[Rd] Question about CHARSXP and garbage collection
Hi, I had a technical question about CHARSXP and garbage collection and couldn't find the answer in the R manual. The question is this. Are CHARSXP garbage collected like any other object, despite being part of the CHARSXP cache? i.e. is the cache being cleaned by garbage collection regularly and therefore, when I am in C code, do I need to protect a CHARSXP? Thanks! Holger [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Package manuals as html page instead of pdf
Hi, I wanted to pose a question to the R developers that I was wondering about for a while. Currently, the standard way of rendering the manual of an R package on CRAN is in the form of a pdf-file. From my perspective, this pdf-file has many drawbacks: - It makes the load (relatively) long - requires at least a plug-in in a browser, - breaks the forward-backward functionality of browser - Does not contain reformattable text so that the monitor space cannot be optimally used when displaying it - Has many page breaks that require space on the monitor and need to be skipped over - Introduces the dependency on latex itself. Therefore, I wanted to ask if the R core team has thought about moving away from pdf-manuals and on to (single page) HTML manuals? I think that would have several advantages, those being - faster loadtimes - could still be sent around as a single file - Are more flexible on how the text would be displayed - forward-backward navigation in the browser and browser full text search would work Of course, printing it would be slightly worse out of an HTML document than it currently is from a pdf. Thank you already for providing comments Holger [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] A package requiring cmake
Hi, I am currently preparing a package for hdf5 that ships and compiles from source on windows. The intention here is to avoid having to ship or download a binary from an unknown source. As a dependency, I need the cmake program installed. Here my question: 1. Is cmake installed on win-builder? If not, could it be installed? If yes, in a specified standard location or available through the PATH variable? 2. How do I specify that a package is only intended for a specific OS? On another note here: The package I am preparing would only compile the binaries on windows. On other systems, I would prefer to have people install them thought native services (e.g. apt-get) to make configuration etc. more manageable for system administrators (even though that puts a little more burden on the end-user on these systems). Second question: Is there a way to specify an OS-specific dependency? As the hdf5lib package is rather large and intended for windows only, I would prefer if it isn't downloaded anywhere else. thanks for your help Holger [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Advice debugging M1Mac check errors
Hi, I wanted to ask if people have good advice on how to debug M1Mac package check errors when you don´t have a Mac? Is a cloud machine the best option or is there something else? Thanks Holger [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Different serialization of functions in interactive vs. batch mode
Hi,
I posted this question to the regular help list, but it seems to be
this is probably a question that is better addressed on r-devel. Sorry
for the double posting.
I am using hash-values to cache certain results in R. This caching
also depends on the hash-value of the function that is being cached
(calculated using the digest package). I noticed that computations
that should already be cached are recomputed when switching from an
interactive session to a BATCH session. Therefore, I wrote a test
script
library(digest)
testfun <- function() {
return(NULL)
}
testval <- "testval"
print(digest(testfun))
print(serialize(testfun, connection = NULL))
and executed it once using input-redirection from a file (testFile.R)
and once copying the code into an interactive R session. The
hash-values of the functions differ. As digest internally relies on
serialize, I also checked there and found that digest is not the
reason for the discrepancy. Instead, the serialized value of the
function already differs between the BATCH and inteactive sessions.
I was wondering if someone knows if
1. Is this a feature or a bug? It feels like a bug to me as all the
inputs are identical, I would expect that the output is identical as
well. Is there something I am overlooking?
2. Is there a way to get consistent hash-values for functions between
BATCH and interactive sessions.
The output from the BATCH and interactive runs are below (as well as
sessionInfo)
Thank you very much for your help!
