Re: [R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info
It is. I will try their mailing list :)
On Wed, Jul 17, 2019 at 4:56 PM Bert Gunter wrote:
> Isn't this a Bioconductor package? If so, shouldn't you be posting on
> their website instead of here?
> (Apologies if I'm mistaken).
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Wed, Jul 17, 2019 at 1:20 PM Spencer Brackett <
> spbracket...@saintjosephhs.com> wrote:
>
>> Good evening,
>>
>> I downloaded the Biobase package in order to utilize the ExpressionSet and
>> other features hosted there to examine annotations for probeset data,
>> which
>> I seek to visualize. I currently have pre-analyzed object located in my
>> environment containing said probeset info, along with gene id and
>> location.
>> After experimenting with the following approaches, I'm am at a loss for as
>> to why the AnnotatedDataFrame function is not being recognized by R.
>>
>> ##Example of some of my attempts and their respective error messages##
>>
>> >AnnotatedDataFrame()
>> Error in AnnotatedDataFrame() : could not find function
>>"AnnotatedDataFrame"
>>
>> signature(object="assayData")
>> object "assayData"
>> > annotatedDataFrameFrom("assayData", byrow=FALSE)
>> Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
>> could not find function "annotatedDataFrameFrom"
>>
>> >as(data.frame, "AnnotatedDataFrame")
>> Error in as(data.frame, "AnnotatedDataFrame") :
>> no method or default for coercing “function” to “AnnotatedDataFrame”
>>
>> Best,
>>
>> Spencer
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info
Isn't this a Bioconductor package? If so, shouldn't you be posting on their
website instead of here?
(Apologies if I'm mistaken).
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Wed, Jul 17, 2019 at 1:20 PM Spencer Brackett <
spbracket...@saintjosephhs.com> wrote:
> Good evening,
>
> I downloaded the Biobase package in order to utilize the ExpressionSet and
> other features hosted there to examine annotations for probeset data, which
> I seek to visualize. I currently have pre-analyzed object located in my
> environment containing said probeset info, along with gene id and location.
> After experimenting with the following approaches, I'm am at a loss for as
> to why the AnnotatedDataFrame function is not being recognized by R.
>
> ##Example of some of my attempts and their respective error messages##
>
> >AnnotatedDataFrame()
> Error in AnnotatedDataFrame() : could not find function
>"AnnotatedDataFrame"
>
> signature(object="assayData")
> object "assayData"
> > annotatedDataFrameFrom("assayData", byrow=FALSE)
> Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
> could not find function "annotatedDataFrameFrom"
>
> >as(data.frame, "AnnotatedDataFrame")
> Error in as(data.frame, "AnnotatedDataFrame") :
> no method or default for coercing “function” to “AnnotatedDataFrame”
>
> Best,
>
> Spencer
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info
I thought it successfully loaded after library(Biobase) but after
implementing your suggested I got the following
Error in library(Biobase) : there is no package called ‘Biobase’
So to download it would I try to rerun with Debug? This is an option given
as part of the return
On Wed, Jul 17, 2019 at 4:37 PM Martin Morgan
wrote:
> Are you remembering to attach the Biobase package to your R session?
>
> > AnnotatedDataFrame()
> Error in AnnotatedDataFrame() :
> could not find function "AnnotatedDataFrame"
> > suppressPackageStartupMessages({ library(Biobase) })
> > AnnotatedDataFrame()
> An object of class 'AnnotatedDataFrame': none
>
> Biobase is a Bioconductor package, so support questions should more
> appropriately go to https://support.bioconductor.org
>
> Martin
>
> On 7/17/19, 4:20 PM, "R-help on behalf of Spencer Brackett" <
> r-help-boun...@r-project.org on behalf of spbracket...@saintjosephhs.com>
> wrote:
>
> Good evening,
>
> I downloaded the Biobase package in order to utilize the ExpressionSet
> and
> other features hosted there to examine annotations for probeset data,
> which
> I seek to visualize. I currently have pre-analyzed object located in my
> environment containing said probeset info, along with gene id and
> location.
> After experimenting with the following approaches, I'm am at a loss
> for as
> to why the AnnotatedDataFrame function is not being recognized by R.
