Re: [R] Building Packages.
В Thu, 21 Mar 2024 18:45:35 + Jorgen Harmse via R-help пишет: > The problem may have been that this package is so important to me > that I put it in .Rprofile. The package was not installed for the new > version of R, so every R session started with an annoying error > message. Presumably a separate session started with R CMD would just > fail without installing the package. This must be the solution to the mystery. I have recently added some code that raised an error (lattice::standard.theme(...), but without a new enough 'lattice' to understand the arguments) to my .Rprofile, and it broke quite a few things related to package development until I fixed my .Rprofile. Congratulations on solving the problem! -- Best regards, Ivan __ 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] Building Packages.
> Turns out that RStudio replaces the install.packages object in the utils > package. > Duncan Murdoch So RStudio unlocks the bindings and alters the exported environment? That seems like another reason to stick to the terminal interface. >> Thank you. tools:::.install_packages works. > I'm glad it works, but it shouldn't be necessary to use (and is not > part of the API: not documented to keep working this way). > Best regards, > Ivan [Krylov] Thank you for letting me know. I hope I can avoid using private functions in future. As noted below, my function seems to work now. > Try setting a breakpoint in system2 before launching your function: > Best regards, > Ivan Now build.package works as written, so there�s nothing to debug. The problem may have been that this package is so important to me that I put it in .Rprofile. The package was not installed for the new version of R, so every R session started with an annoying error message. Presumably a separate session started with R CMD would just fail without installing the package. That�s no longer a problem because the package is now installed. However, I don�t know why the error message wasn�t clearer, and I�m puzzled that I was able to install roxygen2 & devtools. Thank you everyone, and I�m sorry if I didn�t give the right information to diagnose the problem faster. Regards, Jorgen. [[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] Building Packages.
I think this might be a good conversation for someone to have with
the Posit folks
* is there a more transparent way to do what they want?
* either, long-term, by having utils::install_packages() add a
'hook' feature as mentioned by someone
* using a similar method to bspm::enable(), which calls trace() to
add an external hook
* is there a good place for them to put the documentation of what
they're doing?
* can they fix things that are broken (e.g.? handling of paths), and
allow optional arguments to override behaviours that are different from
utils::install.packages (e.g. add a possibility to say force=TRUE to
override the "don't reinstall if already installed")
?
cheers
Ben
On 2024-03-21 11:51 a.m., Duncan Murdoch wrote:
I posted a description of their changes this morning.
Duncan Murdoch
On 21/03/2024 11:37 a.m., avi.e.gr...@gmail.com wrote:
With all this discussion, I shudder to ask this. I may have missed the
answers but the discussion seems to have been about identifying and
solving
the problem rapidly rather than what maybe is best going forward if all
parties agree.
What was the motivation for what RSTUDIO did for their version and the
decision to replace what came with utils unless someone very explicitly
over-rode them by asking for the original? Is their version better in
other
ways? Is there a possibility the two implementations may someday merge
into
something that meets several sets of needs or are they incompatible?
Is there agreement that what broke with the substitution is a valid
use or
is it something that just happens to work on the utils version if not
patched?
-Original Message-
From: R-help On Behalf Of Duncan Murdoch
Sent: Thursday, March 21, 2024 5:53 AM
To: peter dalgaard
Cc: Jorgen Harmse ; r-help@r-project.org; Martin
Maechler
Subject: Re: [R] Building Packages.
Yes, you're right. The version found in the search list entry for
"package:utils" is the RStudio one; the ones found with two or three
colons are the original.
Duncan Murdoch
On 21/03/2024 5:48 a.m., peter dalgaard wrote:
Um, what's with the triple colon? At least on my install, double
seems to
suffice:
identical(utils:::install.packages, utils::install.packages)
[1] TRUE
install.packages
function (...)
.rs.callAs(name, hook, original, ...)
-pd
On 21 Mar 2024, at 09:58 , Duncan Murdoch
wrote:
The good news for Jorgen (who may not be reading this thread any
more) is
that one can still be sure of getting the original install.packages() by
using
utils:::install.packages( ... )
with *three* colons, to get the internal (namespace) version of the
function.
Duncan Murdoch
On 21/03/2024 4:31 a.m., Martin Maechler wrote:
"Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>>> Ivan, can you give more detail on this? I've heard this
>>> issue mentioned, but when I open RStudio and run
>>> find("install.packages") it returns
>>> "utils::install.packages", and running dump() from
>>> within RStudio console and from an external "R
>>> --vanilla" gives identical results.
>>>
>>> I thought at one point this might only refer to the GUI
>>> package-installation interface, but you seem to be
>>> saying it's the install.packages() function as well.
>>>
>>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>>> weirdness only happens on other OSs?
>>
>> On MacOS, I see this:
>>
>> > install.packages function (...) .rs.callAs(name, hook,
>> original, ...)
>>
>> I get the same results as you from find(). I'm not sure
>> what RStudio is doing to give a different value for the
>> function than what find() sees.
> Turns out that RStudio replaces the install.packages
> object in the utils package.
> Duncan Murdoch
Yes, and this has been the case for several years now, and I
have mentioned this several times, too (though some of it
possibly not in a public R-* mailing list).
And yes, that they modify the package environment
as.environment("package:utils")
but leave the
namespace asNamespace("utils")
unchanged, makes it harder to see what's
going on (but also has less severe consequences; if they kept to
the otherwise universal *rule* that the namespace and package must
have
the same objects
apart from those only in the namespace,
people would not even have access to R's true install.packages()
but only see the RStudio fake^Hsubstitute..
We are still not happy with their decision. Also
help(install.pac
Re: [R] Building Packages.
I posted a description of their changes this morning.
Duncan Murdoch
On 21/03/2024 11:37 a.m., avi.e.gr...@gmail.com wrote:
With all this discussion, I shudder to ask this. I may have missed the
answers but the discussion seems to have been about identifying and solving
the problem rapidly rather than what maybe is best going forward if all
parties agree.
What was the motivation for what RSTUDIO did for their version and the
decision to replace what came with utils unless someone very explicitly
over-rode them by asking for the original? Is their version better in other
ways? Is there a possibility the two implementations may someday merge into
something that meets several sets of needs or are they incompatible?
Is there agreement that what broke with the substitution is a valid use or
is it something that just happens to work on the utils version if not
patched?
