Re: [R-pkg-devel] RFC: an interface to manage use of parallelism in packages

[Vladimir Dergachev]

On Wed, 25 Oct 2023, Ivan Krylov wrote:


Summary: at the end of this message is a link to an R package
implementing an interface for managing the use of execution units in R
packages. As a package maintainer, would you agree to use something
like this? Does it look sufficiently reasonable to become a part of R?
Read on for why I made these particular interface choices.

My understanding of the problem stated by Simon Urbanek and Uwe Ligges
[1,2] is that we need a way to set and distribute the CPU core
allowance between multiple packages that could be using very different
methods to achieve parallel execution on the local machine, including
threads and child processes. We could have multiple well-meaning
packages, each of them calling each other using a different parallelism
technology: imagine parallel::makeCluster(getOption('mc.cores'))
combined with parallel::mclapply(mc.cores = getOption('mc.cores')) and
with an OpenMP program that also spawns getOption('mc.cores') threads.
A parallel BLAS or custom multi-threading using std::thread could add
more fuel to the fire.



Hi Ivan,

  Generally, I like the idea. A few comments:

  * from a package developer point of view, I would prefer to have a clear 
idea of how many threads I could use. So having a core R function like 
"getMaxThreads()" or similar would be useful. What that function returns 
could be governed by a package.


  In fact, it might be a good idea to allow to have several packages 
implementing "thread governors" for different situations.


  * it would make sense to think through whether we want (or not) to allow 
package developers to call omp_set_num_threads() or whether this is done 
by R.


  This is hairier than you might think. Allowing it forces every package 
to call omp_set_num_threads() before OMP block, because there is no way to 
know which packaged was called before.


  Not allowing to call omp_set_num_threads() might make it difficult to 
use all the threads, and force R to initialize OpenMP on startup.


 * Speaking of initialization of OpenMP, I have seen situations where 
spawning some regular pthread threads and then initializing OpenMP forces 
all pthread threads to a single CPU.


  I think this is because OpenMP sets thread affinity for all the process 
threads, but only distributes its own.


 * This also raises the question of how affinity is managed. If you have 
called makeForkCluster() to create 10 R instances and then each uses 2 
OpenMP threads, you do not want those occupying only 2 cpu execution 
threads instead of 20.


 * From the user perspective, it might be useful to be able to limit 
number of threads per package by using patterns or regular expressions.
Often, the reason for limiting number of threads is to reduce memory 
usage.


 * Speaking of memory usage, glibc has parameters like MALLOC_ARENA_MAX 
that have great impact on memory usage of multithreaded programs. I 
usually set it to 1, but then I take extra care to make as few memory 
allocation calls as possible within individual threads.


best

Vladimir Dergachev

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[R-pkg-devel] PkgA imports PkgB, and PkgB suggests PkgA?

[Shu Fai Cheung]

Hi All,

I vaguely recall that, on CRAN, if PkgA imports PkgB, then PkgB cannot
import PkgA. (Please correct me if I am wrong.)

How about this?

PkgA imports PkgB (because PkgA has some helper functions for using PkgB)
PkgB suggests PkgA (because some vignettes or examples in PkgB use
those helpers from PkgA)

Is this allowed on CRAN?

Regards,
Shu Fai

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Re: [Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0

[Hervé Pagès]

Forgot to mention that the package actually got installed, but is 
unloadable (not surprisingly):

     > "CoreGx" %in% rownames(installed.packages())
     [1] TRUE

     > suppressWarnings(suppressMessages(library(CoreGx)))
     Error : in method for ‘updateObject’ with signature 
‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
must appear in the method, in the same place at the end of the argument list
     Error: package or namespace load failed for ‘CoreGx’:
      unable to load R code in package ‘CoreGx’

Best,

H.

