Re: [R-pkg-devel] [External] [External] RcmdrPlugin.HH_1.1-48.tar.gz
> Duncan Murdoch
> on Thu, 7 Mar 2024 05:08:40 -0500 writes:
> On 07/03/2024 4:16 a.m., Ivan Krylov wrote:
>> On Wed, 6 Mar 2024 13:46:55 -0500 Duncan Murdoch
>> wrote:
>>
>>> is this just a more or less harmless error, thinking
>>> that the dot needs escaping
>>
>> I think it's this one. You are absolutely right that the
>> dot doesn't need escaping in either TRE (which is what's
>> used inside exportPattern) or PCRE. In PRCE, this regular
>> expression would have worked as intended:
>>
>> # We do match backslashes by mistake. grepl('[\\.]',
>> '\\') # [1] TRUE
>>
>> # In PCRE, this wouldn't have been a mistake.
>> grepl('[\\.]', c('\\', '.'), perl = TRUE) # [1] FALSE
>> TRUE
>>
> Thanks, I didn't realize that escaping in PCRE was
> optional.
> So the default exportPattern line could be
>exportPattern("^[^.]")
> and it would work even if things were changed so that PCRE
> was used instead of TRE.
> Duncan Murdoch
Yes, thank you, Duncan!
.. I had started changing to this much easier pattern already
before reading on ... --> in R-devel; now also with "doc"s (NEWS.Rd,
R-exts.texi)
Martin
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Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation
В Thu, 7 Mar 2024 20:27:29 + "Ruff, Sergej" пишет: > I am refering to Rstudio. I checked the settings and type is set to > "htlm", not text. And I was wondering why the package documentation > opened in a browser when I used @doctype. Do you still have the source package .tar.gz file for which ?bootGSEA would start a browser from inside RStudio? -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation
yes,
I am refering to Rstudio. I checked the settings and type is set to "htlm", not
text. And I was wondering why the package documentation opened in a browser
when I used @doctype. Maybe it has nothing to do with that but I can´t find the
reason why it opened in the browser in the first place.
Von: Jeff Newmiller
Gesendet: Donnerstag, 7. März 2024 20:57:58
An: r-package-devel@r-project.org; Ruff, Sergej; Hadley Wickham
Cc: r-package-devel@r-project.org
Betreff: [EXTERN] Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need
help for r package documentation
What is a "right side window"? Are you mixing up what R does and what RStudio
does? I think I agree with Ivan that this is a question about the environment
in which you are loading the package rather than anything in the package itself.
On March 7, 2024 11:21:06 AM PST, "Ruff, Sergej"
wrote:
>So, in the previous version of the package when we type ?bootGSEA, it opens
>the documentation in webpage (google, firefox…) and when we type ?pkg-function
>opens to the right side window, but now it just opens in the right side
>window. I was wondering why does it not open in webpage now.
>
>
>Von: Ruff, Sergej
>Gesendet: Donnerstag, 7. März 2024 17:56:20
>An: Hadley Wickham
>Cc: r-package-devel@r-project.org
>Betreff: AW: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for
>r package documentation
>
>
>the package is currently available under:
>https://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
>
>
>line 1-31 contains the package information.
>
>
>#' Package contains functions that repeates GSEA using bootstrap samples of
>gene sets. Bootstrap results are
>#' aggregated to a new ranking score. The score can be compared to the gene set
>#' ranking resulting from the standard GSEA.
>#'
>#' So far the functions included in the package are:
>#' \itemize{
>#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
>#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
>boostrap pathway analysis
>#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
>#' \item \code{\link{boot.GO}} Bootstrap GO analysis
>#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
>#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
>#' \item \code{\link{histDiff}} Visualization of difference in ranks
>#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
>#' }
>#'
>#' \tabular{ll}{
>#' Package: \tab bootGSEA\cr
>#' Type: \tab Package\cr
>#' Version: \tab 1.0\cr
>#' Date: \tab 2024-03-05\cr
>#' License: \tab GPL (>= 3)\cr
>#' }
>#'
>#' @author Shamini Hemandhar Kumar, Klaus Jung
>(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
>#'
>#' Maintainer: Shamini Hemandhar Kumar
>(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
>#' @aliases bootGSEA
>#' @title Robustness evaluation of gene set enrichment analysis (GSEA)
>#' @keywords Robustness GSEA
>"_PACKAGE"
>
>
>
>Von: Hadley Wickham
>Gesendet: Donnerstag, 7. März 2024 16:02:15
>An: Ruff, Sergej
>Cc: r-package-devel@r-project.org
>Betreff: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r
>package documentation
>
>Do you have a pointer to the roxygen2 comments that you're using?
