have made smaller contributions (such as code 
patches etc.) but should not show up in the package citation.

"cph"
(Copyright holder) Use for all copyright holders.

Questions: What is the proper attribution in this case?  Bostock is clearly 
cph.  Is that sufficient?  I'm not completely certain about the intentions of 
"com" but it may fit.  "ctb" sounds insufficient and "aut" seems to be a bit 
much (can you be an author of an R package and not know about it?).  Is there a 
CRAN policy about this?

Thanks for any thoughts and guidance.  Bryan

Prof. Bryan Hanson
Dept of Chemistry & Biochemistry
DePauw University
Greencastle IN 46135 USA
academic.depauw.edu/~hanson/index.html
github.com/bryanhanson

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