Holger Hoefling
-
BATCH run (via input redirection):
$ R --vanilla < testFile.R
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 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 redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(digest)
> testfun <- function() {
+ return(NULL)
+ }
> print(digest(testfun))
[1] "b03160b9250f0d5b5bcce42bd86d8e56"
> print(serialize(testfun, connection = NULL))
[1] 58 0a 00 00 00 02 00 03 01 00 00 02 03 00 00 00 04 03 00 00 00 fd 00 00 00
[26] fe 00 00 00 06 00 00 00 01 00 04 00 09 00 00 00 01 7b 00 00 00 02 00 00 00
[51] 06 00 00 00 01 00 04 00 09 00 00 00 06 72 65 74 75 72 6e 00 00 00 02 00 00
[76] 00 fe 00 00 00 fe 00 00 00 fe
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] digest_0.6.4
>
--
Interactive run:
$ R --vanilla
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 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 redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(digest)
> testfun <- function() {
+ return(NULL)
+ }
> print(digest(testfun))
[1] "fada482d2894088b079a8e56b7044862"
> print(serialize(testfun, connection = NULL))
[1] 58 0a 00 00 00 02 00 03 01 00 00 02 03 00 00 00 06 03 00 00 04 02 00 00 00
[26] 01 00 04 00 09 00 00 00 06 73 72 63 72 65 66 00 00 03 0d 00 00 00 08 00 00
[51] 00 01 00 00 00 0c 00 00 00 03 00 00 00 01 00 00 00 0c 00 00 00 01 00 00 00
[76] 01 00 00 00 03 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 07 73 72 63 66
[101] 69 6c 65 00 00 00 04 00 00 00 00 00 00 00 f2 00 00 04 02 00 00 00 01 00 04
[126] 00 09 00 00 00 05 6c 69 6e 65 73 00 00 00 10 00 00 00 01 00 04 00 09 00 00
[151] 00 2b 74 65 73 74 66 75 6e 20 3c 2d 20 66 75 6e 63 74 69 6f 6e 28 29 20 7b
[176] 0a 20 20 20 20 72 65 74 75 72 6e 28 4e 55 4c 4c 29 0a 7d 0a 00 00 04 02 00
[201] 00 00 01 00 04 00 09 00 00 00 08 66 69 6c 65 6e 61 6d 65 00 00 00 10 00 00
[226] 00 01 00 04 00 09 00 00 00 00 00 00 00 fe 00 00 00 fe 00 00 04 02 00 00 00
[251] 01 00 04 00 09 00 00 00 05 63 6c 61 73 73 00 00 00 10 00 00 00 02 00 04 00
[276] 09 00 00 00 0b
Re: [Rd] Different serialization of functions in interactive vs. batch mode
Hi Luke,
Ah - I see - thank you! This at least points me to a way on how to
"fix" this. I tried setting the srcref attribute to NULL, but the hash
value is still different and so is the serialization. So this looks
like it is one difference, but not all of them
Even if all differences were identified - it still leaves me with
different behavior between interactive and batch-mode, though. I am
curious as to why that is. Do you know why in interactive mode the
attribute with the srcref is set, but not in batch mode?
Thanks!
Holger
P.S. I attached the output I get when i set the attributes to NULL
On Wed, Feb 18, 2015 at 3:04 PM, wrote:
> Add
>
> attributes(testfun)
>
> and you will see where the two functions differ.
>
> luke
>
>
> On Wed, 18 Feb 2015, Holger Hoefling wrote:
>
>> Hi,
>>
>> I posted this question to the regular help list, but it seems to be
>> this is probably a question that is better addressed on r-devel. Sorry
>> for the double posting.
>>
>> I am using hash-values to cache certain results in R. This caching
>> also depends on the hash-value of the function that is being cached
>> (calculated using the digest package). I noticed that computations
>> that should already be cached are recomputed when switching from an
>> interactive session to a BATCH session. Therefore, I wrote a test
>> script
>>
>> library(digest)
>> testfun <- function() {
>>return(NULL)
>> }
>> testval <- "testval"
>> print(digest(testfun))
>> print(serialize(testfun, connection = NULL))
>>
>> and executed it once using input-redirection from a file (testFile.R)
>> and once copying the code into an interactive R session. The
>> hash-values of the functions differ. As digest internally relies on
>> serialize, I also checked there and found that digest is not the
>> reason for the discrepancy. Instead, the serialized value of the
>> function already differs between the BATCH and inteactive sessions.
>>
>> I was wondering if someone knows if
>> 1. Is this a feature or a bug? It feels like a bug to me as all the
>> inputs are identical, I would expect that the output is identical as
>> well. Is there something I am overlooking?
>> 2. Is there a way to get consistent hash-values for functions between
>> BATCH and interactive sessions.
>>
>> The output from the BATCH and interactive runs are below (as well as
>> sessionInfo)
>>
>> Thank you very much for your help!