>Hadley
>
>On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
>mailto:sergej.r...@tiho-hannover.de>> wrote:
>Hello,
>
>I need help with a package I am currently developing called bootGSEA.
> I noticed that when I try ‘?bootGSEA’ it goes to the help page in R itself
> but not to the html page (we had this issue last time as well but we solved
> it by adding a documentation to the package itself to the R file) like from
> the before version of the package.
>I tried “_PACKAGE” in the documentation of the package section as @doctype is
>depreceated, but it still doesn’t seem to solve the issue. Do you have any
>idea on this?
>
>
>[[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing
>list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>--
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>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need help for r package documentation
What is a "right side window"? Are you mixing up what R does and what RStudio
does? I think I agree with Ivan that this is a question about the environment
in which you are loading the package rather than anything in the package itself.
On March 7, 2024 11:21:06 AM PST, "Ruff, Sergej"
wrote:
>So, in the previous version of the package when we type ?bootGSEA, it opens
>the documentation in webpage (google, firefox…) and when we type ?pkg-function
>opens to the right side window, but now it just opens in the right side
>window. I was wondering why does it not open in webpage now.
>
>
>Von: Ruff, Sergej
>Gesendet: Donnerstag, 7. März 2024 17:56:20
>An: Hadley Wickham
>Cc: r-package-devel@r-project.org
>Betreff: AW: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for
>r package documentation
>
>
>the package is currently available under:
>https://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
>
>
>line 1-31 contains the package information.
>
>
>#' Package contains functions that repeates GSEA using bootstrap samples of
>gene sets. Bootstrap results are
>#' aggregated to a new ranking score. The score can be compared to the gene set
>#' ranking resulting from the standard GSEA.
>#'
>#' So far the functions included in the package are:
>#' \itemize{
>#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
>#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
>boostrap pathway analysis
>#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
>#' \item \code{\link{boot.GO}} Bootstrap GO analysis
>#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
>#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
>#' \item \code{\link{histDiff}} Visualization of difference in ranks
>#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
>#' }
>#'
>#' \tabular{ll}{
>#' Package: \tab bootGSEA\cr
>#' Type: \tab Package\cr
>#' Version: \tab 1.0\cr
>#' Date: \tab 2024-03-05\cr
>#' License: \tab GPL (>= 3)\cr
>#' }
>#'
>#' @author Shamini Hemandhar Kumar, Klaus Jung
>(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
>#'
>#' Maintainer: Shamini Hemandhar Kumar
>(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
>#' @aliases bootGSEA
>#' @title Robustness evaluation of gene set enrichment analysis (GSEA)
>#' @keywords Robustness GSEA
>"_PACKAGE"
>
>
>
>Von: Hadley Wickham
>Gesendet: Donnerstag, 7. März 2024 16:02:15
>An: Ruff, Sergej
>Cc: r-package-devel@r-project.org
>Betreff: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r
>package documentation
>
>Do you have a pointer to the roxygen2 comments that you're using?
>Hadley
>
>On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
>mailto:sergej.r...@tiho-hannover.de>> wrote:
>Hello,
>
>I need help with a package I am currently developing called bootGSEA.
> I noticed that when I try ‘?bootGSEA’ it goes to the help page in R itself
> but not to the html page (we had this issue last time as well but we solved
> it by adding a documentation to the package itself to the R file) like from
> the before version of the package.
>I tried “_PACKAGE” in the documentation of the package section as @doctype is
>depreceated, but it still doesn’t seem to solve the issue. Do you have any
>idea on this?
>
>
>[[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing
>list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>--
>http://hadley.nz
>
> [[alternative HTML version deleted]]
>
>__
>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] [EXTERN] Re: @doctype is deprecated. need help for r package documentation
So, in the previous version of the package when we type ?bootGSEA, it opens
the documentation in webpage (google, firefox…) and when we type ?pkg-function
opens to the right side window, but now it just opens in the right side window.