On 11/3/23 15:10, Hervé Pagès wrote:
>
> Hi list,
>
> Here is an example:
>
>     hpages@XPS15:~$ R CMD INSTALL CoreGx
>     * installing to library ‘/home/hpages/R/R-4.4.r85388/site-library’
>     * installing *source* package ‘CoreGx’ ...
>     ** using staged installation
>     ** R
>     ** data
>     *** moving datasets to lazyload DB
>     ** inst
>     ** byte-compile and prepare package for lazy loading
>     Error : in method for ‘updateObject’ with signature 
> ‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
> must appear in the method, in the same place at the end of the 
> argument list
>     Error: unable to load R code in package ‘CoreGx’
>     ** help
>     *** installing help indices
>     ** building package indices
>     ** installing vignettes
>     ** testing if installed package can be loaded from temporary location
>     Error : in method for ‘updateObject’ with signature 
> ‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
> must appear in the method, in the same place at the end of the 
> argument list
>     Error: package or namespace load failed for ‘CoreGx’:
>  unable to load R code in package ‘CoreGx’
>     Error: loading failed
>     ** testing if installed package can be loaded from final location
>     Error : in method for ‘updateObject’ with signature 
> ‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
> must appear in the method, in the same place at the end of the 
> argument list
>     Error: package or namespace load failed for ‘CoreGx’:
>  unable to load R code in package ‘CoreGx’
>     Error: loading failed
>     Error : in method for ‘updateObject’ with signature 
> ‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
> must appear in the method, in the same place at the end of the 
> argument list
>     Error: unable to load R code in package ‘CoreGx’
>     ** testing if installed package keeps a record of temporary 
> installation path
>     * DONE (CoreGx)
>
> Many serious errors were ignored. Plus the command returned exit code 0:
>
>     hpages@XPS15:~$ echo $?
>     0
>
> This is with R 4.4, that BioC 3.19 will be based on and that we only 
> started to use recently for our daily builds.
>
> Strangely, we only see this on Linux. On Windows and Mac, we get the 
> usual hard error, as expected. See:
>
> - 
> https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/nebbiolo1-install.html
>
> - 
> https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/palomino3-install.html
>
> - 
> https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/merida1-install.html
>
> To reproduce:
>
>     library(remotes)
>     install_git("https://git.bioconductor.org/packages/CoreGx;)
>
> Thanks,
>
> H.
>
> > sessionInfo()
> R Under development (unstable) (2023-10-22 r85388)
> Platform: x86_64-pc-linux-gnu
> Running under: Ubuntu 23.10
>
> Matrix products: default
> BLAS:   /home/hpages/R/R-4.4.r85388/lib/libRblas.so
> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8    LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_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
>
> time zone: America/Los_Angeles
> tzcode source: system (glibc)
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods base
>
> other attached packages:
> [1] remotes_2.4.2.1
>
> loaded via a namespace (and not attached):
>  [1] processx_3.8.2    compiler_4.4.0    R6_2.5.1 rprojroot_2.0.3
>  [5] cli_3.6.1 prettyunits_1.2.0 tools_4.4.0 crayon_1.5.2
>  [9] desc_1.4.2    callr_3.7.3   pkgbuild_1.4.2 ps_1.7.5
>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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[Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0

[Hervé Pagès]

Hi list,

Here is an example:

     hpages@XPS15:~$ R CMD INSTALL CoreGx
     * installing to library ‘/home/hpages/R/R-4.4.r85388/site-library’
     * installing *source* package ‘CoreGx’ ...
     ** using staged installation
     ** R
     ** data
     *** moving datasets to lazyload DB
     ** inst
     ** byte-compile and prepare package for lazy loading
     Error : in method for ‘updateObject’ with signature 
‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
must appear in the method, in the same place at the end of the argument list
     Error: unable to load R code in package ‘CoreGx’
     ** help
     *** installing help indices
     ** building package indices
     ** installing vignettes
     ** testing if installed package can be loaded from temporary location
     Error : in method for ‘updateObject’ with signature 
‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
must appear in the method, in the same place at the end of the argument list
     Error: package or namespace load failed for ‘CoreGx’:
  unable to load R code in package ‘CoreGx’
     Error: loading failed
     ** testing if installed package can be loaded from final location
     Error : in method for ‘updateObject’ with signature 
‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
must appear in the method, in the same place at the end of the argument list
     Error: package or namespace load failed for ‘CoreGx’:
  unable to load R code in package ‘CoreGx’
     Error: loading failed
     Error : in method for ‘updateObject’ with signature 
‘object="CoreSet"’:  arguments (‘verbose’) after ‘...’ in the generic 
must appear in the method, in the same place at the end of the argument list
     Error: unable to load R code in package ‘CoreGx’
     ** testing if installed package keeps a record of temporary 
installation path
     * DONE (CoreGx)

Many serious errors were ignored. Plus the command returned exit code 0:

     hpages@XPS15:~$ echo $?
     0

This is with R 4.4, that BioC 3.19 will be based on and that we only 
started to use recently for our daily builds.

Strangely, we only see this on Linux. On Windows and Mac, we get the 
usual hard error, as expected. See:

- 
https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/nebbiolo1-install.html

- 
https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/palomino3-install.html

- 
https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/merida1-install.html

To reproduce:

     library(remotes)
     install_git("https://git.bioconductor.org/packages/CoreGx;)

Thanks,

H.

 > sessionInfo()
R Under development (unstable) (2023-10-22 r85388)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 23.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.4.r85388/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8    LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_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

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

other attached packages:
[1] remotes_2.4.2.1

loaded via a namespace (and not attached):
  [1] processx_3.8.2    compiler_4.4.0    R6_2.5.1 rprojroot_2.0.3
  [5] cli_3.6.1 prettyunits_1.2.0 tools_4.4.0 crayon_1.5.2
  [9] desc_1.4.2    callr_3.7.3   pkgbuild_1.4.2 ps_1.7.5

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?

[Johannes Griss]

Hi everyone,

For a while the build system reported an error that our ReactomeGSA 
package cannot be build due to the missing dependency of the 
"ReactomeGSA.data" package which is required to build the vignettes and 
is listed in the "Suggests" section.


ReactomeGSA.data seems to building fine though but depends on ReactomeGSA.

Unfortunately, I cannot figure out how I could solve this issue.

Thanks for your help!

