Re: [Bioc-devel] Stackoverflow Bounty: pkgdown R package build_site function causes dependent packages unable to be loaded

[Hervé Pagès]

Hi Marcin,

You posted this 7 months ago, it has been viewed 100 times, and nobody
commented or tried to answer. I don't know if a bounty is going to help
though.

To me, a much more effective way to get people help you is by providing
enough information so that people can easily reproduce the problem.
Honestly, right now, I don't see how people could easily reproduce
this. I guess most people have never heard of pkgdown, or don't know
where to find it, or don't know how to install it, or don't know which
version you used. They don't know which version of R or RTCGA you used
either, or what you did before calling pkgdown::build_site(), or what
platform you are on.

So if you manage to provide code that people can just copy/paste in
a fresh session in order to see the problem, that will greatly help.
Your code should show how to install pkgdown (don't assume people have
it installed already). After your code has loaded all the required
packages, show the output of your sessionInfo().

This is general advice for any bug report. I don't know if you found
a bug but it could be (hard to tell without being able to reproduce).

Also did you try to contact the pkgdown folks? This is probably a more
efficient way to report a bug than using stackoverflow.

Cheers,
H.


On 12/15/2016 07:21 AM, Marcin Kosiński wrote:

I am trying to build a pkgdown documentation for Bioconductor package.
I have wrote about it on the stackoverflow
http://stackoverflow.com/questions/36874972/pkgdown-r-package-build-site-function-causes-dependent-packages-unable-to-be-loa
but the question didn't receivew the expected attention.

I have started a bounty, looking to give 50 points of my reputation for the
best answer.

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--
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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Re: [Rd] New leap second end of 2016 / beginning 2017 (depending on TZ)

[Martin Maechler]

> Martin Maechler 
> on Wed, 14 Dec 2016 17:04:22 +0100 writes:

> As R is sophisticated enough to track leap seconds,
> ?.leap.seconds

> we'd need to update our codes real soon now again:

> https://en.wikipedia.org/wiki/Leap_second

> (and those of you who want second precision in R in 2017 need to start
> working with 'R patched' or 'R devel' ...)

I've been told offline, that the above could be considered as
FUD .. which I hope nobody read from it.

Furthermore, there seems to be wide disagreement about the
usefulness of leap seconds, and how computers (and OSs) should
deal with them.
One recent approach (e.g. by Google) is to "smear the leap
second" into the system (by somehow "throttling" time servers ;-)..

(and no, I even less would want this to become a long thread, so
 please refrain if you can ...)

Martin

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[Rd] print.POSIXct doesn't seem to use tz argument, as per its example

[Jennifer Lyon]

On the documentation page for DateTimeClasses, in the Examples section,
there are the following two lines:

format(.leap.seconds) # the leap seconds in your time zone
print(.leap.seconds, tz = "PST8PDT")  # and in Seattle's

The second line (using print) seems to ignore the tz argument, and prints
the dates in my time zone, while:

format(.leap.seconds, tz = "PST8PDT")

does print the dates in PST. The code in
https://github.com/wch/r-source/blob/trunk/src/library/base/R/datetime.R
around line 234 looks like the ... argument is passed to print, not to
format.

print.POSIXct <-
print.POSIXlt <- function(x, ...)
{
max.print <- getOption("max.print", L)
if(max.print < length(x)) {
print(format(x[seq_len(max.print)], usetz = TRUE), ...)
cat(' [ reached getOption("max.print") -- omitted',
length(x) - max.print, 'entries ]\n')
} else print(if(length(x)) format(x, usetz = TRUE)
 else paste(class(x)[1L], "of length 0"), ...)
invisible(x)
}

The documentation for print() on this page seems to be silent on tz as an
argument, but I do believe the example using print() does not work as
advertised.

Thanks.

Jen
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

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

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Re: [Rd] Parallel compression support for saving to rds/rdata files?

