Re: [R-pkg-devel] Help package checks using valgrind

> On 23 May 2017, at 23:40 , Merlise Clyde, Ph.D. wrote: > > I am trying to resolve the Additional Issues reported by CRAN @ > https://www.stats.ox.ac.uk/pub/bdr/memtests/valgrind/BAS-Ex.Rout for my > package BAS which calls C and Fortran. > > The output from the above URL is

[R-pkg-devel] Help package checks using valgrind

I am trying to resolve the Additional Issues reported by CRAN @ https://www.stats.ox.ac.uk/pub/bdr/memtests/valgrind/BAS-Ex.Rout for my package BAS which calls C and Fortran. The output from the above URL is not particularly informative (at least to me) for identifying where the problems are

[R-pkg-devel] cvDetect: an R + OpenCV + Windows webcam/photo face/palm/finger detection demo package

Hi all, Since I had't found any R + OpenCV face recognition package through Google, so I made a demo package cvDetect , which shows webcam/picture face/palm/finger recognition capability in R. Currently it's for Windows only, since I don't have webcams in my Linux systems so far. My

[Rd] Getting an R bugzilla account

Hi All, I have a fix to this bug ( https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16454) and would like to submit a patch to the bug report on Bugzilla. I'd also like to start going through some of the other Windows-specific issues and start fixing those. The bug submission instructions

Re: [Bioc-devel] openbabel 2.4.1

Hi Kevin, I'll update this (with Herve's help) and will let you know when it's done. Valerie On 05/22/2017 01:21 PM, Kevin Horan wrote: > The package ChemmineOB depends on the external library OpenBabel. There > is now a new version of it, version 2.4.1. Could you please install this > on

[Rd] Allow dot in RHS of update.formula's old formula

Feature request: I want to use update.formula to subtract an intercept (or other) term from a formula with a dot on the RHS. However, as this causes an error, I propose a patch below. Thus, I want: > update.formula(y ~ ., ~ . -1) [1] y ~ . - 1 Instead I get this error: Error in

[Bioc-devel] How can I fix a vignette error in tokay1

Hi, I get the next error when tokay1 runs my vignette.rmd file: LaTeX Error: File `framed.sty 'not found. How can I fix this error? Regards. -- Juan David Henao Maestría en Bioinformática Universidad Nacional de Colombia [[alternative HTML version deleted]]

Re: [Bioc-devel] mzR: pwiz is now the default backend

actually, I got quite some segfaults lately with the Ramp backend (was default up to now). With the pwiz backend I don't get them anymore. Also, in xcms we were manually setting the backend to pwiz and did not experience any problems. cheers, jo On 23 May 2017, at 18:35, Laurent Gatto

Re: [R-pkg-devel] CRAN and cmake

On 2017-05-23 10:56 AM, Dirk Eddelbuettel wrote: On 23 May 2017 at 10:34, Thibault Vatter wrote: | Hi, | | Back in 2015, there was a discussion on this list about CRAN and cmake. | | As explained by Gabor at the time, it would be useful to have cmake in a R | package. | | Furthermore, Gregory

Re: [Bioc-devel] mzR: pwiz is now the default backend

On 23 May 2017 16:26, Vladislav Petyuk wrote: > Are there going to be any noticeable changes for the package users? Does > it break compatibility? Do I need to install something extra (like > ProteoWizard)? In theory, we don't expect any downstream effects: no breaks, no extra dependencies,

Re: [Rd] [PATCH] Ensure correct order of evaluation in macro

On 23/05/2017 11:47 AM, Sahil Kang wrote: Hi Duncan, Would you merge this patch? I'm planning on sending larger patches in the next few days that fix other macros I've seen, but I figured​ it'd be best to start with a smaller patch. No, I generally try to leave the macro stuff to others.