Kind regards,
Johannes

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Re: [R-pkg-devel] [r-package-devel] Win.Metafile and package check - "Found the platform-specific device:"

[Vladimir Dergachev]

On Fri, 3 Nov 2023, wayne.w.jo...@shell.com wrote:


Dear R-Package-Devel,

As part of GWSDAT package (https://github.com/waynegitshell/GWSDAT) we support 
the option to output plots to a WMF 
(https://r-graphics.org/recipe-output-vector-wmf) format if, and only if,  the 
user is on Windows. However, when I run the package checks on here it complains 
about using a platform specific function with the following message:

 Found the platform-specific device:
   'win.metafile'
 dev.new() is the preferred way to open a new device, in the unlikely
 event one is needed.

In my opinion this is a false positive - and a similar issue has previously 
been reported here: 
https://stackoverflow.com/questions/70585796/unable-to-understand-1-note-in-devtoolscheck-caused-by-a-platform-specific-d

Any ideas on how I modify the code and package submission to automatically pass 
the checks?


Two suggestions:

  * let users specify the graphics device they want

  * reading manpage for dev.new() it accepts a bunch of options - there is 
probably a way to request the metafile device you want. But I could not 
find that in documentation.


best

Vladimir Dergachev



Thanks,

Wayne




Wayne Jones
Principal Data Scientist
Decarbonisation Data Science

Tel: +44 (0) 207 934 4330
Projects and Technology, Shell Research Limited, Shell Centre, York Road, 
London, SE1 7NA
Email: wayne.w.jo...@shell.com
Intranet: 
Shell.ai
Internet: www.shell.ai


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Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

[J C Nash]

Yes. An initial space does the trick. Thanks. J

On 2023-11-03 11:48, Serguei Sokol wrote:

Le 03/11/2023 à 15:54, J C Nash a écrit :

I've spent a couple of hours with an Rmarkdown document where I
was describing some spherical coordinates made up of a radius r and
some angles. I wanted to fix the radius at 1.

In my Rmarkdown text I wrote

    Thus we have `r = 1` ...

To avoid a confusion between inline code and fixed font typesetting, could it be

    Thus we have ` r = 1` ...

(with a space after an opening quote)?

Best,
Serguei.



This caused failure to render with "unexpected =". I was using Rstudio
at first and didn't see the error msg.

If I use "radius R" and `R = 1`, things are fine, or `r=1` with no space,
but the particular "(quote) r (space)" seems to trigger code block processing.

Perhaps this note can save others some wasted time.

I had thought (obviously incorrectly) that one needed ```{r something}
to start the code chunk.

JN

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Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

[Serguei Sokol]

Le 03/11/2023 à 15:54, J C Nash a écrit :

I've spent a couple of hours with an Rmarkdown document where I
was describing some spherical coordinates made up of a radius r and
some angles. I wanted to fix the radius at 1.

In my Rmarkdown text I wrote

    Thus we have `r = 1` ...
To avoid a confusion between inline code and fixed font typesetting, 
could it be


   Thus we have ` r = 1` ...

(with a space after an opening quote)?

Best,
Serguei.



This caused failure to render with "unexpected =". I was using Rstudio
at first and didn't see the error msg.

If I use "radius R" and `R = 1`, things are fine, or `r=1` with no space,
but the particular "(quote) r (space)" seems to trigger code block 
processing.


Perhaps this note can save others some wasted time.

I had thought (obviously incorrectly) that one needed ```{r something}
to start the code chunk.

JN

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Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

[Jeff Newmiller via R-package-devel]

A code chunk does always begin with a triple backtick at the beginning of a 
line. The term for what you encountered is "inline code" used to embed computed 
results into the markdown text as though you had typed them directly.

Check out 
https://www.r-bloggers.com/2017/12/how-to-show-r-inline-code-blocks-in-r-markdown
 for relevant discussion.

On November 3, 2023 7:54:22 AM PDT, J C Nash  wrote:
>I've spent a couple of hours with an Rmarkdown document where I
>was describing some spherical coordinates made up of a radius r and
>some angles. I wanted to fix the radius at 1.
>
>In my Rmarkdown text I wrote
>
>   Thus we have `r = 1` ...
>
>This caused failure to render with "unexpected =". I was using Rstudio
>at first and didn't see the error msg.
>
>If I use "radius R" and `R = 1`, things are fine, or `r=1` with no space,
>but the particular "(quote) r (space)" seems to trigger code block processing.
>
>Perhaps this note can save others some wasted time.
>
>I had thought (obviously incorrectly) that one needed ```{r something}
>to start the code chunk.
>
>JN
>
>__
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-- 
Sent from my phone. Please excuse my brevity.

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Re: [Bioc-devel] EpiCompare: transferring maintainership

[Kern, Lori via Bioc-devel]

We will need to create a BiocCredentials account for Tom Roberts if he does not 
have one yet.  We would need to know what email Tom would like for access there 
as well as if they have a github id?   I can create the account and allow 
access.
After access to the package, it will be up to the new maintainer to change the 
DESCRIPTION file and push to git.bioconductor.org.  It will also be good to 
sign up both here on the bioc-devel mailing list as well as the support site.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sera Choi 

Sent: Friday, November 3, 2023 11:17 AM
To: bioc-devel@r-project.org 
Cc: Skene, Nathan G ; tomroberts.wor...@gmail.com 

Subject: [Bioc-devel] EpiCompare: transferring maintainership

Hi Bioconductor team,

I'm currently the maintainer of Bioconductor package, EpiCompare. I'm
writing to request transfer of maintainership to Tom Roberts (
tomroberts.wor...@gmail.com). Please could you let me know what is
required?