-Original Message-
From: R-help On Behalf Of Duncan Murdoch
Sent: Thursday, March 21, 2024 5:53 AM
To: peter dalgaard
Cc: Jorgen Harmse ; r-help@r-project.org; Martin Maechler
Subject: Re: [R] Building Packages.
Yes, you're right. The version found in the search list entry for
"package:utils" is the RStudio one; the ones found with two or three
colons are the original.
Duncan Murdoch
On 21/03/2024 5:48 a.m., peter dalgaard wrote:
Um, what's with the triple colon? At least on my install, double seems to
suffice:
identical(utils:::install.packages, utils::install.packages)
[1] TRUE
install.packages
function (...)
.rs.callAs(name, hook, original, ...)
-pd
On 21 Mar 2024, at 09:58 , Duncan Murdoch
wrote:
The good news for Jorgen (who may not be reading this thread any more) is
that one can still be sure of getting the original install.packages() by
using
utils:::install.packages( ... )
with *three* colons, to get the internal (namespace) version of the
function.
Duncan Murdoch
On 21/03/2024 4:31 a.m., Martin Maechler wrote:
"Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>>> Ivan, can you give more detail on this? I've heard this
>>> issue mentioned, but when I open RStudio and run
>>> find("install.packages") it returns
>>> "utils::install.packages", and running dump() from
>>> within RStudio console and from an external "R
>>> --vanilla" gives identical results.
>>>
>>> I thought at one point this might only refer to the GUI
>>> package-installation interface, but you seem to be
>>> saying it's the install.packages() function as well.
>>>
>>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>>> weirdness only happens on other OSs?
>>
>> On MacOS, I see this:
>>
>> > install.packages function (...) .rs.callAs(name, hook,
>> original, ...)
>>
>> I get the same results as you from find(). I'm not sure
>> what RStudio is doing to give a different value for the
>> function than what find() sees.
> Turns out that RStudio replaces the install.packages
> object in the utils package.
> Duncan Murdoch
Yes, and this has been the case for several years now, and I
have mentioned this several times, too (though some of it
possibly not in a public R-* mailing list).
And yes, that they modify the package environment
as.environment("package:utils")
but leave the
namespace asNamespace("utils")
unchanged, makes it harder to see what's
going on (but also has less severe consequences; if they kept to
the otherwise universal *rule* that the namespace and package must have
the same objects
apart from those only in the namespace,
people would not even have access to R's true install.packages()
but only see the RStudio fake^Hsubstitute..
We are still not happy with their decision. Also
help(install.packages) goes to R's documentation of R's
install.packages, so there's even more misleading of useRs.
Martin
__
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] Building Packages.
With all this discussion, I shudder to ask this. I may have missed the
answers but the discussion seems to have been about identifying and solving
the problem rapidly rather than what maybe is best going forward if all
parties agree.
What was the motivation for what RSTUDIO did for their version and the
decision to replace what came with utils unless someone very explicitly
over-rode them by asking for the original? Is their version better in other
ways? Is there a possibility the two implementations may someday merge into
something that meets several sets of needs or are they incompatible?
Is there agreement that what broke with the substitution is a valid use or
is it something that just happens to work on the utils version if not
patched?
-Original Message-
From: R-help On Behalf Of Duncan Murdoch
Sent: Thursday, March 21, 2024 5:53 AM
To: peter dalgaard
Cc: Jorgen Harmse ; r-help@r-project.org; Martin Maechler
Subject: Re: [R] Building Packages.
Yes, you're right. The version found in the search list entry for
"package:utils" is the RStudio one; the ones found with two or three
colons are the original.
Duncan Murdoch
On 21/03/2024 5:48 a.m., peter dalgaard wrote:
> Um, what's with the triple colon? At least on my install, double seems to
suffice:
>
>> identical(utils:::install.packages, utils::install.packages)
> [1] TRUE
>> install.packages
> function (...)
> .rs.callAs(name, hook, original, ...)
>
>
> -pd
>
>> On 21 Mar 2024, at 09:58 , Duncan Murdoch
wrote:
>>
>> The good news for Jorgen (who may not be reading this thread any more) is
that one can still be sure of getting the original install.packages() by
using
>>
>> utils:::install.packages( ... )
>>
>> with *three* colons, to get the internal (namespace) version of the
function.
>>
>> Duncan Murdoch
>>
>>
>> On 21/03/2024 4:31 a.m., Martin Maechler wrote:
>>>>>>>> "Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
>>> > On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>>> >> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>>> >>> Ivan, can you give more detail on this? I've heard this
>>> >>> issue mentioned, but when I open RStudio and run
>>> >>> find("install.packages") it returns
>>> >>> "utils::install.packages", and running dump() from
>>> >>> within RStudio console and from an external "R
>>> >>> --vanilla" gives identical results.
>>> >>>
>>> >>> I thought at one point this might only refer to the GUI
>>> >>> package-installation interface, but you seem to be
>>> >>> saying it's the install.packages() function as well.
>>> >>>
>>> >>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>>> >>> weirdness only happens on other OSs?
>>> >>
>>> >> On MacOS, I see this:
>>> >>
>>> >> > install.packages function (...) .rs.callAs(name, hook,
>>> >> original, ...)
>>> >>
>>> >> I get the same results as you from find(). I'm not sure
>>> >> what RStudio is doing to give a different value for the
>>> >> function than what find() sees.
>>> > Turns out that RStudio replaces the install.packages
>>> > object in the utils package.
>>> > Duncan Murdoch
>>> Yes, and this has been the case for several years now, and I
>>> have mentioned this several times, too (though some of it
>>> possibly not in a public R-* mailing list).
>>> And yes, that they modify the package environment
>>>as.environment("package:utils")
>>> but leave the
>>>namespace asNamespace("utils")
>>> unchanged, makes it harder to see what's
>>> going on (but also has less severe consequences; if they kept to
>>> the otherwise universal *rule* that the namespace and package must have
the same objects
>>> apart from those only in the namespace,
>>> people would not even have access to R's true install.packages()
>>> but only see the RStudio fake^Hsubstitute..
>>> We are still not happy with their decision. Also
>>> help(install.packages) goes to R's documentation of R's
>>> install.packages, so there's even more misleading of useRs.
>>> Martin
>>>
>>
>> __
>> R
Re: [R] Building Packages.
Is your Fedora machine using the bspm package with bspm::enable() in
the .Rprofile (to install binary packages from the r2u repository)?
bspm adds a hook by using trace() on install.packages, which makes it
look like this.