I was wondering why does it not open in webpage now.
Von: Ruff, Sergej
Gesendet: Donnerstag, 7. März 2024 17:56:20
An: Hadley Wickham
Cc: r-package-devel@r-project.org
Betreff: AW: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r
package documentation
the package is currently available under:
https://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
line 1-31 contains the package information.
#' Package contains functions that repeates GSEA using bootstrap samples of
gene sets. Bootstrap results are
#' aggregated to a new ranking score. The score can be compared to the gene set
#' ranking resulting from the standard GSEA.
#'
#' So far the functions included in the package are:
#' \itemize{
#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
boostrap pathway analysis
#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
#' \item \code{\link{boot.GO}} Bootstrap GO analysis
#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
#' \item \code{\link{histDiff}} Visualization of difference in ranks
#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
#' }
#'
#' \tabular{ll}{
#' Package: \tab bootGSEA\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0\cr
#' Date: \tab 2024-03-05\cr
#' License: \tab GPL (>= 3)\cr
#' }
#'
#' @author Shamini Hemandhar Kumar, Klaus Jung
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
#'
#' Maintainer: Shamini Hemandhar Kumar
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
#' @aliases bootGSEA
#' @title Robustness evaluation of gene set enrichment analysis (GSEA)
#' @keywords Robustness GSEA
"_PACKAGE"
Von: Hadley Wickham
Gesendet: Donnerstag, 7. März 2024 16:02:15
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r
package documentation
Do you have a pointer to the roxygen2 comments that you're using?
Hadley
On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
mailto:sergej.r...@tiho-hannover.de>> wrote:
Hello,
I need help with a package I am currently developing called bootGSEA.
I noticed that when I try ‘?bootGSEA’ it goes to the help page in R itself but
not to the html page (we had this issue last time as well but we solved it by
adding a documentation to the package itself to the R file) like from the
before version of the package.
I tried “_PACKAGE” in the documentation of the package section as @doctype is
depreceated, but it still doesn’t seem to solve the issue. Do you have any idea
on this?
[[alternative HTML version deleted]]
__
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Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need help for r package documentation
the package is currently available under:
https://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
line 1-31 contains the package information.
#' Package contains functions that repeates GSEA using bootstrap samples of
gene sets. Bootstrap results are
#' aggregated to a new ranking score. The score can be compared to the gene set
#' ranking resulting from the standard GSEA.
#'
#' So far the functions included in the package are:
#' \itemize{
#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
boostrap pathway analysis
#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
#' \item \code{\link{boot.GO}} Bootstrap GO analysis
#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
#' \item \code{\link{histDiff}} Visualization of difference in ranks
#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
#' }
#'
#' \tabular{ll}{
#' Package: \tab bootGSEA\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0\cr
#' Date: \tab 2024-03-05\cr
#' License: \tab GPL (>= 3)\cr
#' }
#'
#' @author Shamini Hemandhar Kumar, Klaus Jung
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
#'
#' Maintainer: Shamini Hemandhar Kumar
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
#' @aliases bootGSEA
#' @title Robustness evaluation of gene set enrichment analysis (GSEA)
#' @keywords Robustness GSEA
"_PACKAGE"
Von: Hadley Wickham
Gesendet: Donnerstag, 7. März 2024 16:02:15
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r
package documentation
Do you have a pointer to the roxygen2 comments that you're using?
Hadley
On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
mailto:sergej.r...@tiho-hannover.de>> wrote:
Hello,
I need help with a package I am currently developing called bootGSEA.
I noticed that when I try ‘?bootGSEA’ it goes to the help page in R itself but
not to the html page (we had this issue last time as well but we solved it by
adding a documentation to the package itself to the R file) like from the
before version of the package.
I tried “_PACKAGE” in the documentation of the package section as @doctype is
depreceated, but it still doesn’t seem to solve the issue. Do you have any idea
on this?