Thanks so much!

Best wishes,
Sera

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[Bioc-devel] EpiCompare: transferring maintainership

[Sera Choi]

Hi Bioconductor team,

I'm currently the maintainer of Bioconductor package, EpiCompare. I'm
writing to request transfer of maintainership to Tom Roberts (
tomroberts.wor...@gmail.com). Please could you let me know what is
required?

Thanks so much!

Best wishes,
Sera

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[R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

[J C Nash]

I've spent a couple of hours with an Rmarkdown document where I
was describing some spherical coordinates made up of a radius r and
some angles. I wanted to fix the radius at 1.

In my Rmarkdown text I wrote

   Thus we have `r = 1` ...

This caused failure to render with "unexpected =". I was using Rstudio
at first and didn't see the error msg.

If I use "radius R" and `R = 1`, things are fine, or `r=1` with no space,
but the particular "(quote) r (space)" seems to trigger code block processing.

Perhaps this note can save others some wasted time.

I had thought (obviously incorrectly) that one needed ```{r something}
to start the code chunk.

JN

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[Rd] svd() of a 30000 by 30000 matrix segfaults: 32-bit length overflow in LAPACK?

[Ivan Krylov]

Dear Dr. Robert M Flight, dear R-developers,

By an accident, I've noticed this problem reported on Mastodon [1].

On a computer with ≥32G of RAM, running the following code (which may
take 5 CPU-hours and allocate 27G of RAM!) results in a segfault:

n_val <- 3
tmp_matrix <- matrix(rnorm((n_val ^ 2) / 2), nrow = n_val, ncol = n_val)
svd_res <- svd(tmp_matrix)

Tim Taylor says [2] that this doesn't fail for a 2 by 2 matrix,
which suggests a 32-bit integer overflow: 3*3*8 is 7.2e9, which
is more than 4.3e9, which is more than 2^32, while 2*2*8 is
3.2e9, slightly below the threshold.

Here's the backtrace from the crash:

#0  0x7462ac71 in dlasd3 (nl=468, nr=467, sqre=1, k=921, d=..., q=..., 
ldq=921, dsigma=..., u=...,
ldu=3, u2=..., ldu2=936, vt=..., ldvt=3, vt2=..., ldvt2=937, 
idxc=..., ctot=..., z=..., info=0)
at ../../../../src/modules/lapack/dlapack.f:82312
#1  0x7464578b in dlasd1 (nl=468, nr=467, sqre=1, d=..., 
alpha=-0.58048560936028271,
beta=-0.40955467846435345, u=..., ldu=3, vt=..., ldvt=3, idxq=..., 
iwork=..., work=..., info=0)
at ../../../../src/modules/lapack/dlapack.f:81271
#2  0x74681bf2 in dlasd0 (n=29964, sqre=0, d=..., e=..., u=..., 
ldu=3, vt=..., ldvt=3, smlsiz=25,
iwork=..., work=..., info=0) at 
../../../../src/modules/lapack/dlapack.f:80956
#3  0x7468fd5e in dbdsdc (uplo=..., compq=..., n=3, d=..., e=..., 
u=..., ldu=3, vt=...,
ldvt=3, q=..., iq=..., work=..., iwork=..., info=0, _uplo=1, _compq=1)
at ../../../../src/modules/lapack/dlapack.f:1525
#4  0x746c1f81 in dgesdd (jobz=..., m=3, n=3, a=..., lda=3, 
s=..., u=..., ldu=3, vt=...,
ldvt=3, work=..., lwork=201, iwork=..., info=0, _jobz=1)
at ../../../../src/modules/lapack/dlapack.f:23312
#5  0x74c5550f in La_svd (jobu=, x=, 
s=0x57b88670, u=0x7ffbc379f010,
vt=0x7ffa1652a010) at ../../../../src/include/Rinlinedfuns.h:120

The place of the crash and the state of the registers suggests some
kind of buffer overrun:

(gdb) frame 0
#0  0x7462ac71 in dlasd3 (nl=468, nr=467, sqre=1, k=921, d=..., q=..., 
ldq=921, dsigma=..., u=...,
ldu=3, u2=..., ldu2=936, vt=..., ldvt=3, vt2=..., ldvt2=937, 
idxc=..., ctot=..., z=..., info=0)
at ../../../../src/modules/lapack/dlapack.f:82312
82312   Q( J, I ) = U( JC, I ) / TEMP
(gdb) disas
...
   0x7462ac60 <+1824>:  movslq -0x4(%r10,%rdx,4),%rsi
   0x7462ac65 <+1829>:  add%r12,%rsi
   0x7462ac68 <+1832>:  movsd  (%rcx,%rsi,8),%xmm1
   0x7462ac6d <+1837>:  divsd  %xmm0,%xmm1
=> 0x7462ac71 <+1841>:  movsd  %xmm1,(%rbx,%rdx,8)
...
(gdb) info reg
rbx0x745c38d8  140737293072600
rcx0x7ffbc379f040  140719293067328
rdx0xe5229
rsi0x517d2c5340460

0x745c38d8 looks precariously close to the end of the valid
userspace address range for processes typically running on my computer.
I was also able to reproduce this with OpenBLAS (0.3.5, LAPACK 3.8.0).