>>
>> Holger Hoefling
>>
>> -
>> BATCH run (via input redirection):
>>
>> $ R --vanilla < testFile.R
>>
>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>> Copyright (C) 2014 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 redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> library(digest)
>>> testfun <- function() {
>>
>> + return(NULL)
>> + }
>>>
>>> print(digest(testfun))
>>
>> [1] "b03160b9250f0d5b5bcce42bd86d8e56"
>>>
>>> print(serialize(testfun, connection = NULL))
>>
>> [1] 58 0a 00 00 00 02 00 03 01 00 00 02 03 00 00 00 04 03 00 00 00 fd 00
>> 00 00
>> [26] fe 00 00 00 06 00 00 00 01 00 04 00 09 00 00 00 01 7b 00 00 00 02 00
>> 00 00
>> [51] 06 00 00 00 01 00 04 00 09 00 00 00 06 72 65 74 75 72 6e 00 00 00 02
>> 00 00
>> [76] 00 fe 00 00 00 fe 00 00 00 fe
>>>
>>> sessionInfo()
>>
>> R version 3.1.0 (2014-04-10)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] digest_0.6.4
>>>
>>>
>>
>> --
>> Interactive run:
>>
>> $ R --vanilla
>>
>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>
Re: [Rd] Different serialization of functions in interactive vs. batch mode
Luke, thank you so much - that solves my problem!
Holger
On Wed, Feb 18, 2015 at 3:56 PM, wrote:
> On Wed, 18 Feb 2015, Holger Hoefling wrote:
>
>> Hi Luke,
>>
>> Ah - I see - thank you! This at least points me to a way on how to
>> "fix" this. I tried setting the srcref attribute to NULL, but the hash
>> value is still different and so is the serialization. So this looks
>> like it is one difference, but not all of them
>
>
> when source attributes are attached they are attached to calls within
> the body as well, so
>
> > attributes(body(testfun))
> $srcref
> $srcref[[1]]
> ...
>
>> Even if all differences were identified - it still leaves me with
>> different behavior between interactive and batch-mode, though. I am
>> curious as to why that is. Do you know why in interactive mode the
>> attribute with the srcref is set, but not in batch mode?
>
>
> I can't speak to why the default for the keep.source option is
> different in the two cases, but you can set it to be the same: in
> interactive mode
>
> > options(keep.source = FALSE)
> > testfun <- function() {return(NULL)}
> > digest(testfun)
> [1] "b03160b9250f0d5b5bcce42bd86d8e56"
>
> Or use options(keep.source = TRUE) in the other case.
>
> Best,
>
> luke
>
>
>>
>> Thanks!
>>
>> Holger
>>
>> P.S. I attached the output I get when i set the attributes to NULL
>>
>>
>> On Wed, Feb 18, 2015 at 3:04 PM, wrote:
>>>
>>> Add
>>>
>>> attributes(testfun)
>>>
>>> and you will see where the two functions differ.
>>>
>>> luke
>>>
>>>
>>> On Wed, 18 Feb 2015, Holger Hoefling wrote:
>>>
>>>> Hi,
>>>>
>>>> I posted this question to the regular help list, but it seems to be
>>>> this is probably a question that is better addressed on r-devel. Sorry
>>>> for the double posting.
>>>>
>>>> I am using hash-values to cache certain results in R. This caching
>>>> also depends on the hash-value of the function that is being cached
>>>> (calculated using the digest package). I noticed that computations
>>>> that should already be cached are recomputed when switching from an
>>>> interactive session to a BATCH session. Therefore, I wrote a test
>>>> script
>>>>
>>>> library(digest)
>>>> testfun <- function() {
>>>>return(NULL)
>>>> }
>>>> testval <- "testval"
>>>> print(digest(testfun))
>>>> print(serialize(testfun, connection = NULL))
>>>>
>>>> and executed it once using input-redirection from a file (testFile.R)
>>>> and once copying the code into an interactive R session. The
>>>> hash-values of the functions differ. As digest internally relies on
>>>> serialize, I also checked there and found that digest is not the
>>>> reason for the discrepancy. Instead, the serialized value of the
>>>> function already differs between the BATCH and inteactive sessions.
>>>>
>>>> I was wondering if someone knows if
>>>> 1. Is this a feature or a bug? It feels like a bug to me as all the
>>>> inputs are identical, I would expect that the output is identical as
>>>> well. Is there something I am overlooking?