My guess is that if you start with --vanilla *or* run bspm::disable()
that you'll get back to the original-as-installed version.
Even if you have RStudio installed you could change the association
in your GUI file browser to open R files in emacs by default ...
cheers
Ben Bolker
On 2024-03-21 4:40 a.m., Martin Maechler wrote:
Ben Bolker
on Wed, 20 Mar 2024 13:25:33 -0400 writes:
>Hmm, looks platform-specific. Under Linux both RStudio
> and external R console return
> a0b52513622c41c11e3ef57c7a485767
> for digest::digest(install.packages)
Well, platform-specific maybe, notably probably the *RStudio*-version
matters (for once).
One one of our public compute-machines running Linux Fedora 38
(I don't have RStudio installed on my desktop as I loathe it
badly to see RStudio start up when I click at an *R script in
the OS gui file browser ... !:!P:!)(*&))
I definitely see
R.version.string
[1] "R version 4.3.3 Patched (2024-02-29 r86162)"
RStudio.Version()$version
[1] ‘2023.12.1.402’
install.packages
function (...)
.rs.callAs(name, hook, original, ...)
No need for any hashes to see that install.packages is not the
one from R.
---
Concluding from your, Ben's, finding I'd guess that Posit
finally decided to move away from this very unfriendly idea of
sneakily replacing a base R function ?
That would actually give raise to some applause..
Martin
> On 2024-03-20 1:20 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
Ivan, can you give more detail on this? I've heard
this issue mentioned, but when I open RStudio and run
find("install.packages") it returns
"utils::install.packages", and running dump() from
within RStudio console and from an external "R
--vanilla" gives identical results.
I thought at one point this might only refer to
the GUI package-installation interface, but you seem to
be saying it's the install.packages() function as well.
Running an up-to-date RStudio on Linux, FWIW --
maybe weirdness only happens on other OSs?
>>>
>>> On MacOS, I see this:
>>>
>>> > install.packages function (...) .rs.callAs(name,
>>> hook, original, ...)
>>>
>>> I get the same results as you from find(). I'm not sure
>>> what RStudio is doing to give a different value for the
>>> function than what find() sees.
>>
>> Turns out that RStudio replaces the install.packages
>> object in the utils package.
>>
>> Duncan Murdoch
>>
>>>
>>> Duncan Murdoch
>>>
Ben Bolker
On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
> В Wed, 20 Mar 2024 16:02:27 + Jorgen Harmse via
> R-help пишет:
>
>>> install.packages(tar,type='source',repos=NULL)
>>
Error in library(jhBase) : there is no package called
>> ‘jhBase’
>>
Execution halted
>>
Warning in install.packages(tar, type = "source", repos =
>> NULL) :
>>
installation of package
>>
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
had non-zero exit status
>
> Using RStudio? It happens to override install.packages
> with a function that doesn't quite handle file
> paths. Try utils::install.packages(tar, type =
> "source", repos = NULL).
>
__
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.
--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of
working hours.
__
R-help@r-project.org
Re: [R] Building Packages.
Yes, you're right. The version found in the search list entry for
"package:utils" is the RStudio one; the ones found with two or three
colons are the original.
Duncan Murdoch
On 21/03/2024 5:48 a.m., peter dalgaard wrote:
Um, what's with the triple colon? At least on my install, double seems to
suffice:
identical(utils:::install.packages, utils::install.packages)
[1] TRUE
install.packages
function (...)
.rs.callAs(name, hook, original, ...)
-pd
On 21 Mar 2024, at 09:58 , Duncan Murdoch wrote:
The good news for Jorgen (who may not be reading this thread any more) is that
one can still be sure of getting the original install.packages() by using
utils:::install.packages( ... )
with *three* colons, to get the internal (namespace) version of the function.
Duncan Murdoch
On 21/03/2024 4:31 a.m., Martin Maechler wrote:
"Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>>> Ivan, can you give more detail on this? I've heard this
>>> issue mentioned, but when I open RStudio and run
>>> find("install.packages") it returns
>>> "utils::install.packages", and running dump() from
>>> within RStudio console and from an external "R
>>> --vanilla" gives identical results.
>>>
>>> I thought at one point this might only refer to the GUI
>>> package-installation interface, but you seem to be
>>> saying it's the install.packages() function as well.
>>>
>>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>>> weirdness only happens on other OSs?
>>
>> On MacOS, I see this:
>>
>> > install.packages function (...) .rs.callAs(name, hook,
>> original, ...)
>>
>> I get the same results as you from find(). I'm not sure
>> what RStudio is doing to give a different value for the
>> function than what find() sees.
> Turns out that RStudio replaces the install.packages
> object in the utils package.
> Duncan Murdoch
Yes, and this has been the case for several years now, and I
have mentioned this several times, too (though some of it
possibly not in a public R-* mailing list).
And yes, that they modify the package environment
as.environment("package:utils")
but leave the
namespace asNamespace("utils")
unchanged, makes it harder to see what's
going on (but also has less severe consequences; if they kept to
the otherwise universal *rule* that the namespace and package must have the
same objects
apart from those only in the namespace,
people would not even have access to R's true install.packages()
but only see the RStudio fake^Hsubstitute..
We are still not happy with their decision. Also
help(install.packages) goes to R's documentation of R's
install.packages, so there's even more misleading of useRs.
Martin
__
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] Building Packages.
Um, what's with the triple colon? At least on my install, double seems to
suffice:
> identical(utils:::install.packages, utils::install.packages)
[1] TRUE
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
-pd
> On 21 Mar 2024, at 09:58 , Duncan Murdoch wrote:
>
> The good news for Jorgen (who may not be reading this thread any more) is
> that one can still be sure of getting the original install.packages() by using
>
>utils:::install.packages( ... )
>
> with *three* colons, to get the internal (namespace) version of the function.
>
> Duncan Murdoch
>
>
> On 21/03/2024 4:31 a.m., Martin Maechler wrote:
>>> "Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
>> > On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>> >> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>> >>> Ivan, can you give more detail on this? I've heard this
>> >>> issue mentioned, but when I open RStudio and run
>> >>> find("install.packages") it returns
>> >>> "utils::install.packages", and running dump() from
>> >>> within RStudio console and from an external "R
>> >>> --vanilla" gives identical results.
>> >>>
>> >>> I thought at one point this might only refer to the GUI
>> >>> package-installation interface, but you seem to be
>> >>> saying it's the install.packages() function as well.