>
> ##Example of some of my attempts and their respective error messages##
>
> >AnnotatedDataFrame()
> Error in AnnotatedDataFrame() : could not find function
>"AnnotatedDataFrame"
>
> signature(object="assayData")
> object "assayData"
> > annotatedDataFrameFrom("assayData", byrow=FALSE)
> Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
> could not find function "annotatedDataFrameFrom"
>
> >as(data.frame, "AnnotatedDataFrame")
> Error in as(data.frame, "AnnotatedDataFrame") :
> no method or default for coercing “function” to “AnnotatedDataFrame”
>
> Best,
>
> Spencer
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info
Are you remembering to attach the Biobase package to your R session?
> AnnotatedDataFrame()
Error in AnnotatedDataFrame() :
could not find function "AnnotatedDataFrame"
> suppressPackageStartupMessages({ library(Biobase) })
> AnnotatedDataFrame()
An object of class 'AnnotatedDataFrame': none
Biobase is a Bioconductor package, so support questions should more
appropriately go to https://support.bioconductor.org
Martin
On 7/17/19, 4:20 PM, "R-help on behalf of Spencer Brackett"
wrote:
Good evening,
I downloaded the Biobase package in order to utilize the ExpressionSet and
other features hosted there to examine annotations for probeset data, which
I seek to visualize. I currently have pre-analyzed object located in my
environment containing said probeset info, along with gene id and location.
After experimenting with the following approaches, I'm am at a loss for as
to why the AnnotatedDataFrame function is not being recognized by R.
##Example of some of my attempts and their respective error messages##
>AnnotatedDataFrame()
Error in AnnotatedDataFrame() : could not find function
"AnnotatedDataFrame"
signature(object="assayData")
object "assayData"
> annotatedDataFrameFrom("assayData", byrow=FALSE)
Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
could not find function "annotatedDataFrameFrom"
>as(data.frame, "AnnotatedDataFrame")
Error in as(data.frame, "AnnotatedDataFrame") :
no method or default for coercing “function” to “AnnotatedDataFrame”
Best,
Spencer
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with save/load across R versions and OS
Hi, I managed to transfer my object trough dput/dget and a text file export. I will look into stripping the function for the reprex creation when I have more time (this is a ginormous function)... Thanks to your input and Bert's - Original Message - From: "Duncan Murdoch" To: "Sebastien Bihorel" Cc: r-help@r-project.org Sent: Wednesday, July 17, 2019 3:04:46 PM Subject: Re: [R] Problem with save/load across R versions and OS On 17/07/2019 2:02 p.m., Sebastien Bihorel wrote: > Hi, > > Indeed the S4 object is a class provided by a contributed package. However, > the windows machine that reads the .rds fine does not even have the package > installed. > > I also confirm that I used readRDS (loadRDS was a typo on my part, sorry). > > In this case, I cannot provide a reprex as the contributed package function > that creates the S4 object connects to a local database with secured access. > I could send the code, but only the authorized people could run it. This is > not the ideal situation for problem solving... > > I was wondering if there was a pathway through serialize / unserialize. I > tried but I could not find the way to properly write and read the serialized > object. I don't know about that approach. You can probably produce a reprex, it'll just be work: copy the function from the contributed package, and edit it so that the line that reads from the database just generates some fake data in a similar format. If you can make it reproducible, then cut out as much stuff as possible, keeping it reproducible, and post the final minimal reprex. It's likely to take some time, but also likely to lead to a solution (either by you, when you notice a bug in the contributed package and can fix it, or by one of us, when you post the reprex and we dig in). Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info
Good evening,
I downloaded the Biobase package in order to utilize the ExpressionSet and
other features hosted there to examine annotations for probeset data, which
I seek to visualize. I currently have pre-analyzed object located in my
environment containing said probeset info, along with gene id and location.
After experimenting with the following approaches, I'm am at a loss for as
to why the AnnotatedDataFrame function is not being recognized by R.