We seem to be overflowing the WORK array. The DGESDD documentation says
that for JOBZ = 'S', WORK must be of length >= 4*mn*mn + 7*mn, where
mn = min(M, N). For M = N = 3, this comes out to 360021, while
the actual length of the WORK array is only 201 (as returned from a
previous call to DGESDD with LWORK = -1).

I think this is caused by an overflow in the value of the BDSPAC
variable. At the point where MINWRK is assigned (MAX(MINWRK,MAXWRK) to
become LWORK later), the following can be observed:

22721   MINWRK = 3*N + MAX( M, BDSPAC )
0x77e9a2e0cmp%ecx,%esi
(gdb) p M
$48 = 3
(gdb) p BDSPAC
$49 = 
(gdb) p $ecx
$50 = -1594847296
(gdb) p $esi
$51 = 3

The debugger insists that the BDSPAC variable is optimised out for most
of the duration of its existence, but it can be proven that it
overflows:

22613  BDSPAC = 3*N*N + 4*N
(gdb) ptype BDSPAC
type = integer(kind=4)
(gdb) p BDSPAC
$60 = 
(gdb) p (int32_t)(3*M*M + 4*M)
$61 = -1594847296

Is there anything R can do at this point, given the required length of
LWORK being impossible to represent using a signed 32-bit integer?

-- 
Best regards,
Ivan

[1] https://mastodon.social/@rmflight/111341279750995911

[2] https://mastodon.social/@_timtay...@fosstodon.org/111341425112070441

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Re: [Bioc-devel] gwasurvivr is looking for a new owner/maintainer

[Abbas Rizvi]

Ali - I'll email you separately!

If any other folks are interested, please still inquire as we figure out
the ownership handoff.

Thank you!

Abbas

On Fri, Nov 3, 2023 at 9:01 AM Ali Sajid Imami 
wrote:

> I am definitely interested, as I am working heavily with GWAS data now.
>
> > On Nov 3, 2023, at 8:36 AM, Abbas Rizvi  wrote:
> >
> > Dear Bioconductor Developers,
> >
> > We are looking for a new primary owner for gwasurvivr
> >  >.
> > This package allows users to build multivariate Cox models on
> typed/imputed
> > GWAS data. It seems to have quite a few regular users and has been cited
> > <
> https://scholar.google.ca/scholar?oi=bibs=en=770317402630660857>
> for
> > a number of research projects. We don't have time to support this
> > project/package any longer.
> >
> > Revamping this package and expanding its usage could be an excellent part
> > of one's MS or PhD projects. I am happy to onboard anyone to the package
> > code base and work with them on the needs and feature updates that are
> > needed.
> >
> > Please let me know if you are interested.
> >
> > - Abbas
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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[R-pkg-devel] [r-package-devel] Win.Metafile and package check - "Found the platform-specific device:"

[Wayne.W.Jones]

Dear R-Package-Devel,

As part of GWSDAT package (https://github.com/waynegitshell/GWSDAT) we support 
the option to output plots to a WMF 
(https://r-graphics.org/recipe-output-vector-wmf) format if, and only if,  the 
user is on Windows. However, when I run the package checks on here it complains 
about using a platform specific function with the following message:

  Found the platform-specific device:
'win.metafile'
  dev.new() is the preferred way to open a new device, in the unlikely
  event one is needed.

In my opinion this is a false positive - and a similar issue has previously 
been reported here: 
https://stackoverflow.com/questions/70585796/unable-to-understand-1-note-in-devtoolscheck-caused-by-a-platform-specific-d

Any ideas on how I modify the code and package submission to automatically pass 
the checks?

Thanks,

Wayne




Wayne Jones
Principal Data Scientist
Decarbonisation Data Science

Tel: +44 (0) 207 934 4330
Projects and Technology, Shell Research Limited, Shell Centre, York Road, 
London, SE1 7NA
Email: wayne.w.jo...@shell.com
Intranet: 
Shell.ai
Internet: www.shell.ai


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[Bioc-devel] gwasurvivr is looking for a new owner/maintainer

[Abbas Rizvi]

Dear Bioconductor Developers,

We are looking for a new primary owner for gwasurvivr
.
This package allows users to build multivariate Cox models on typed/imputed
GWAS data. It seems to have quite a few regular users and has been cited
 for
a number of research projects. We don't have time to support this
project/package any longer.

Revamping this package and expanding its usage could be an excellent part
of one's MS or PhD projects. I am happy to onboard anyone to the package
code base and work with them on the needs and feature updates that are
needed.

Please let me know if you are interested.

- Abbas

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Vladimir Dergachev]

On Wed, 1 Nov 2023, David Hugh-Jones wrote:


Aside from the package question, surely the other issue here is that Prof
Ripley’s email is extraordinarily rude. Any paid employee would be sacked
for that. I appreciate R and CRAN are volunteer-run organisations, but I
don’t think that should be an excuse for this level of, frankly, toxicity.
Why is he allowed to get away with it?