[Simon Urbanek]

> On Dec 15, 2016, at 12:08 AM, Kenny Bell  wrote:
> 
> Hi,
> 
> I have tried to follow the instructions in the ``save`` documentation and
> it doesn't seem to work (see below):
> 
> mydata <- do.call(rbind, rep(iris, 1))
> con <- pipe("pigz -p8 > fname.gz", "wb");
> save(mydata, file = con); close(con) # This runs
> 
> R.utils::gunzip("fname.gz", "fname.RData", overwrite = TRUE)
> load("fname.RData") # Error: error reading from connection
> 
> First question: Should the above work?
> 


Not really, gzip is a bad example, because it doesn't really support parallel 
compression (since a gzip stream cannot be chopped into blocks by design), but 
you can do it with bzip2:

mydata <- do.call(rbind, rep(iris, 1))
con <- pipe("pbzip2 -p8 > fname.bz2", "wb")
save(mydata, file = con)
close(con) 

load("fname.bz2")

you can also use parallel read:

load(pipe("pbzip2 -dc fname.bz2"))

Cheers,
Simon



> Second question: Is it possible to make this dummy friendly by allowing
> "pigz" as an option for ``compress`` in saveRDS and save? And in such a way
> that the decompressing is hidden from the user like normal?
> 
> Thanks!
> Kenny
> 
> 
> -- 
> Kendon Bell
> Email: km...@berkeley.edu
> Phone: (510) 612-3375
> 
> Ph.D. Candidate
> Department of Agricultural & Resource Economics
> University of California, Berkeley
> 
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> 
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> 

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Re: [Bioc-devel] .git folders in the repository

[王棣台]

Hi,

I am the author of the package 'anamiR'.
It might be a mistake I made when I was learning how to use git-SVN.

I think I have corrected it.

Many thanks,
Ti-Tai Wang

從: Bioc-devel [bioc-devel-boun...@r-project.org] 代表 Wolfgang Huber 
[wolfgang.hu...@embl.de]
寄件日期: 2016年12月15日 下午 04:43
至: bioc-devel@r-project.org
主旨: [Bioc-devel] .git folders in the repository

Today I get, after “svn up"
whuber@boltzmann:~/madman/Rpacks$ find . -name .git -exec du -sh {} \;
 17M./anamiR/anamiR/.git
 56K./RareVariantVis/.git

Probably the “.git" folders should not be checked in?

Best wishes
Wolfgang

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[Bioc-devel] Stackoverflow Bounty: pkgdown R package build_site function causes dependent packages unable to be loaded

[Marcin Kosiński]

I am trying to build a pkgdown documentation for Bioconductor package.
I have wrote about it on the stackoverflow
http://stackoverflow.com/questions/36874972/pkgdown-r-package-build-site-function-causes-dependent-packages-unable-to-be-loa
but the question didn't receivew the expected attention.

I have started a bounty, looking to give 50 points of my reputation for the
best answer.

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Shepherd, Lori]

$error
[1] "At least 80% of man pages documenting exported objects must have
runnable examples. The following pages do not:"

This ERROR occurs when man pages are included without runnable examples.  You 
have examples in it looks like 5/12 of your man pages (~42%). We encourage 80%

$warning
[1] "Add non-empty \\value sections to the following man pages:
man/filterBycombStringency.Rd"

Most man pages encourage a \value{} section describing the output of the 
function or what would be returned.  This is asking that you add this section 
to this specific man page with information about what the function returns.


On quick glance I think you would cite the references in the bibliography with 
the tag
Vahid_Jalili_MSPC_2015  not the title "Using combined evidence from replicates 
to evaluate ChIP-seq peaks"




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 Jurat Shayidin 

Sent: Thursday, December 15, 2016 7:17:42 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Quick question about result of R CMD check and R CMD 
BiocCheck

Dear BiocDevel :