##Example of some of my attempts and their respective error messages##
>AnnotatedDataFrame()
Error in AnnotatedDataFrame() : could not find function
"AnnotatedDataFrame"
signature(object="assayData")
object "assayData"
> annotatedDataFrameFrom("assayData", byrow=FALSE)
Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
could not find function "annotatedDataFrameFrom"
>as(data.frame, "AnnotatedDataFrame")
Error in as(data.frame, "AnnotatedDataFrame") :
no method or default for coercing “function” to “AnnotatedDataFrame”
Best,
Spencer
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with save/load across R versions and OS
On 17/07/2019 2:02 p.m., Sebastien Bihorel wrote: Hi, Indeed the S4 object is a class provided by a contributed package. However, the windows machine that reads the .rds fine does not even have the package installed. I also confirm that I used readRDS (loadRDS was a typo on my part, sorry). In this case, I cannot provide a reprex as the contributed package function that creates the S4 object connects to a local database with secured access. I could send the code, but only the authorized people could run it. This is not the ideal situation for problem solving... I was wondering if there was a pathway through serialize / unserialize. I tried but I could not find the way to properly write and read the serialized object. I don't know about that approach. You can probably produce a reprex, it'll just be work: copy the function from the contributed package, and edit it so that the line that reads from the database just generates some fake data in a similar format. If you can make it reproducible, then cut out as much stuff as possible, keeping it reproducible, and post the final minimal reprex. It's likely to take some time, but also likely to lead to a solution (either by you, when you notice a bug in the contributed package and can fix it, or by one of us, when you post the reprex and we dig in). Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with save/load across R versions and OS
Hi, Indeed the S4 object is a class provided by a contributed package. However, the windows machine that reads the .rds fine does not even have the package installed. I also confirm that I used readRDS (loadRDS was a typo on my part, sorry). In this case, I cannot provide a reprex as the contributed package function that creates the S4 object connects to a local database with secured access. I could send the code, but only the authorized people could run it. This is not the ideal situation for problem solving... I was wondering if there was a pathway through serialize / unserialize. I tried but I could not find the way to properly write and read the serialized object. Thanks - Original Message - From: "Duncan Murdoch" To: "Sebastien Bihorel" , r-help@r-project.org Sent: Wednesday, July 17, 2019 10:42:13 AM Subject: Re: [R] Problem with save/load across R versions and OS On 17/07/2019 4:39 a.m., Sebastien Bihorel wrote: > Hi, > > I am trying to transfer an S4 object from a machine working with CentOS 7.2 / > R 3.4.3 to another one running Linux Mint 19 / R 3.6.0. If I save the object > using saveRDS in obj.rds, loadRDS returns an "unknown input format" error on > my Linux Mint machine. Interestingly enough, obj.rds loads just fine in a 3rd > machine running Windows Server 2012 / R 3.4.3. I tried also using save and > load and various values of the ascii and compression arguments, but still no > cigar... > > Do you have recommendations on how to successfully transfer my object to my > Linux Mint machine? > Normally such a transfer should just work. Reasons why it might not: - The error is being triggered by a contributed package somehow. Do contributed package versions match? - There's no loadRDS function in base R, the base R function is readRDS. If that's not just a typo above, then the loadRDS function you're using doesn't work. Use the base package functions instead. - There's a bug in R. In any case, we can't do much to help you without a reproducible example. Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with save/load across R versions and OS
Hi, Yes, I tried save/load... same failure. But I did not yet try dump/source or dput/dget. I will From: "Bert Gunter" To: "Sebastien Bihorel" Cc: "R-help" Sent: Wednesday, July 17, 2019 10:27:24 AM Subject: Re: [R] Problem with save/load across R versions and OS Did you try plain save/load ?? Also ?dump/source ?dput/dget Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jul 17, 2019 at 1:38 AM Sebastien Bihorel < [ mailto:sebastien.biho...@cognigencorp.com | sebastien.biho...