>> >>>
>> >>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>> >>> weirdness only happens on other OSs?
>> >>
>> >> On MacOS, I see this:
>> >>
>> >> > install.packages function (...) .rs.callAs(name, hook,
>> >> original, ...)
>> >>
>> >> I get the same results as you from find(). I'm not sure
>> >> what RStudio is doing to give a different value for the
>> >> function than what find() sees.
>> > Turns out that RStudio replaces the install.packages
>> > object in the utils package.
>> > Duncan Murdoch
>> Yes, and this has been the case for several years now, and I
>> have mentioned this several times, too (though some of it
>> possibly not in a public R-* mailing list).
>> And yes, that they modify the package environment
>> as.environment("package:utils")
>> but leave the
>> namespace asNamespace("utils")
>> unchanged, makes it harder to see what's
>> going on (but also has less severe consequences; if they kept to
>> the otherwise universal *rule* that the namespace and package must have the
>> same objects
>> apart from those only in the namespace,
>> people would not even have access to R's true install.packages()
>> but only see the RStudio fake^Hsubstitute..
>> We are still not happy with their decision. Also
>> help(install.packages) goes to R's documentation of R's
>> install.packages, so there's even more misleading of useRs.
>> Martin
>>
>
> __
> 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.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
__
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] Building Packages.
The good news for Jorgen (who may not be reading this thread any more)
is that one can still be sure of getting the original install.packages()
by using
utils:::install.packages( ... )
with *three* colons, to get the internal (namespace) version of the
function.
Duncan Murdoch
On 21/03/2024 4:31 a.m., Martin Maechler wrote:
"Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>>> Ivan, can you give more detail on this? I've heard this
>>> issue mentioned, but when I open RStudio and run
>>> find("install.packages") it returns
>>> "utils::install.packages", and running dump() from
>>> within RStudio console and from an external "R
>>> --vanilla" gives identical results.
>>>
>>> I thought at one point this might only refer to the GUI
>>> package-installation interface, but you seem to be
>>> saying it's the install.packages() function as well.
>>>
>>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>>> weirdness only happens on other OSs?
>>
>> On MacOS, I see this:
>>
>> > install.packages function (...) .rs.callAs(name, hook,
>> original, ...)
>>
>> I get the same results as you from find(). I'm not sure
>> what RStudio is doing to give a different value for the
>> function than what find() sees.
> Turns out that RStudio replaces the install.packages
> object in the utils package.
> Duncan Murdoch
Yes, and this has been the case for several years now, and I
have mentioned this several times, too (though some of it
possibly not in a public R-* mailing list).
And yes, that they modify the package environment
as.environment("package:utils")
but leave the
namespace asNamespace("utils")
unchanged, makes it harder to see what's
going on (but also has less severe consequences; if they kept to
the otherwise universal *rule* that the namespace and package must have the
same objects
apart from those only in the namespace,
people would not even have access to R's true install.packages()
but only see the RStudio fake^Hsubstitute..
We are still not happy with their decision. Also
help(install.packages) goes to R's documentation of R's
install.packages, so there's even more misleading of useRs.
Martin
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Re: [R] Building Packages.
> Ben Bolker
> on Wed, 20 Mar 2024 13:25:33 -0400 writes:
>Hmm, looks platform-specific. Under Linux both RStudio
> and external R console return
> a0b52513622c41c11e3ef57c7a485767
> for digest::digest(install.packages)
Well, platform-specific maybe, notably probably the *RStudio*-version
matters (for once).
One one of our public compute-machines running Linux Fedora 38
(I don't have RStudio installed on my desktop as I loathe it
badly to see RStudio start up when I click at an *R script in
the OS gui file browser ... !:!P:!)(*&))
I definitely see
> R.version.string
[1] "R version 4.3.3 Patched (2024-02-29 r86162)"
> RStudio.Version()$version
[1] ‘2023.12.1.402’
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
>
No need for any hashes to see that install.packages is not the
one from R.
---
Concluding from your, Ben's, finding I'd guess that Posit
finally decided to move away from this very unfriendly idea of
sneakily replacing a base R function ?
That would actually give raise to some applause..
Martin
> On 2024-03-20 1:20 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
Ivan, can you give more detail on this? I've heard
this issue mentioned, but when I open RStudio and run
find("install.packages") it returns
"utils::install.packages", and running dump() from
within RStudio console and from an external "R
--vanilla" gives identical results.
I thought at one point this might only refer to
the GUI package-installation interface, but you seem to
be saying it's the install.packages() function as well.
Running an up-to-date RStudio on Linux, FWIW --
maybe weirdness only happens on other OSs?
>>>
>>> On MacOS, I see this:
>>>
>>> > install.packages function (...) .rs.callAs(name,
>>> hook, original, ...)
>>>
>>> I get the same results as you from find(). I'm not sure
>>> what RStudio is doing to give a different value for the
>>> function than what find() sees.
>>
>> Turns out that RStudio replaces the install.packages
>> object in the utils package.
>>
>> Duncan Murdoch
>>
>>>
>>> Duncan Murdoch
>>>
Ben Bolker
On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
> В Wed, 20 Mar 2024 16:02:27 + Jorgen Harmse via
> R-help пишет:
>
>>> install.packages(tar,type='source',repos=NULL)
>>
> Error in library(jhBase) : there is no package called
>> ‘jhBase’
>>
> Execution halted
>>
> Warning in install.packages(tar, type = "source", repos =
>> NULL) :
>>
> installation of package
>
>>
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
> had non-zero exit status
>
> Using RStudio? It happens to override install.packages
> with a function that doesn't quite handle file
> paths. Try utils::install.packages(tar, type =
> "source", repos = NULL).
>
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>>>
>>
> __
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> more, see https://stat.ethz.ch/mailman/listinfo/r-help
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> http://www.R-project.org/posting-guide.html and provide
> commented, minimal, self-contained, reproducible code.
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Re: [R] Building Packages.
> "Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
>>> Ivan, can you give more detail on this? I've heard this
>>> issue mentioned, but when I open RStudio and run
>>> find("install.packages") it returns
>>> "utils::install.packages", and running dump() from
>>> within RStudio console and from an external "R
>>> --vanilla" gives identical results.
>>>
>>> I thought at one point this might only refer to the GUI
>>> package-installation interface, but you seem to be
>>> saying it's the install.packages() function as well.
>>>
>>> Running an up-to-date RStudio on Linux, FWIW -- maybe
>>> weirdness only happens on other OSs?
