Hello Anna,
The speed of parallel computing depends on many factors. To avoid any
potential confounders, Please try to use this code for timing (assuming you
still have all the variables you used in your example)
```
parallel_param <- SnowParam(workers = ncores, type = "SOCK", tasks =
Hi,
It seems like the enclosed environment does not work well with the
loop. Here is a simple example
```
FuncGenerator <- function(value){
function() message(value)
}
funcSets <- list()
for(i in 1:2)
funcSets[[i]] <- FuncGenerator(i)
environment(funcSets[[1]])$value
# [1] 2
Hi all,
>From the document of 'setTimeLimit', it states "Setting any limit has
a small overhead – well under 1% on the systems measured.", but
something is wrong with my benchmark code, enabling the time limit
makes my benchmark 1x slower than the benchmark without the limit.
Below is an example
uments linked to OneDrive (either by your choice
> or by some administrator setting a group policy)? If so, ou could unlink it
> using OneDrive's settings dialog. Or you could set R_USER to avoid using
> ...\Documents.
>
> -Bill
>
> On Mon, Nov 22, 2021 at 8:4
Hi, I have a new win system and try to install R as usual. Somehow,
the environment variable "R_LIBS_USER" is incorrectly pointed to a
Onedrive folder. Since "R_LIBS_USER" depends on "R_USER", the root
problem then becomes why "R_USER" is the path to the Onedrive. I did
an exhausting search in the
it still fails and says it doesn't find the function
> "mandatory_is_vars()" which is a function exported by the package
> >
> > On 10/25/21, 13:49, "Jiefei Wang" wrote:
> >
> > What do you mean by "exported functions are inv
I mean that trying to modify the code of one of the functions that raises
> errors and setting the option "exportglobals = TRUE" on SnowParam, somehow it
> still fails and says it doesn't find the function "mandatory_is_vars()" which
> is a function exported by the package
&g
What do you mean by "exported functions are invisible to SnowParam
workers"? Please provide more details. If you call 'bplapply' with a
function from your package, it should be visible to the worker.
___
Bioc-devel@r-project.org mailing list
Hi Giulia,
One of your errors is raised from L1288 in the file "analysis-functions.R"
if (getOption("ISAnalytics.verbose") == TRUE) { ... }
The error message is "argument is of length zero". Usually, this means
something is wrong with the global option. Then I see at L4812 in
Dear all,
We are preparing for the new devel branch for Bioc 3.15, so we look
for suggestions for BiocParallel from our community. If you think
there is anything we can improve, please feel free to leave your
comments here: https://github.com/Bioconductor/BiocParallel/issues/160
Cheers,
Jiefei
Hi,
If you are a newbie to the terminal, all you need to do is to extract
the R code from your vignette using `R CMD Stangle
xcms-lcms-ms.Rmd`(assume you are under the vignettes directory). Then
use `R -d valgrind -f xcms-lcms-ms.R` to check for the memory issue.
In the ideal case, it can
t; the onintrEx() function, etc. A good source on signal handling is e.g.
> http://www.linusakesson.net/programming/tty/
>
> Best
> Tomas
>
> On 7/20/21 9:55 AM, Jiefei Wang wrote:
> > Hi all,
> >
> > I just notice this interesting problem a few days bef
Hi all,
I just notice this interesting problem a few days before, but I cannot
find an answer for it. Say if you have a long-running job in a cluster
made by the parallel package and you decide to stop the execution by
pressing ctr + c in the terminal or the stop button in Rstudio for
some
Hi Gabor,
Calling back to an R function from the ALTREP function is not safe.
There has been a heated discussion on why you should not do it and
that the main reason that we do not have any R level ALTREP API. If
you are interested in it you can find it from this issue:
s before backticks could be used to make
> symbol literals for symbols that included odd things like spaces and
> dollar signs.
>
> -Bill
>
> On Sat, Mar 27, 2021 at 7:49 AM Jiefei Wang wrote:
> >
> > Thanks, Duncan. Below is the repost of my question in plain text mode.
purpose as the above example works for both list and S4 system.