@cognigencorp.com ] > wrote: Hi, I am trying to transfer an S4 object from a machine working with CentOS 7.2 / R 3.4.3 to another one running Linux Mint 19 / R 3.6.0. If I save the object using saveRDS in obj.rds, loadRDS returns an "unknown input format" error on my Linux Mint machine. Interestingly enough, obj.rds loads just fine in a 3rd machine running Windows Server 2012 / R 3.4.3. I tried also using save and load and various values of the ascii and compression arguments, but still no cigar... Do you have recommendations on how to successfully transfer my object to my Linux Mint machine? Thanks Sebastien __ [ mailto:R-help@r-project.org | R-help@r-project.org ] mailing list -- To UNSUBSCRIBE and more, see [ https://stat.ethz.ch/mailman/listinfo/r-help | https://stat.ethz.ch/mailman/listinfo/r-help ] PLEASE do read the posting guide [ http://www.r-project.org/posting-guide.html | http://www.R-project.org/posting-guide.html ] and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with save/load across R versions and OS
On 17/07/2019 4:39 a.m., Sebastien Bihorel wrote: Hi, I am trying to transfer an S4 object from a machine working with CentOS 7.2 / R 3.4.3 to another one running Linux Mint 19 / R 3.6.0. If I save the object using saveRDS in obj.rds, loadRDS returns an "unknown input format" error on my Linux Mint machine. Interestingly enough, obj.rds loads just fine in a 3rd machine running Windows Server 2012 / R 3.4.3. I tried also using save and load and various values of the ascii and compression arguments, but still no cigar... Do you have recommendations on how to successfully transfer my object to my Linux Mint machine? Normally such a transfer should just work. Reasons why it might not: - The error is being triggered by a contributed package somehow. Do contributed package versions match? - There's no loadRDS function in base R, the base R function is readRDS. If that's not just a typo above, then the loadRDS function you're using doesn't work. Use the base package functions instead. - There's a bug in R. In any case, we can't do much to help you without a reproducible example. Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with save/load across R versions and OS
Did you try plain save/load ?? Also ?dump/source ?dput/dget Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jul 17, 2019 at 1:38 AM Sebastien Bihorel < sebastien.biho...@cognigencorp.com> wrote: > Hi, > > I am trying to transfer an S4 object from a machine working with CentOS > 7.2 / R 3.4.3 to another one running Linux Mint 19 / R 3.6.0. If I save the > object using saveRDS in obj.rds, loadRDS returns an "unknown input format" > error on my Linux Mint machine. Interestingly enough, obj.rds loads just > fine in a 3rd machine running Windows Server 2012 / R 3.4.3. I tried also > using save and load and various values of the ascii and compression > arguments, but still no cigar... > > Do you have recommendations on how to successfully transfer my object to > my Linux Mint machine? > > Thanks > > Sebastien > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 3.6.1
I think that would depend on whether the bug was in the install program or not. In this case I would not bet on that being the problem. I would either look for a patched release that addresses the bug, or roll back to 3.5.3. You might have luck with 3.6.0, but given that was when the major feature update occurred that option seems risky to me. On July 17, 2019 8:13:53 AM CDT, Spencer Graves wrote: > What might be the likely outcomes of an attempt to reinstall >3.6.1? > > > And might that depend on whether the current 3.6.1 was >uninstalled first? > > > Spencer > > >On 2019-07-17 07:17, Jeff Newmiller wrote: >> It would never make sense for such messages to reflect normal and >> expected operation, so hypothesizing about intentionally changing >> stack behavior doesn't make sense. >> >> The default format for saveRDS changed in 3.6.0. There may be bugs >> associated with that, but rolling back to 3.6.0 would just trade >bugs. >> >> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html >> >> On July 16, 2019 8:56:28 PM CDT, Jan Galkowski >> wrote: >>> Did something seriously change in R 3.6.1 at least for Windows in >terms >>> of stack impacts? >>> >>> I'm encountering many problems with the 00UNLOCK, needing to disable >>> locking during installations. >>> >>> And I'm encountering >>> Error: C stack usage 63737888 is too close to the limit >>> for cases I did not before, even when all I'm doing is serializing >an >>> object to be saved with *saveRDS* or even *save.image(.)*. >>> >>> Yes, I know, I did not append a minimally complete example. Just >wanted >>> to see if it was just me, or if anyone else was seeing this. >>> >>> It's on Windows 7 HE and I've run *R* here for years. >>> >>> My inclination is to drop back to 3.6.0 if it is just me or if no >one >>> knows about this problem. >>> >>> Thanks, >>> >>> - Jan Galkowski. >>> >>> >>> [[alternative HTML version deleted]] >>> >>> __ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 3.6.1