>>
>> On MacOS, I see this:
>>
>> > install.packages function (...) .rs.callAs(name, hook,
>> original, ...)
>>
>> I get the same results as you from find(). I'm not sure
>> what RStudio is doing to give a different value for the
>> function than what find() sees.
> Turns out that RStudio replaces the install.packages
> object in the utils package.
> Duncan Murdoch
Yes, and this has been the case for several years now, and I
have mentioned this several times, too (though some of it
possibly not in a public R-* mailing list).
And yes, that they modify the package environment
as.environment("package:utils")
but leave the
namespace asNamespace("utils")
unchanged, makes it harder to see what's
going on (but also has less severe consequences; if they kept to
the otherwise universal *rule* that the namespace and package must have the
same objects
apart from those only in the namespace,
people would not even have access to R's true install.packages()
but only see the RStudio fake^Hsubstitute..
We are still not happy with their decision. Also
help(install.packages) goes to R's documentation of R's
install.packages, so there's even more misleading of useRs.
Martin
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building Packages.
В Wed, 20 Mar 2024 19:26:53 +
Jorgen Harmse пишет:
> Thank you. tools:::.install_packages works.
I'm glad it works, but it shouldn't be necessary to use (and is not
part of the API: not documented to keep working this way).
Since you're already using devtools, perhaps devtools::install will
succeed. But it's not obvious why utils::install.packages() is failing,
and it should still be called by devtools::install().
> It happens that one of the functions in my package is a utility to
> build packages. I guess I should change the install step.
Try setting a breakpoint in system2 before launching your function:
debugonce(system2)
build.package('/path/to/the/source/tree')
This should land you in R's "browser" (see help(browser) for how to use
it). At this point, what is `command` and what are the `args`? If you
remove c("CMD", "INSTALL") from the `args` vector and give the rest as
the argument to .install_packages() in a fresh process, will it break
in a similar manner?
Browse[2]> command
[1] "/usr/lib/R/bin/R"
Browse[2]> args
[1] "CMD" "INSTALL" "-l"
"'/home/ivan/R/x86_64-pc-linux-gnu-library/4.2'"
"'/home/ivan/path/to/package_1.0.tar.gz'"
# (start a new process)
tools:::.install_packages(c(
'-l',
# you'll have to manually unquote the file paths:
# the strings above are for both R and the command line shell
# to interpret, but here we're only giving them to R, not the shell
"/home/ivan/R/x86_64-pc-linux-gnu-library/4.2",
"/home/ivan/path/to/package_1.0.tar.gz"
))
--
Best regards,
Ivan
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building Packages.
Thank you. tools:::.install_packages works.
It happens that one of the functions in my package is a utility to build
packages. I guess I should change the install step.
Regards,
Jorgen.
#' Build package from source
#'
#' \code{roxygen2} & \code{devtools} have several steps to build a package, and
#' \code{build.package} wraps them in one function. It can also clean up
#' and protect the description file.
#'
#' @param package.dir the directory with the package files arranged as expected
by
#' \code{roxygen2} except as noted below
#' @param clean whether to remove old \code{Rd} files before starting
#' @param install whether to install the package after building it, which may
make the latest
#' version available in the current R session
#'
#' @note The description file should be in \code{DESC.source} rather than
\code{DESCRIPTION}.
#' \code{build.package} will then overwrite the machine-generated
\code{DESCRIPTION} from the
#' previous build with the true source.
#'
#' @return \code{invisible()}
#'
#' @export
build.package <- function(package.dir,clean=TRUE,install=TRUE)
{ if (!require(roxygen2))
stop("Please install roxygen2 and its dependencies.")
if (!require(devtools))
stop("Please install devtools and its dependencies.")
if ( file.exists(file.path(package.dir,"DESC.source") -> DESC.source) )
file.copy(DESC.source, file.path(package.dir,"DESCRIPTION"), overwrite=TRUE)
roxygenise(package.dir,clean=clean)
tar <- devtools::build(package.dir)
if (install)
install.packages(tar,type='source',repos=NULL)
invisible()
}
From: Ivan Krylov
Date: Wednesday, March 20, 2024 at 14:12
To: Jorgen Harmse
Cc: Jorgen Harmse via R-help
Subject: [EXTERNAL] Re: [R] Building Packages.
� Wed, 20 Mar 2024 17:00:34 +
Jorgen Harmse �:
> Thank you, but I think I was already using utils.
>
> Regards,
> Jorgen.
>
>
> > environment(install.packages)
>
>
>
> > utils::install.packages('/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz',type='source',repos=NULL)
> >
>
> Error in library(jhBase) : there is no package called �jhBase�
Sorry, then it has been my mistake to blame RStudio for this.
We can try debugging this. If you start a fresh R process and run
tools:::.install_packages(path_to_tarball), the installation will (try
to) proceed in the current process instead of a child process. Once it
fails, traceback() will be available to show you where the error
condition has been raised. What does it say?
Alternatively,
1. Check the package R files for stray library() calls. Generally,
packages should not be calling library().
2. Try a "binary search" approach. Make a copy of your package code but
remove half of the files (or half of the functions if they live in a
single file). Keep removing a half (or go to the other half) depending
on whether the same error keeps happening.
Good luck!
--
Best regards,
Ivan
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building Packages.
В Wed, 20 Mar 2024 17:00:34 +
Jorgen Harmse пишет:
> Thank you, but I think I was already using utils.
>
> Regards,
> Jorgen.
>
>
> > environment(install.packages)
>
>
>
> > utils::install.packages('/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz',type='source',repos=NULL)
> >
>
> Error in library(jhBase) : there is no package called ‘jhBase’
Sorry, then it has been my mistake to blame RStudio for this.
We can try debugging this. If you start a fresh R process and run
tools:::.install_packages(path_to_tarball), the installation will (try
to) proceed in the current process instead of a child process. Once it
fails, traceback() will be available to show you where the error
condition has been raised. What does it say?
Alternatively,
1. Check the package R files for stray library() calls. Generally,
packages should not be calling library().
2. Try a "binary search" approach. Make a copy of your package code but
remove half of the files (or half of the functions if they live in a
single file). Keep removing a half (or go to the other half) depending
on whether the same error keeps happening.
Good luck!
--
Best regards,
Ivan
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building Packages.
I was thinking of making it Open Source, but I haven’t yet. It’s mostly a
collection of small utility functions (more oxygen comments than actual code).