>>>> 2. Is there a way to get consistent hash-values for functions between
>>>> BATCH and interactive sessions.
>>>>
>>>> The output from the BATCH and interactive runs are below (as well as
>>>> sessionInfo)
>>>>
>>>> Thank you very much for your help!
>>>>
>>>> Holger Hoefling
>>>>
>>>> -
>>>> BATCH run (via input redirection):
>>>>
>>>> $ R --vanilla < testFile.R
>>>>
>>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>>> Copyright (C) 2014 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 redistribute it under certain conditions.
>>>> Type 'license()' or 'licence()' for distribution details.
>>>>
>>>> R is a collaborative project with many contributors.
>>>> Type 'contributors()' for more informa
Re: [Rd] Different serialization of functions in interactive vs. batch mode
Hi Gabriel,
thanks for your reply - it does solve the problem of my toy function,
but does come with some other problems though.
a) as.list(f)[[1]] yields an expression, not a function. In order to
go the route you are suggesting, I would more likely use "deparse" in
order to get the original back
b) and more seriously - as.list strips the environment of the function
(and thus associated information) as well as information about parent
environments. For the execution of a function, this would however be
crucial. This is also why a pure "deparse" alone in my opinion would
not work.
Thanks
Holger
On Wed, Feb 18, 2015 at 3:36 PM, Gabriel Becker wrote:
> Holger,
>
> For me (see session info) using
>
> digest(as.list(f))
>
> gets around this problem.
>
> ~G
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_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
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] digest_0.6.8
>
>
>
>
> On Wed, Feb 18, 2015 at 6:22 AM, Holger Hoefling wrote:
>>
>> Hi Luke,
>>
>> Ah - I see - thank you! This at least points me to a way on how to
>> "fix" this. I tried setting the srcref attribute to NULL, but the hash
>> value is still different and so is the serialization. So this looks
>> like it is one difference, but not all of them
>>
>> Even if all differences were identified - it still leaves me with
>> different behavior between interactive and batch-mode, though. I am
>> curious as to why that is. Do you know why in interactive mode the
>> attribute with the srcref is set, but not in batch mode?
>>
>> Thanks!
>>
>> Holger
>>
>> P.S. I attached the output I get when i set the attributes to NULL
>>
>>
>> On Wed, Feb 18, 2015 at 3:04 PM, wrote:
>> > Add
>> >
>> > attributes(testfun)
>> >
>> > and you will see where the two functions differ.
>> >
>> > luke
>> >
>> >
>> > On Wed, 18 Feb 2015, Holger Hoefling wrote:
>> >
>> >> Hi,
>> >>
>> >> I posted this question to the regular help list, but it seems to be
>> >> this is probably a question that is better addressed on r-devel. Sorry
>> >> for the double posting.
>> >>
>> >> I am using hash-values to cache certain results in R. This caching
>> >> also depends on the hash-value of the function that is being cached
>> >> (calculated using the digest package). I noticed that computations
>> >> that should already be cached are recomputed when switching from an
>> >> interactive session to a BATCH session. Therefore, I wrote a test
>> >> script
>> >>
>> >> library(digest)
>> >> testfun <- function() {
>> >>return(NULL)
>> >> }
>> >> testval <- "testval"
>> >> print(digest(testfun))
>> >> print(serialize(testfun, connection = NULL))
>> >>
>> >> and executed it once using input-redirection from a file (testFile.R)
>> >> and once copying the code into an interactive R session. The
>> >> hash-values of the functions differ. As digest internally relies on
>> >> serialize, I also checked there and found that digest is not the
>> >> reason for the discrepancy. Instead, the serialized value of the
>> >> function already differs between the BATCH and inteactive sessions.
>> >>
>> >> I was wondering if someone knows if
>> >> 1. Is this a feature or a bug? It feels like a bug to me as all the
>> >> inputs are identical, I would expect that the output is identical as
>> >> well. Is there something I am overlooking?
>> >> 2. Is there a way to get consistent hash-values for functions between
>> >> BATCH and interactive sessions.
>> >>
>> >> The output from the BATCH and interactive runs are below (as well as
>> >> sessionInfo)
>> >>
>> >> Thank you very much for your help!
>> >>
>> >> Holger Hoefling
>> >>
>> >> -
>&g
