On 11/03/2015 3:09 PM, Dan Tenenbaum wrote:
- Original Message -
From: Duncan Murdoch murdoch.dun...@gmail.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: r-devel@r-project.org
Sent: Wednesday, March 11, 2015 12:06:48 PM
Subject: Re: [Rd] Notes on building a gcc toolchain for
Using R-devel, I get
R-devel
R Under development (unstable) (2015-03-09 r67969) -- Unsuffered
Consequences
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to
On Tue, Mar 10, 2015 at 12:56 PM, Hui hui...@savvyrookies.com wrote:
Thanks. However I got http error 999.
There is an additional complication here that linkedin doesn't want you to
scrape the website and denies requests form non-browser clients. To get
around this you need to set the
On 12/03/2015 13:51, Prof J C Nash (U30A) wrote:
Are other developers finding R 3.1.3 problematic because vignette
building requires pandoc 1.12.3, while Linux Mint 17 / Ubuntu 14.04 have
1.12.2.1? R 3.1.2 seems to work fine.
R has no built-in support for non-Sweave vignettes, and there is no
Are other developers finding R 3.1.3 problematic because vignette
building requires pandoc 1.12.3, while Linux Mint 17 / Ubuntu 14.04 have
1.12.2.1? R 3.1.2 seems to work fine.
I'd very much like to avoid having to build as large a Linux package as
pandoc, which has given me issues outside of R
Good evening.
Testing the most recent version of Rtools, the build stops about when
text.c is being compiled in the tools package (just after R.Lapack). The
compilation is looking for gcc in C:, even though RTOOLS is set for another
drive, and the compilation has successfully run until this
The subject line is in error, as the issue must be in R-devel.tar.gz
as running the same Rtools on last night's download of
R-devel_2015-03-09.tar.gz successfully navigates that error.
The error exists in R-devel_2015-03-12.tar.gz and
R-devel_2015-03-12.tar.gz and R-devel_2015-03-10.tar.gz, but
The following changes may be responsible:
src\gnuwin32\fixed\Makefile lines 31 and 47 where version 9 has '-e
s|BINPREF =|BINPREF = $(BINPREF)| \' and version 10 has '-e
's|BINPREF =|BINPREF ?= $$(RTOOLS)gcc492_64/bin/|' \'.
Or, it may have been the addition of RTOOLS ?= C:/Rtools/ on line 17
of
Removing the extra '$' from $$(RTOOLS) solves the issue.
Thank you,
Avi
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Thanks Brian.
Indeed, the vignette is in markdown form. When I updated my system to
R 3.1.3 I ran update.packages() and this seems to have upset things
(including R-studio processing of markdown files).
I tried removing rmarkdown and reverting to an older version so that my
sessionInfo() is
What he said
This doesn't make any sense from an API perspective. When would a user ever
expect to see unnamed assay matrices?
--t
On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
allowing positional matching strikes me as being far too fragile.
- Original Message -
From: John Nash profjcn...@gmail.com
To: Prof Brian Ripley rip...@stats.ox.ac.uk, r-devel@r-project.org
Sent: Thursday, March 12, 2015 8:15:42 AM
Subject: Re: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3
Thanks Brian.
Indeed, the vignette is in markdown
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any sense from an API perspective. When would a user ever
expect to see unnamed assay matrices?
When there's a single assay?
--t
On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com
On 12 March 2015 at 08:41, arilamst...@gmail.com wrote:
| But I don't know if this is the best way to do this, or if there is
| anything else to consider. I have never had to manage package dependencies
| outside of CRAN, and have always thought of CRAN as being a closed
| ecosystem, where there
On 12 March 2015 at 09:40, arilamst...@gmail.com wrote:
| Thanks Dirk. I'm looking at it now.
|
| At first glance your documentation brings up a good limitation of simply
| telling users to type devtools::install_github(). Namely, what happens when
| the census bureau updates their shapefiles,
Thanks Dirk. I'm looking at it now.
At first glance your documentation brings up a good limitation of simply
telling users to type devtools::install_github(). Namely, what happens
when the census bureau updates their shapefiles, and I subsequently decide
to update the package? Or if I discover an
I've just uploaded a minor update (3.3.0.1957) to Rtools33, adding the
cygpath.exe utility. That utility converts between Windows style paths
like D:/Rtools and Cygwin style paths like /cygdrive/d/Rtools. It may
be useful in configuration files if your external library expects to
find gcc
Yes, a single-assay SummarizedExperiment would be the most common case
for unnamed assays. But I think at the very least there should be a
warning on unnamed assays.
On 3/12/15 9:24 AM, Martin Morgan wrote:
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any
Dan's suggestion to get latest pandoc got me part of the way to a
workaround. The other part was removing references in the vignette to
alpha versions of some software.
For info: pandoc 1.13.2 seems to have some bugs for conversion of LaTeX
to html or epub still (or at least the error messages
Hi Dirk,
I'm interested in pursing this but I haven't been able to figure how to to
make it work. Here's what I have so far:
install.packages(drat)
library(drat)
addRepo(arilamstein)
I (obviously) have a copy of the choroplethrZip github repo locally. I
typed:
git checkout gh-pages
git push
Hi
I am seeking to understand why the methods package (to be specific
`methods:::.findOrCopyClass` when called by `setIs` when called by
`setClass`) emits a warning message such as
` class SpatialLinesNULL is defined (with package slot 'rgeos') but no
metadata object found to revise
- Original Message -
From: Duncan Murdoch murdoch.dun...@gmail.com
Cc: r-devel@r-project.org
Sent: Thursday, March 12, 2015 10:17:23 AM
Subject: Re: [Rd] Notes on building a gcc toolchain for Rtools (but not
multilib)
I've just uploaded a minor update (3.3.0.1957) to
This is a question for the folks who are developing the C part of the R
implementation, and not about R debugging.
I'm curious what tools developers use to debug the C implementation on
Mac OS and Linux (my two platforms). And, if you happen to use gdb,
whether anyone has any macros to
Ari,
On 12 March 2015 at 14:29, arilamst...@gmail.com wrote:
| I'm interested in pursing this but I haven't been able to figure how to to
make
| it work. Here's what I have so far:
|
| install.packages(drat)
| library(drat)
| addRepo(arilamstein)
|
| I (obviously) have a copy of the
Hi all,
This is relevant (and possibly quite important) to all package maintainers
whose packages contain C or C++ code, or depend on one that does.
A new toolchain is available for building R and R packages on Windows. This
toolchain uses gcc 4.9.2 whereas the old one used gcc 4.6.3.
Another
On OSX I suggest using lldb instead of gdb, it works better with the
toolchain. If you want C level profiling, try Instruments, it is part of
xcode.
See also
http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Debugging-compiled-code
Gabor
On Thu, Mar 12, 2015 at 5:55 PM, Mick Jordan
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