Best,
Jiefei
On Sat, Mar 27, 2021 at 10:20 PM Duncan Murdoch
wrote:
>
> On 27/03/2021 10:16 a.m., Jiefei Wang wrote:
> > Hi all,
> >
> > I'm trying to get the field value of a reference object by the field
Hi all,
I'm trying to get the field value of a reference object by the field name,
but the dollar symbol behaves quite unusual. See example below
*.foo <- setRefClass("foo",fields = list(a = "integer"
))x <- .foo$new(a=1L)## This is OKx$a## This is OK`$`(x, "a")##
Bugzilla sounds like a good place to start, I will send an email to acquire
an account.
Best,
Jiefei
On Sun, Nov 22, 2020 at 6:57 AM wrote:
> On Sat, 21 Nov 2020, Jiefei Wang wrote:
>
> > Hello,
> >
> > I have two related ALTREP questions. It seems like there is no way to
> &g
Hello,
I have two related ALTREP questions. It seems like there is no way to
assign attributes to an ALTREP vector without using C++ code. To be more
specifically, I want to make an ALTREP matrix, I have tried the following R
code but none of them work.
```
.Internal(inspect(1:6))
t; >con <- file(filePath, "wrb")
> >writeBin(rep(0.0,10),con)
> >close(con)
> >
> >library(simplemmap)
> >x <- mmap(filePath, "double")
> >saveRDS(x, file = "x.Rds")
> >
> >## in a separ
Hi all,
I am not able to export an ALTREP object when `gctorture` is on in the
worker. The package simplemmap can be used to reproduce the problem. See
the example below
```
## Create a temporary file
filePath <- tempfile()
con <- file(filePath, "wrb")
writeBin(rep(0.0,10),con)
close(con)
there is no such
function in R to get the class of an ALTREP object for the SEXP struct is
very compact and this less-important information might not be stored when
an ALTREP object is created.
Best,
Jiefei
On Mon, Oct 19, 2020 at 8:37 PM Jiefei Wang wrote:
> Thank Denes for the clarification, glad to see
s to the OP's own package :) I
> > think Jiefei would like to know how one can "officially" determine if an
> > arbitrary ALTERP object belongs to a class that he owns.
> >
> > Regards,
> > Denes
> >
> >
> > On 10/19/20 10:22 AM, Benjami
Hi all,
I would like to determine if an ALTREP object is from my package, I see
there is a function `ALTREP_CLASS` defined in RInternal.h but its return
value is neither a `R_altrep_class_t` object nor an STRSXP representing a
class name. I do not know how to correctly use it. Any suggestions?
Hi Gabriel, here is a simple package for reproducing the problem.
https://github.com/Jiefei-Wang/testPkg
Best,
Jiefei
On Thu, Oct 8, 2020 at 5:04 AM Gabriel Becker wrote:
> Jiefei,
>
> Where does the code for your altrep class live?
>
> Thanks,
> ~G
>
> On Wed, Oct 7
Hi all,
The coercion function defined for the ALTREP object will not be called by R
when an assignment operation implicitly introduces coercion for a large
ALTREP object.
For example, If I create a vector of length 10, the ALTREP coercion
function seems to work fine.
```
> x <- 1:10
> y <-
ciences Institute
> Building 145
> Australian National University
>
> Phone: 61-2-61250730
> E-mail: conrad.bur...@anu.edu.au
> Web page: http://maths.anu.edu.au/people/conrad-burden
>
>
> On 17 Sep 2020, at 8:36 pm, Jiefei Wang wrote:
>
>
Hi Conrad,
Just a friendly reminder, there is a bug in your package. Here is the build
result from the link you provided:
==
--- Error message ---
--- failure: length > 1 in coercion to logical ---
--- call from argument ---
columns < 1 || columns >
Hi Henry,
It seems like you are using a Bioconductor package. Why not directly ask
the author of the package(eswri...@pitt.edu)?
JFYI, here is the link for the package, it seems like the author has
written a lot of documentation for the package:
a global lock you
>> need to keep in mind that any function in the R API can signal an
>> error and execute a longjmp, so you need to make sure you have set a
>> top level context in your thread.
>>
>> Best,
>>
>> luke
>>
>> On Sun,
Hi,
I am curious about whether there exist thread-safe functions in
`Rinternals.h`. I know that R is single-threaded designed, but for the
simple and straightforward functions like `DATAPTR` and `INTEGER_GET_REGION`,
are these functions safe to call in a multi-thread environment?
Best,
Jiefei
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