So one thing to keep in mind that doing volunteer public facing work tends 
to expose people to all kinds of unreasonable requests.


Those who endure often become more direct, and that's fine. Or, and 
people in commercial companies can be very direct too.


One thing that helps is to be extra-polite to a person who is doing a lot 
of volunteer work, and who is likely way oversubscribed.


Focusing on practical matters, if you take a step back things look 
pretty good:


Your package has dependency on a package that you have not written and
that is maintained outside CRAN. It was bound to break sooner or later.

However, the last time you updated bioOED was in 2019 and there was no 
need to do anything for more than 3 years. That's amazing ! And probably 
made possible by being a little bit too direct on occasion.


best

Vladimir Dergachev



David


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Re: [Bioc-devel] Add a package to BiocCredentials

[Yunshun Chen via Bioc-devel]

Hi Lori,

Thanks for that.

Yes, I can confirm that Mengbo Li is one of the scider authors and maintainers. 
Could you please grant Mengbo access to scider on Bioc git?

Best,
Yunshun


From: Kern, Lori 
Sent: Friday, November 3, 2023 22:15
To: bioc-devel@r-project.org ; Mengbo Li 

Cc: Yunshun Chen 
Subject: Re: Add a package to BiocCredentials

Yunchun Chen as the current maintainer can you please confirm this request?


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Mengbo Li via 
Bioc-devel 
Sent: Friday, November 3, 2023 5:12 AM
To: bioc-devel@r-project.org 
Cc: Yunshun Chen 
Subject: [Bioc-devel] Add a package to BiocCredentials

Dear core team,

Hope this email finds you well. Could I please have scider 
(https://secure-web.cisco.com/1Dl9WFFykg45Tdw8lYQGZVVBEqpo7LEB9FTe9nej7_P_i8sLW6ap8WOz2vz7pAMkhqULPLN5QgVJVB5N0RcA_MROioNJwneusXiG9NpAlL_Uw3_pDoE3zOuEYLdI4-Cv6SUn3kaHkB9SCDdDAkB19x8Jmm2eVXfiihblp-aD8d4jCLzUAmIJT_GQWLboOxjeJvq-7EGiRTZOi8Q0PEKKn7z3x0-i2qg5EjBXmHYTr4UyBE3KiMfcRdIdhnQNG-Cx35FhF94_SUbBQvBLfKi6q2shhOJhMSA9QqghhPiqYGMUJ6pPh2kj96KirwVBG8qrT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fscider.html)
 added to my Bioc git credentials? The email address is 
li...@wehi.edu.au. I have also cc-ed the current 
maintainer of the package.

Many thanks,
Mengbo

[WEHI Logo]


Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia

http://secure-web.cisco.com/1K1BiFTNEdSY2DDCe1DG2wQiBjEPrfF7izI_9faFlAsvTibbBQmbrS0ykAuNo6hr-20mDZTQBPrij2XVAyMkf7m44YLxPiMirDXId6PfTjChBJJVxa24agUcGv90AcmDp8apyf0V2Y0KxVcoUgDw-gSX0Z4V-WPFArWvGU-YahlmmKwAMLXj-1v4KOGi9nJLZTyPZm0nVJj99GkRp_VTP4x4Wkzrb9bFqq_m7EU5623y7b7CwkZsvcn3JcCgqDTwOB3eJjvdoXqigHj8S1w1k39vj6DNzYBppFd8mY7QrClfLLh_NFsLPmewTUqmyKjBC/http%3A%2F%2Fwww.wehi.edu.au

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[David Hugh-Jones]

Guys,

Martin, I am very sorry you spent all that time. I am sceptical that this
is a correct interpretation of the law, given what I see on Twitter daily,
and I would not take a university as an authority on this. But that is
neither here nor there – if I made you waste your time, that's my bad and
I'm sorry.

More generally, I have absolutely no wish to spend time beating up on any
individual – and people have kindly sent comments off-list that gave me
context about the specific case. But persistent rudeness is harmful, and
there ought to be a way to address it. Many projects use codes of conduct
for this purpose.

David


On Fri, 3 Nov 2023 at 11:15, Martin Maechler 
wrote:

> Dear R-package-devel readers *and* notably writers,
>
> In Europe there are (diverse) laws about privacy etc, and those,
> (and/or some politeness) do not allow
> free citing of private e-mail communications in public
> nor ad hominem remarks in such public communication.
>
> For this reason, I (as mailing list co-maintainer, and notably
> responsible for the lawfulness of the public mailing list archives on
> our web server) now spent about 2 hours  to carefully obey such
> privacy requirements (carefully editing + recreating all the html
> archives).
> {In another similar case, my employer, ETH Zurich, did urge me
> "from above" to spend my time with such a tedious and ungratifying job ...}
> This is *NOT* something I'd be happy to redo.
>
> So *please* do not misuse such a public mailing list and do keep
> your private opinions private in such a case in the future!
>
> > Spencer Graves  on Thu, 2 Nov 2023 15:29:29 -0500 writes:
>
> > On 11/2/23 2:52 PM, Rolf Turner wrote:
> >>
> >> On Wed, 1 Nov 2023 16:10:34 + David Hugh-Jones wrote:
> >>
> >>> Aside from the package question, surely the other issue
> >>> here is that ’s email is extraordinarily
> >>> rude. Any paid employee would be sacked for that. I
> >>> appreciate R and CRAN are volunteer-run organisations,
> >>> but I don’t think that should be an excuse for this
> >>> level of, frankly, toxicity. Why is he allowed to get
> >>> away with it?
> >>>
> >>> David
>
> >>
> >> I've just had a look at the initial posting in this
> >> thread
> >>
> >> and can see nothing rude or offensive in the email
> >> that was copied and pasted into that  posting.
> >>
> >> I find *your* email far more offensive than anything that
> >>  has ever written.  Get a life.
> >>
> >> cheers,
> >>
> >> Rolf Turner
> >>
> >> P.S.  See fortunes::fortune(88).
> >>
> >> R. T.
>
>
> > Hi, David:
>
>
> []
>
>
> > I've been in the military, and I've learned to ignore
> > the tone and look for the value in comments I
> > receive. I've learned a lot from , and
> > others. When the tone seemed less supportive or even
> > insulting, I'm very glad the person took the time to
> > comment and didn't decide not to reply for fear of
> > offending me. I'm more productive and a better human for
> > all the help I've gotten from this and other R-related
> > lists.
>
>
> > fortunes::fortune('Spencer Graves')
>
> which can you get 4 different answers; using `showMatches` argument
> (which I think I had added), e.g. now gives
>
> > fortune("Spencer Graves", showMatches = TRUE)
> Matching row numbers: 90, 124, 177, 271
>
> Rolf Turner: In the middle of a Saturday morning (in my Time Zone!) I send
> out a plea for help, and in
> just over 20 minutes my problem is solved!
> I don't think you get service like that anywhere else. This R-help list is
> BLOODY AMAZING!
> Spencer Graves: 'The sun never sets on the (former) British Empire.'
> Today, it never sets on R-Help.
>-- Rolf Turner and Spencer Graves
>   R-help (May 2005)
>
> and then
>
> > fortune(90)
>
> Our great-great grandchildren as yet unborn may read some of the stupid
> questions and/or answers that I
> and perhaps others give from time to time. I'd rather get flamed for
> saying something stupid in public on
> this list than to continue to provide substandard service to the people
> with whom I work because I
> perpetrated the same mistake in an environment in which no one questioned
> so effectively my errors.
>-- Spencer Graves (in a discussion on whether answers on R-help should
> be more polite)
>   R-help (December 2004)
>
> > sg
>
> Martin
>
>
> --
> Martin Maechler
> ETH Zurich  and  R Core team
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Martin Maechler]

Dear R-package-devel readers *and* notably writers,

In Europe there are (diverse) laws about privacy etc, and those,
(and/or some politeness) do not allow
free citing of private e-mail communications in public
nor ad hominem remarks in such public communication.

For this reason, I (as mailing list co-maintainer, and notably
responsible for the lawfulness of the public mailing list archives on
our web server) now spent about 2 hours  to carefully obey such
privacy requirements (carefully editing + recreating all the html archives).
{In another similar case, my employer, ETH Zurich, did urge me
"from above" to spend my time with such a tedious and ungratifying job ...}
This is *NOT* something I'd be happy to redo.

So *please* do not misuse such a public mailing list and do keep
your private opinions private in such a case in the future!

> Spencer Graves  on Thu, 2 Nov 2023 15:29:29 -0500 writes:

> On 11/2/23 2:52 PM, Rolf Turner wrote:
>> 
>> On Wed, 1 Nov 2023 16:10:34 + David Hugh-Jones wrote:
>> 
>>> Aside from the package question, surely the other issue
>>> here is that ’s email is extraordinarily
>>> rude. Any paid employee would be sacked for that. I
>>> appreciate R and CRAN are volunteer-run organisations,
>>> but I don’t think that should be an excuse for this
>>> level of, frankly, toxicity. Why is he allowed to get
>>> away with it?
>>> 
>>> David

>> 
>> I've just had a look at the initial posting in this
>> thread
>>
>> and can see nothing rude or offensive in the email
>> that was copied and pasted into that  posting.
>> 
>> I find *your* email far more offensive than anything that
>>  has ever written.  Get a life.
>> 
>> cheers,
>> 
>> Rolf Turner
>> 
>> P.S.  See fortunes::fortune(88).
>> 
>> R. T.


> Hi, David:


[]


> I've been in the military, and I've learned to ignore
> the tone and look for the value in comments I
> receive. I've learned a lot from , and
> others. When the tone seemed less supportive or even
> insulting, I'm very glad the person took the time to
> comment and didn't decide not to reply for fear of
> offending me. I'm more productive and a better human for
> all the help I've gotten from this and other R-related
> lists.