What might be the likely outcomes of an attempt to reinstall 3.6.1? And might that depend on whether the current 3.6.1 was uninstalled first? Spencer On 2019-07-17 07:17, Jeff Newmiller wrote: It would never make sense for such messages to reflect normal and expected operation, so hypothesizing about intentionally changing stack behavior doesn't make sense. The default format for saveRDS changed in 3.6.0. There may be bugs associated with that, but rolling back to 3.6.0 would just trade bugs. https://cran.r-project.org/doc/manuals/r-devel/NEWS.html On July 16, 2019 8:56:28 PM CDT, Jan Galkowski wrote: Did something seriously change in R 3.6.1 at least for Windows in terms of stack impacts? I'm encountering many problems with the 00UNLOCK, needing to disable locking during installations. And I'm encountering Error: C stack usage 63737888 is too close to the limit for cases I did not before, even when all I'm doing is serializing an object to be saved with *saveRDS* or even *save.image(.)*. Yes, I know, I did not append a minimally complete example. Just wanted to see if it was just me, or if anyone else was seeing this. It's on Windows 7 HE and I've run *R* here for years. My inclination is to drop back to 3.6.0 if it is just me or if no one knows about this problem. Thanks, - Jan Galkowski. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 3.6.1
It would never make sense for such messages to reflect normal and expected operation, so hypothesizing about intentionally changing stack behavior doesn't make sense. The default format for saveRDS changed in 3.6.0. There may be bugs associated with that, but rolling back to 3.6.0 would just trade bugs. https://cran.r-project.org/doc/manuals/r-devel/NEWS.html On July 16, 2019 8:56:28 PM CDT, Jan Galkowski wrote: >Did something seriously change in R 3.6.1 at least for Windows in terms >of stack impacts? > >I'm encountering many problems with the 00UNLOCK, needing to disable >locking during installations. > >And I'm encountering > >> Error: C stack usage 63737888 is too close to the limit > >for cases I did not before, even when all I'm doing is serializing an >object to be saved with *saveRDS* or even *save.image(.)*. > >Yes, I know, I did not append a minimally complete example. Just wanted >to see if it was just me, or if anyone else was seeing this. > >It's on Windows 7 HE and I've run *R* here for years. > >My inclination is to drop back to 3.6.0 if it is just me or if no one >knows about this problem. > >Thanks, > > - Jan Galkowski. > > > [[alternative HTML version deleted]] > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R 3.6.1
Did something seriously change in R 3.6.1 at least for Windows in terms of stack impacts? I'm encountering many problems with the 00UNLOCK, needing to disable locking during installations. And I'm encountering > Error: C stack usage 63737888 is too close to the limit for cases I did not before, even when all I'm doing is serializing an object to be saved with *saveRDS* or even *save.image(.)*. Yes, I know, I did not append a minimally complete example. Just wanted to see if it was just me, or if anyone else was seeing this. It's on Windows 7 HE and I've run *R* here for years. My inclination is to drop back to 3.6.0 if it is just me or if no one knows about this problem. Thanks, - Jan Galkowski. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with save/load across R versions and OS
Hi, I am trying to transfer an S4 object from a machine working with CentOS 7.2 / R 3.4.3 to another one running Linux Mint 19 / R 3.6.0. If I save the object using saveRDS in obj.rds, loadRDS returns an "unknown input format" error on my Linux Mint machine. Interestingly enough, obj.rds loads just fine in a 3rd machine running Windows Server 2012 / R 3.4.3. I tried also using save and load and various values of the ascii and compression arguments, but still no cigar... Do you have recommendations on how to successfully transfer my object to my Linux Mint machine? Thanks Sebastien __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] dbparser v1.0.2: DrugBank XML Database Parser
Hello, Kindly check the new release of dbparser v1.0.2 on https://cran.r-project.org/web/packages/dbparser/index.html The new release include: - Fix zip file location issue - Replace Secondary and third keys columns from drug framework with other_keys column that contains any other keys that might exist in addition to the primary key - Add average-mass, monoisotopic-mass and calculated-properties parsers. - Support saving parsed drugs related parsed database as csv As always, contributions and bug reports are welcome on https://dainanahan.github.io/dbparser/index.html Best Regards, Mohammed Ali MSc in Applied Data Science & Big Data mohammed@edu.dsti.institute +20 01000481973 eg.linkedin.com/in/mohammedali85 ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