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] @doctype is deprecated. need help for r package documentation
Do you have a pointer to the roxygen2 comments that you're using? Hadley On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej wrote: > Hello, > > I need help with a package I am currently developing called bootGSEA. > I noticed that when I try ‘?bootGSEA’ it goes to the help page in R > itself but not to the html page (we had this issue last time as well but we > solved it by adding a documentation to the package itself to the R file) > like from the before version of the package. > I tried “_PACKAGE” in the documentation of the package section as @doctype > is depreceated, but it still doesn’t seem to solve the issue. Do you have > any idea on this? > > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > -- http://hadley.nz [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] RFC: C backtraces for R CMD check via just-in-time debugging
Hi Ivan,
Here is the piece of code I currently use:
void backtrace_dump(void)
{
unw_cursor_tcursor;
unw_context_t context;
unw_getcontext();
unw_init_local(, );
while (unw_step() > 0)
{
unw_word_t offset, pc;
charfname[64];
unw_get_reg(, UNW_REG_IP, );
fname[0] = '\0';
(void) unw_get_proc_name(, fname, 64, );
fprintf(stderr, "0x%016lx : (%s+0x%lx)\n", pc-(long)backtrace_dump,
fname, offset);
}
}
To make it safe, one can simply replace fprintf() with a function that
stores information into a buffer.
Several things to point out:
* printing pc-(long)backtrace_dump works around address randomization,
so that if you attach the debugger you can find the location again by
using backtrace_dump+0 (it does not have to be backtrace_dump, any
symbol will do)
* this works even if the symbols are stripped, in which case it finds an
offset relative to the nearest available symbol - there are always some
from the loader. Of course, in this case you should use the offsets and
the debugger to find out whats wrong
* you can call backtrace_dump() from anywhere, does not have to be a
signal handler. I've taken to calling it when my programs detect some
abnormal situation, so I can see the call chain.
* this should work as a package, but I am not sure whether the offsets
between package symbols and R symbols would be static or not. For R it
might be a good idea to also print a table of offsets between some R
symbol and all the loaded C packages R_init_RMVL(), at least initially.
* R ought to know where packages are loaded, we might want to be clever
and print out information on which package contains which function, or
there might be identical R_init_RMVL() printouts.
best
Vladimir Dergachev
On Thu, 7 Mar 2024, Ivan Krylov wrote:
On Tue, 5 Mar 2024 18:26:28 -0500 (EST)
Vladimir Dergachev wrote:
I use libunwind in my programs, works quite well, and simple to use.
Happy to share the code if there is interest..
Do you mean that you use libunwind in signal handlers? An example on
how to produce a backtrace without calling any async-signal-unsafe
functions would indeed be greatly useful.
Speaking of shared objects injected using LD_PRELOAD, I've experimented
some more, and I think that none of them would work with R without
additional adjustments. They install their signal handler very soon
after the process starts up, and later, when R initialises, it
installs its own signal handler, overwriting the previous one. For this
scheme to work, either R would have to cooperate, remembering a pointer
to the previous signal handler and calling it at some point (which
sounds unsafe), or the injected shared object would have to override
sigaction() and call R's signal handler from its own (which sounds
extremely unsafe).
Without that, if we want C-level backtraces, we either need to patch R
to produce them (using backtrace() and limiting this to glibc systems
or using libunwind and paying the dependency cost) or to use a debugger.
--
Best regards,
Ivan
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Re: [R-pkg-devel] [External] [External] RcmdrPlugin.HH_1.1-48.tar.gz
Le 07/03/2024 à 11:08, Duncan Murdoch a écrit :
On 07/03/2024 4:16 a.m., Ivan Krylov wrote:
On Wed, 6 Mar 2024 13:46:55 -0500
Duncan Murdoch wrote:
is this just a more or less harmless error, thinking that
the dot needs escaping
I think it's this one. You are absolutely right that the dot doesn't
need escaping in either TRE (which is what's used inside exportPattern)
or PCRE. In PRCE, this regular expression would have worked as intended:
# We do match backslashes by mistake.
grepl('[\\.]', '\\')
# [1] TRUE
# In PCRE, this wouldn't have been a mistake.
grepl('[\\.]', c('\\', '.'), perl = TRUE)
# [1] FALSE TRUE
Thanks, I didn't realize that escaping in PCRE was optional.