I built the package on my Windows machine a few months ago, but my Mac first
wouldn’t install roygen2 & devtools and now (with the latest version of R)
won’t install the tarball that they create. (A work-around that I might try
again is to build the package under Windows and ship the tarball to my Mac.)
Regards,
Jorgen.
Example:
#' Adjust number of columns used in printing
#'
#' Use \code{\link{options}} to determine the current number of columns,
increment
#' or decrement, and pass the result as \code{width} in a second call to
\code{options}.
#'
#' @param dw signed amount by which to increment the number of columns
#'
#' @return a list with the old value of \code{options('width')}
#'
#' @export
width <- function(dw) options(width = options('width')[[1L]] + as.integer(dw))
From: Duncan Murdoch
Date: Wednesday, March 20, 2024 at 12:09
To: Jorgen Harmse , Ivan Krylov , Jorgen
Harmse via R-help
Subject: [EXTERNAL] Re: [R] Building Packages.
Is the source for your package online somewhere?
Duncan Murdoch
On 20/03/2024 1:00 p.m., Jorgen Harmse via R-help wrote:
> Thank you, but I think I was already using utils.
>
> Regards,
> Jorgen.
>
>
>> environment(install.packages)
>
>
>
>> utils::install.packages('/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz',type='source',repos=NULL)
>
> Error in library(jhBase) : there is no package called �jhBase�
>
> Execution halted
>
> Warning in
> utils::install.packages("/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz",
> :
>
>installation of package
> �/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz�
> had non-zero exit status
>
>
> From: Ivan Krylov
> Date: Wednesday, March 20, 2024 at 11:14
> To: Jorgen Harmse via R-help
> Cc: Jorgen Harmse
> Subject: [EXTERNAL] Re: [R] Building Packages.
> � Wed, 20 Mar 2024 16:02:27 +
> Jorgen Harmse via R-help �:
>
>>> install.packages(tar,type='source',repos=NULL)
>>
>> Error in library(jhBase) : there is no package called �jhBase�
>>
>> Execution halted
>>
>> Warning in install.packages(tar, type = "source", repos = NULL) :
>>
>>installation of package
>> �/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz�
>> had non-zero exit status
>
> Using RStudio? It happens to override install.packages with a function
> that doesn't quite handle file paths. Try utils::install.packages(tar,
> type = "source", repos = NULL).
>
> --
> Best regards,
> Ivan
>
>[[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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Re: [R] Building Packages.
Hmm, looks platform-specific. Under Linux both RStudio and external
R console return
a0b52513622c41c11e3ef57c7a485767
for digest::digest(install.packages)
On 2024-03-20 1:20 p.m., Duncan Murdoch wrote:
On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
On 20/03/2024 12:37 p.m., Ben Bolker wrote:
Ivan, can you give more detail on this? I've heard this issue
mentioned, but when I open RStudio and run find("install.packages") it
returns "utils::install.packages", and running dump() from within
RStudio console and from an external "R --vanilla" gives identical
results.
I thought at one point this might only refer to the GUI
package-installation interface, but you seem to be saying it's the
install.packages() function as well.
Running an up-to-date RStudio on Linux, FWIW -- maybe weirdness
only
happens on other OSs?
On MacOS, I see this:
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
I get the same results as you from find(). I'm not sure what RStudio is
doing to give a different value for the function than what find() sees.
Turns out that RStudio replaces the install.packages object in the utils
package.
Duncan Murdoch
Duncan Murdoch
Ben Bolker
On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
В Wed, 20 Mar 2024 16:02:27 +
Jorgen Harmse via R-help пишет:
install.packages(tar,type='source',repos=NULL)
Error in library(jhBase) : there is no package called ‘jhBase’
Execution halted
Warning in install.packages(tar, type = "source", repos = NULL) :
installation of package
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
had non-zero exit status
Using RStudio? It happens to override install.packages with a function
that doesn't quite handle file paths. Try utils::install.packages(tar,
type = "source", repos = NULL).
__
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Re: [R] Building Packages.
В Wed, 20 Mar 2024 12:37:39 -0400
Ben Bolker пишет:
> Ivan, can you give more detail on this? I've heard this issue
> mentioned, but when I open RStudio and run find("install.packages")
> it returns "utils::install.packages", and running dump() from within
> RStudio console and from an external "R --vanilla" gives identical
> results.
Has this been fixed in a recent RStudio version? This is what I get on
a Windows virtual machine:
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
> install.packages(file.choose())
Installing package into ‘C:/Users/User/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘C:\path\to\mypackage_1.0.tar.gz’ is not available
for this version of R
A version of this package for your version of R might be available
elsewhere, see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> utils::install.packages(file.choose())
Installing package into ‘C:/Users/User/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from 'pkgs'
* installing *source* package 'mypackage' ...
** using staged installation
** libs
--
Best regards,
Ivan
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Re: [R] Building Packages.
On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
On 20/03/2024 12:37 p.m., Ben Bolker wrote:
Ivan, can you give more detail on this? I've heard this issue
mentioned, but when I open RStudio and run find("install.packages") it
returns "utils::install.packages", and running dump() from within
RStudio console and from an external "R --vanilla" gives identical results.
I thought at one point this might only refer to the GUI
package-installation interface, but you seem to be saying it's the
install.packages() function as well.
Running an up-to-date RStudio on Linux, FWIW -- maybe weirdness only
happens on other OSs?
On MacOS, I see this:
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
I get the same results as you from find(). I'm not sure what RStudio is
doing to give a different value for the function than what find() sees.
Turns out that RStudio replaces the install.packages object in the utils
package.
Duncan Murdoch
Duncan Murdoch
Ben Bolker
On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
В Wed, 20 Mar 2024 16:02:27 +
Jorgen Harmse via R-help пишет:
install.packages(tar,type='source',repos=NULL)
Error in library(jhBase) : there is no package called ‘jhBase’
Execution halted
Warning in install.packages(tar, type = "source", repos = NULL) :
installation of package
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
had non-zero exit status
Using RStudio? It happens to override install.packages with a function
that doesn't quite handle file paths. Try utils::install.packages(tar,
type = "source", repos = NULL).
__
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Re: [R] Building Packages.
Is the source for your package online somewhere?
Duncan Murdoch
On 20/03/2024 1:00 p.m., Jorgen Harmse via R-help wrote:
Thank you, but I think I was already using utils.