> fortunes::fortune('Spencer Graves')

which can you get 4 different answers; using `showMatches` argument
(which I think I had added), e.g. now gives

> fortune("Spencer Graves", showMatches = TRUE)
Matching row numbers: 90, 124, 177, 271 

Rolf Turner: In the middle of a Saturday morning (in my Time Zone!) I send out 
a plea for help, and in
just over 20 minutes my problem is solved!
I don't think you get service like that anywhere else. This R-help list is 
BLOODY AMAZING!
Spencer Graves: 'The sun never sets on the (former) British Empire.' Today, it 
never sets on R-Help.
   -- Rolf Turner and Spencer Graves
  R-help (May 2005)

and then

> fortune(90)

Our great-great grandchildren as yet unborn may read some of the stupid 
questions and/or answers that I
and perhaps others give from time to time. I'd rather get flamed for saying 
something stupid in public on
this list than to continue to provide substandard service to the people with 
whom I work because I
perpetrated the same mistake in an environment in which no one questioned so 
effectively my errors.
   -- Spencer Graves (in a discussion on whether answers on R-help should be 
more polite)
  R-help (December 2004)

> sg

Martin


--
Martin Maechler
ETH Zurich  and  R Core team

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Re: [Bioc-devel] Add a package to BiocCredentials

[Kern, Lori via Bioc-devel]

Yunchun Chen as the current maintainer can you please confirm this request?


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Mengbo Li via 
Bioc-devel 
Sent: Friday, November 3, 2023 5:12 AM
To: bioc-devel@r-project.org 
Cc: Yunshun Chen 
Subject: [Bioc-devel] Add a package to BiocCredentials

Dear core team,

Hope this email finds you well. Could I please have scider 
(https://secure-web.cisco.com/1Dl9WFFykg45Tdw8lYQGZVVBEqpo7LEB9FTe9nej7_P_i8sLW6ap8WOz2vz7pAMkhqULPLN5QgVJVB5N0RcA_MROioNJwneusXiG9NpAlL_Uw3_pDoE3zOuEYLdI4-Cv6SUn3kaHkB9SCDdDAkB19x8Jmm2eVXfiihblp-aD8d4jCLzUAmIJT_GQWLboOxjeJvq-7EGiRTZOi8Q0PEKKn7z3x0-i2qg5EjBXmHYTr4UyBE3KiMfcRdIdhnQNG-Cx35FhF94_SUbBQvBLfKi6q2shhOJhMSA9QqghhPiqYGMUJ6pPh2kj96KirwVBG8qrT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fscider.html)
 added to my Bioc git credentials? The email address is 
li...@wehi.edu.au. I have also cc-ed the current 
maintainer of the package.

Many thanks,
Mengbo

[WEHI Logo]


Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia

http://secure-web.cisco.com/1K1BiFTNEdSY2DDCe1DG2wQiBjEPrfF7izI_9faFlAsvTibbBQmbrS0ykAuNo6hr-20mDZTQBPrij2XVAyMkf7m44YLxPiMirDXId6PfTjChBJJVxa24agUcGv90AcmDp8apyf0V2Y0KxVcoUgDw-gSX0Z4V-WPFArWvGU-YahlmmKwAMLXj-1v4KOGi9nJLZTyPZm0nVJj99GkRp_VTP4x4Wkzrb9bFqq_m7EU5623y7b7CwkZsvcn3JcCgqDTwOB3eJjvdoXqigHj8S1w1k39vj6DNzYBppFd8mY7QrClfLLh_NFsLPmewTUqmyKjBC/http%3A%2F%2Fwww.wehi.edu.au

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WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional 
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to country and community.

Private and confidential
The content of this e-mail and any attachments may be private and confidential, 
intended only for use of the individual or entity named. If you are not the 
intended recipient of this message you must not read, forward, print, copy, 
disclose, use or store in any way the information this e-mail or any attachment 
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[Bioc-devel] Add a package to BiocCredentials

[Mengbo Li via Bioc-devel]

Dear core team,

Hope this email finds you well. Could I please have scider 
(https://bioconductor.org/packages/release/bioc/html/scider.html) added to my 
Bioc git credentials? The email address is 
li...@wehi.edu.au. I have also cc-ed the current 
maintainer of the package.

Many thanks,
Mengbo

[WEHI Logo]


Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia

www.wehi.edu.au

Twitter  |  
Facebook  |  
Instagram  |  
Youtube  |  
LinkedIn


WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional 
owners of the land where our campuses are located and the continuing connection 
to country and community.

Private and confidential
The content of this e-mail and any attachments may be private and confidential, 
intended only for use of the individual or entity named. If you are not the 
intended recipient of this message you must not read, forward, print, copy, 
disclose, use or store in any way the information this e-mail or any attachment 
contains. If you are not the intended recipient, please notify the sender 
immediately and delete or destroy all copies of this e-mail and any attachment.

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[Bioc-devel] problems when updating MOSim package

[Sonia Tarazona]

Dear Lori,

We have made some changes in the MOSim package and we are now trying to
update the package in Bioconductor.

However, we cannot make it. This is the error message we get:

PS W:\MOSim> git push upstream devel
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

However, we could do it last time with the same computer and credentials.
We have checked the ssh keys in my computer, GitHub and Bioconductor and
everything seems to be fine.

Could you help us with this?

Thanks,

Sonia Tarazona

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