I got confused about the message from R CMD BiocCheck, and R CMD check on
my packages. Precisely speaking, R CMD check throws an error that my unit
test is failed, zero warning, 2 notes; instead R CMD BiocCheck complain
with one error that no runnable example found, one warning (I don't
undersand this warning, becuase R CMD check doesn't report this), 4 notes.
I don't understand the result of R CMD BiocCheck, can't figure out the
exact issue . However, result of R CMD check is more clear and
self-explanatory. I did add example for each of my function, R CMD check
okay with it, but R CMD BiocCheck complain about this, Why ? How to address
the issues raised by R CMD BiocCheck ?  R CMD BiocCheck gave me following
message :

$error
[1] "At least 80% of man pages documenting exported objects must have
runnable examples. The following pages do not:"

$warning
[1] "Add non-empty \\value sections to the following man pages:
man/filterBycombStringency.Rd"



Plus, I tried to attach bibliography.bib files on my package's vignette,
but Rstudio didn't print out the bibliography information at the end of
.Rmd file. How can I make this happen ? I did push all recent changes to
github , so everything is synchronized. Is
that possible to kindly ask Bioconductor team to briefly review my packages
and getting valuable opinion to improve my work? I am grad students and
very few experiences in Bioinformatics field (not in this major), so my
very first R package might have a lot of issues, getting possible
contribution would be highly appreciated. Many thanks to Bioconductor team.

Best regards :

--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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[Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Jurat Shayidin]

Dear BiocDevel :

I got confused about the message from R CMD BiocCheck, and R CMD check on
my packages. Precisely speaking, R CMD check throws an error that my unit
test is failed, zero warning, 2 notes; instead R CMD BiocCheck complain
with one error that no runnable example found, one warning (I don't
undersand this warning, becuase R CMD check doesn't report this), 4 notes.
I don't understand the result of R CMD BiocCheck, can't figure out the
exact issue . However, result of R CMD check is more clear and
self-explanatory. I did add example for each of my function, R CMD check
okay with it, but R CMD BiocCheck complain about this, Why ? How to address
the issues raised by R CMD BiocCheck ?  R CMD BiocCheck gave me following
message :

$error
[1] "At least 80% of man pages documenting exported objects must have
runnable examples. The following pages do not:"

$warning
[1] "Add non-empty \\value sections to the following man pages:
man/filterBycombStringency.Rd"



Plus, I tried to attach bibliography.bib files on my package's vignette,
but Rstudio didn't print out the bibliography information at the end of
.Rmd file. How can I make this happen ? I did push all recent changes to
github , so everything is synchronized. Is
that possible to kindly ask Bioconductor team to briefly review my packages
and getting valuable opinion to improve my work? I am grad students and
very few experiences in Bioinformatics field (not in this major), so my
very first R package might have a lot of issues, getting possible
contribution would be highly appreciated. Many thanks to Bioconductor team.

Best regards :

-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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[Rd] Parallel compression support for saving to rds/rdata files?

[Kenny Bell]

Hi,

I have tried to follow the instructions in the ``save`` documentation and
it doesn't seem to work (see below):

mydata <- do.call(rbind, rep(iris, 1))
con <- pipe("pigz -p8 > fname.gz", "wb");
save(mydata, file = con); close(con) # This runs

R.utils::gunzip("fname.gz", "fname.RData", overwrite = TRUE)
load("fname.RData") # Error: error reading from connection

First question: Should the above work?

Second question: Is it possible to make this dummy friendly by allowing
"pigz" as an option for ``compress`` in saveRDS and save? And in such a way
that the decompressing is hidden from the user like normal?

Thanks!
Kenny


-- 
Kendon Bell
Email: km...@berkeley.edu
Phone: (510) 612-3375

Ph.D. Candidate
Department of Agricultural & Resource Economics
University of California, Berkeley

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[Bioc-devel] .git folders in the repository

[Wolfgang Huber]

Today I get, after “svn up"
whuber@boltzmann:~/madman/Rpacks$ find . -name .git -exec du -sh {} \;
 17M./anamiR/anamiR/.git
 56K./RareVariantVis/.git

Probably the “.git" folders should not be checked in?

Best wishes
Wolfgang

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