Regards,
Jorgen.
environment(install.packages)
utils::install.packages('/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz',type='source',repos=NULL)
Error in library(jhBase) : there is no package called �jhBase�
Execution halted
Warning in
utils::install.packages("/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz",
:
installation of package
�/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz� had
non-zero exit status
From: Ivan Krylov
Date: Wednesday, March 20, 2024 at 11:14
To: Jorgen Harmse via R-help
Cc: Jorgen Harmse
Subject: [EXTERNAL] Re: [R] Building Packages.
� Wed, 20 Mar 2024 16:02:27 +
Jorgen Harmse via R-help �:
install.packages(tar,type='source',repos=NULL)
Error in library(jhBase) : there is no package called �jhBase�
Execution halted
Warning in install.packages(tar, type = "source", repos = NULL) :
installation of package
�/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz�
had non-zero exit status
Using RStudio? It happens to override install.packages with a function
that doesn't quite handle file paths. Try utils::install.packages(tar,
type = "source", repos = NULL).
--
Best regards,
Ivan
[[alternative HTML version deleted]]
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Re: [R] Building Packages.
On 20/03/2024 12:37 p.m., Ben Bolker wrote:
Ivan, can you give more detail on this? I've heard this issue
mentioned, but when I open RStudio and run find("install.packages") it
returns "utils::install.packages", and running dump() from within
RStudio console and from an external "R --vanilla" gives identical results.
I thought at one point this might only refer to the GUI
package-installation interface, but you seem to be saying it's the
install.packages() function as well.
Running an up-to-date RStudio on Linux, FWIW -- maybe weirdness only
happens on other OSs?
On MacOS, I see this:
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
I get the same results as you from find(). I'm not sure what RStudio is
doing to give a different value for the function than what find() sees.
Duncan Murdoch
Ben Bolker
On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
В Wed, 20 Mar 2024 16:02:27 +
Jorgen Harmse via R-help пишет:
install.packages(tar,type='source',repos=NULL)
Error in library(jhBase) : there is no package called ‘jhBase’
Execution halted
Warning in install.packages(tar, type = "source", repos = NULL) :
installation of package
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
had non-zero exit status
Using RStudio? It happens to override install.packages with a function
that doesn't quite handle file paths. Try utils::install.packages(tar,
type = "source", repos = NULL).
__
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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.
__
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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] Building Packages.
Thank you, but I think I was already using utils.
Regards,
Jorgen.
> environment(install.packages)
> utils::install.packages('/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz',type='source',repos=NULL)
Error in library(jhBase) : there is no package called �jhBase�
Execution halted
Warning in
utils::install.packages("/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz",
:
installation of package
�/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz� had
non-zero exit status
From: Ivan Krylov
Date: Wednesday, March 20, 2024 at 11:14
To: Jorgen Harmse via R-help
Cc: Jorgen Harmse
Subject: [EXTERNAL] Re: [R] Building Packages.
� Wed, 20 Mar 2024 16:02:27 +
Jorgen Harmse via R-help �:
> > install.packages(tar,type='source',repos=NULL)
>
> Error in library(jhBase) : there is no package called �jhBase�
>
> Execution halted
>
> Warning in install.packages(tar, type = "source", repos = NULL) :
>
> installation of package
> �/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz�
> had non-zero exit status
Using RStudio? It happens to override install.packages with a function
that doesn't quite handle file paths. Try utils::install.packages(tar,
type = "source", repos = NULL).
--
Best regards,
Ivan
[[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] Building Packages.
Ivan, can you give more detail on this? I've heard this issue
mentioned, but when I open RStudio and run find("install.packages") it
returns "utils::install.packages", and running dump() from within
RStudio console and from an external "R --vanilla" gives identical results.
I thought at one point this might only refer to the GUI
package-installation interface, but you seem to be saying it's the
install.packages() function as well.
Running an up-to-date RStudio on Linux, FWIW -- maybe weirdness only
happens on other OSs?
Ben Bolker
On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
В Wed, 20 Mar 2024 16:02:27 +
Jorgen Harmse via R-help пишет:
install.packages(tar,type='source',repos=NULL)
Error in library(jhBase) : there is no package called ‘jhBase’
Execution halted
Warning in install.packages(tar, type = "source", repos = NULL) :
installation of package
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
had non-zero exit status
Using RStudio? It happens to override install.packages with a function
that doesn't quite handle file paths. Try utils::install.packages(tar,
type = "source", repos = NULL).
__
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] Building Packages.
В Wed, 20 Mar 2024 16:02:27 + Jorgen Harmse via R-help пишет: > > install.packages(tar,type='source',repos=NULL) > > Error in library(jhBase) : there is no package called ‘jhBase’ > > Execution halted > > Warning in install.packages(tar, type = "source", repos = NULL) : > > installation of package > ‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’ > had non-zero exit status Using RStudio? It happens to override install.packages with a function that doesn't quite handle file paths. Try utils::install.packages(tar, type = "source", repos = NULL). -- Best regards, Ivan __ 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] Building Packages.
I have a source file with oxygen-style comments (and description & licence
files), and I’m trying to build a package. oxygen & devtools seem to work, and
the tarball exists, but install.packages balks. Does anyone know what’s
happening?
Regards,
Jorgen Harmse.
> roxygenise(package.dir,clean=TRUE)
Setting `RoxygenNote` to "7.3.1"
✖ roxygen2 requires "Encoding: UTF-8"
ℹ Current encoding is NA
ℹ Loading jhBase
Warning: ── Conflicts
──
jhBase conflicts
──
✖ `andNotNA` masks `jhBase::andNotNA()`.
✖ `array.named` masks `jhBase::array.named()`.
✖ `arrayInd.inv` masks `jhBase::arrayInd.inv()`.
… and more.
ℹ Did you accidentally source a file rather than using `load_all()`?
Run `rm(list = c("andNotNA", "array.named", "arrayInd.inv",
"as.POSIXct_orig", "build.package", "colon", "file.info", "file.path",
"files.removeDup", "fprintf", "grepi", "grepiv", "grepv", "grepvi", "ifelses",
"index", "load.env", "load.list", "matrix.sq", "merges", "mm", "orNA",
"pattern.NA", "plots", "printf",
"save.env", "subs", "symmDiff", "vector.named", "width"))` to remove the
conflicts.