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

Yes, what Joris posts about is exactly what I noted in my March 9th post to R-devel. The behaviour is sort of documented, but not in the clearest manner (in my opinion). Like I say, my ultimate conclusion was that the silent coercion of numerics to integers by sprintf() was a handy convenience,

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

https://github.com/Rdatatable/data.table/issues/2171 The fix was easy, it's just surprising to see the behavior change almost on a whim. Just wanted to point it out in case this is unknown behavior, but Evan seems to have found this as well. On Tue, May 23, 2017 at 12:00 PM, Michael Chirico

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

Astute observation. And of course we should be passing integer when we use %d. It's an edge case in how we printed ITime objects in data.table: On Tue, May 23, 2017 at 11:53 AM, Joris Meys wrote: > I initially thought this is "documented behaviour". ?sprintf says: > >

Re: [R-pkg-devel] CRAN and cmake

My bad, my question was not precise enough: by "an R package containing cmake", I meant "an R package containing cmake itself" in order to be able to use cmake e.g. when building an R package from source. A little bit of context: I am trying to write an R interface to a C++ library where cmake

Re: [Bioc-devel] mzR: pwiz is now the default backend

Are there going to be any noticeable changes for the package users? Does it break compatibility? Do I need to install something extra (like ProteoWizard)? On Tue, May 23, 2017 at 9:10 AM Laurent Gatto wrote: > > Dear developer, > > For those who use mzR to access raw mass

[Bioc-devel] mzR: pwiz is now the default backend

Dear developer, For those who use mzR to access raw mass spectrometry data, please note that we have change the default backend from Ramp to pwiz. The old backend is still available using openMSfile(filename, backend = "Ramp") See https://github.com/sneumann/mzR/issues/84 for details.

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

I initially thought this is "documented behaviour". ?sprintf says: Numeric variables with __exactly integer__ values will be coerced to integer. (emphasis mine). Turns out this only works when the first value is numeric and not NA, as shown by the following example: > sprintf("%d",

Re: [Rd] [PATCH] Ensure correct order of evaluation in macro

Hi Duncan, Would you merge this patch? I'm planning on sending larger patches in the next few days that fix other macros I've seen, but I figured​ it'd be best to start with a smaller patch. Thanks, Sahil __ R-devel@r-project.org mailing list

[R-pkg-devel] CRAN and cmake

Hi, Back in 2015, there was a discussion on this list about CRAN and cmake. As explained by Gabor at the time, it would be useful to have cmake in a R package. Furthermore, Gregory mentioned that there was something available on GitHub: https://github.com/stnava/cmaker Since it seems that the

Re: [Rd] Inconsistency in handling of numeric input with %d by sprintf

Hi Michael, I posted something on this topic to R-devel several weeks ago, but never got a response. My ultimate conclusion is that sprintf() isn't super consistent in how it handles coercion: sometimes it'll coerce real to integer without complaint, other times it won't. (My particular email had

Re: [Rd] help pages base R not rendered correctly?

> On 23 May 2017, at 15:56 , Joris Meys wrote: > > Hi Duncan, > > that explains, thank you. If nobody finds the time to fix that, I might > give it a shot myself this summer. Barbeque is overrated. I beg to differ! Chances of rain are underestimated, though (in .be as in

Re: [Rd] help pages base R not rendered correctly?

Hi Duncan, that explains, thank you. If nobody finds the time to fix that, I might give it a shot myself this summer. Barbeque is overrated. Cheers Joris On Tue, May 23, 2017 at 3:10 PM, Duncan Murdoch wrote: > On 23/05/2017 8:39 AM, Joris Meys wrote: > >> Hi all, >>

Re: [Rd] help pages base R not rendered correctly?

On 23/05/2017 8:39 AM, Joris Meys wrote: Hi all, Don't know if this is a known issue, but I couldn't find anything so I report anyway. When checking eg ?qr in both RStudio and the naked R IDE, the help page is rendered incorrectly. More specifically, any use of \bold{...} is printed as is,