Escaping is optional only in brackets []. Without them it becomes
mandatory if we want to catch just "." not any character :
grepl('.', c('\\', '.'), perl = TRUE)
#[1] TRUE TRUE
Best,
Serguei.
So the default exportPattern line could be
exportPattern("^[^.]")
and it would work even if things were changed so that PCRE was used
instead of TRE.
Duncan Murdoch
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Re: [R-pkg-devel] @doctype is deprecated. need help for r package documentation
В Thu, 7 Mar 2024 10:37:51 +
"Ruff, Sergej" пишет:
> I noticed that when I try _?bootGSEA_ it goes to the help page in R
> itself but not to the html page
That's up to the user to choose. help(bootGSEA, help_type = 'html')
should get you to the HTML documentation; help(bootGSEA, help_type =
'text') should give you plain text. The default depends on
options(help_type=...). On Windows, you get a choice during
installation of R; this gets recorded in file.path(R.home('etc'),
'Rprofile.site').
--
Best regards,
Ivan
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[R-pkg-devel] @doctype is deprecated. need help for r package documentation
Hello, I need help with a package I am currently developing called bootGSEA. I noticed that when I try �?bootGSEA� it goes to the help page in R itself but not to the html page (we had this issue last time as well but we solved it by adding a documentation to the package itself to the R file) like from the before version of the package. I tried �_PACKAGE� in the documentation of the package section as @doctype is depreceated, but it still doesn�t seem to solve the issue. Do you have any idea on this? [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [External] [External] RcmdrPlugin.HH_1.1-48.tar.gz
On 07/03/2024 4:16 a.m., Ivan Krylov wrote:
On Wed, 6 Mar 2024 13:46:55 -0500
Duncan Murdoch wrote:
is this just a more or less harmless error, thinking that
the dot needs escaping
I think it's this one. You are absolutely right that the dot doesn't
need escaping in either TRE (which is what's used inside exportPattern)
or PCRE. In PRCE, this regular expression would have worked as intended:
# We do match backslashes by mistake.
grepl('[\\.]', '\\')
# [1] TRUE
# In PCRE, this wouldn't have been a mistake.
grepl('[\\.]', c('\\', '.'), perl = TRUE)
# [1] FALSE TRUE
Thanks, I didn't realize that escaping in PCRE was optional.
So the default exportPattern line could be
exportPattern("^[^.]")
and it would work even if things were changed so that PCRE was used
instead of TRE.
Duncan Murdoch
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Re: [R-pkg-devel] RFC: C backtraces for R CMD check via just-in-time debugging
On Tue, 5 Mar 2024 18:26:28 -0500 (EST) Vladimir Dergachev wrote: > I use libunwind in my programs, works quite well, and simple to use. > > Happy to share the code if there is interest.. Do you mean that you use libunwind in signal handlers? An example on how to produce a backtrace without calling any async-signal-unsafe functions would indeed be greatly useful. Speaking of shared objects injected using LD_PRELOAD, I've experimented some more, and I think that none of them would work with R without additional adjustments. They install their signal handler very soon after the process starts up, and later, when R initialises, it installs its own signal handler, overwriting the previous one. For this scheme to work, either R would have to cooperate, remembering a pointer to the previous signal handler and calling it at some point (which sounds unsafe), or the injected shared object would have to override sigaction() and call R's signal handler from its own (which sounds extremely unsafe). Without that, if we want C-level backtraces, we either need to patch R to produce them (using backtrace() and limiting this to glibc systems or using libunwind and paying the dependency cost) or to use a debugger. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [External] [External] RcmdrPlugin.HH_1.1-48.tar.gz
On Wed, 6 Mar 2024 13:46:55 -0500
Duncan Murdoch wrote:
> is this just a more or less harmless error, thinking that
> the dot needs escaping
I think it's this one. You are absolutely right that the dot doesn't
need escaping in either TRE (which is what's used inside exportPattern)
or PCRE. In PRCE, this regular expression would have worked as intended:
# We do match backslashes by mistake.
grepl('[\\.]', '\\')
# [1] TRUE
# In PCRE, this wouldn't have been a mistake.
grepl('[\\.]', c('\\', '.'), perl = TRUE)
# [1] FALSE TRUE
--
Best regards,
Ivan
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