Writing NAMESPACE
Writing printf.Rd
Writing width.Rd
Writing pattern.NA.Rd
Writing ddply.ns.Rd
Writing as.POSIXct_orig.Rd
Writing mm.Rd
Writing orNA.Rd
Writing merges.Rd
Writing index.Rd
Writing save.env.Rd
Writing build.package.Rd
Writing plots.Rd
Writing ifelses.Rd
Writing subs.Rd
Writing array.named.Rd
Writing grepv.Rd
Writing symmDiff.Rd
Writing file.info.Rd
Writing file.path.Rd
Writing files.removeDup.Rd
Writing arrayInd.inv.Rd
> tar <- devtools::build(package.dir)
── R CMD build
✔ checking for file
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase/DESCRIPTION’ ...
─ preparing ‘jhBase’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘jhBase_1.0.1.tar.gz’
> file.info(tar)
size
isdir mode mtime ctime atime uid gid
uname grname
/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz 14030
FALSE 644 2024-03-20 10:49:10 2024-03-20 10:49:10 2024-03-20 10:49:10 503 20
jharmse staff
> install.packages(tar,type='source',repos=NULL)
Error in library(jhBase) : there is no package called ‘jhBase’
Execution halted
Warning in install.packages(tar, type = "source", repos = NULL) :
installation of package
‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’ had
non-zero exit status
[[alternative HTML version deleted]]
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Re: [R] building packages: R Help for package foo vs. HTML Help?
Michael Friendly wrote: Uwe Ligges wrote: Michael Friendly wrote: In building a package, what are the settings in the package files or the build commands that determine whether the compiled HTML help windows have the window title R Help for package foo vs. HTML Help? Michael, can you give an example for a page with title HTML Help? I only found the R Help for package foo version during a quick inspection of a few examples. Sure: library(vcd); ?mosaic library(heplots); ?heplot library(car); ?Anova library(rgl); ?shade3d # --- I believe up until just the latest version (rgl_0.81.708) I downloaded from R-Forge I get R Help for package [foo] for all of these. I have absolutely no idea why it is different on your machine. Best wishes, Uwe Here's my sessionInfo: sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] vcd_1.1-1 colorspace_0.95 MASS_7.2-44 rgl_0.81.708 [5] heplots_0.8-0 car_1.2-8 I often have quite a few help files active, and it is much more convenient to navigate among them if the window has an informative title. If this is simple to test for in the build process, can/should this be tested for (with a warning) or even enforced/automatically generated in the scripts? -Michael __ R-help@r-project.org mailing list 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] building packages: R Help for package foo vs. HTML Help?
Uwe Ligges wrote: Michael Friendly wrote: Uwe Ligges wrote: Michael Friendly wrote: In building a package, what are the settings in the package files or the build commands that determine whether the compiled HTML help windows have the window title R Help for package foo vs. HTML Help? Michael, can you give an example for a page with title HTML Help? I only found the R Help for package foo version during a quick inspection of a few examples. Sure: library(vcd); ?mosaic library(heplots); ?heplot library(car); ?Anova library(rgl); ?shade3d # --- I believe up until just the latest version (rgl_0.81.708) I downloaded from R-Forge I get R Help for package [foo] for all of these. I have absolutely no idea why it is different on your machine. I see the HTML Help message for some pages in CHM help, not in HTML help. I'm not sure what the pattern is that leads to this. Duncan Murdoch Best wishes, Uwe Here's my sessionInfo: sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] vcd_1.1-1 colorspace_0.95 MASS_7.2-44 rgl_0.81.708 [5] heplots_0.8-0 car_1.2-8 I often have quite a few help files active, and it is much more convenient to navigate among them if the window has an informative title. If this is simple to test for in the build process, can/should this be tested for (with a warning) or even enforced/automatically generated in the scripts? -Michael __ R-help@r-project.org mailing list 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 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] building packages: R Help for package foo vs. HTML Help?
In building a package, what are the settings in the package files or the build commands that determine whether the compiled HTML help windows have the window title R Help for package foo vs. HTML Help? I often have quite a few help files active, and it is much more convenient to navigate among them if the window has an informative title. If this is simple to test for in the build process, can/should this be tested for (with a warning) or even enforced/automatically generated in the scripts? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list 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] building packages: R Help for package foo vs. HTML Help?
Michael Friendly wrote: In building a package, what are the settings in the package files or the build commands that determine whether the compiled HTML help windows have the window title R Help for package foo vs. HTML Help? Michael, can you give an example for a page with title HTML Help? I only found the R Help for package foo version during a quick inspection of a few examples. Best wishes, Uwe I often have quite a few help files active, and it is much more convenient to navigate among them if the window has an informative title. If this is simple to test for in the build process, can/should this be tested for (with a warning) or even enforced/automatically generated in the scripts? -Michael __ R-help@r-project.org mailing list 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] building packages: R Help for package foo vs. HTML Help?
Uwe Ligges wrote: Michael Friendly wrote: In building a package, what are the settings in the package files or the build commands that determine whether the compiled HTML help windows have the window title R Help for package foo vs. HTML Help? Michael, can you give an example for a page with title HTML Help? I only found the R Help for package foo version during a quick inspection of a few examples. Sure: library(vcd); ?mosaic library(heplots); ?heplot library(car); ?Anova library(rgl); ?shade3d # --- I believe up until just the latest version (rgl_0.81.708) I downloaded from R-Forge Here's my sessionInfo: sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] vcd_1.1-1 colorspace_0.95 MASS_7.2-44 rgl_0.81.708 [5] heplots_0.8-0 car_1.2-8 I often have quite a few help files active, and it is much more convenient to navigate among them if the window has an informative title. If this is simple to test for in the build process, can/should this be tested for (with a warning) or even enforced/automatically generated in the scripts? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list 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] building packages for Linux vs. Windows
Erin Hodgess wrote:
Hi R People:
I sure that this is a really easy question, but here goes:
I'm trying to build a package that will run on both Linux and Windows.
However, there are several commands in a section that will be
different in Linux than they are in Windows.
Erin
Several people have indicated how to do this, but I encourage you to be
sure you really need to do it. Many things can be made to work the same
way on all OSs, and packages are much easier to maintain if you do not
have several variants. You might consider posting a few example of
where you find this necessary, and ask if there is an OS independent way
to do it.
Paul Gilbert
Would I be better off just to build two separate packages, please?
If just one is needed, how could I determine which system is running
in order to use the correct command, please?
Thanks in advance,
Erin
La version française suit le texte anglais.
This email may contain privileged and/or confidential in...{{dropped:26}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] building packages for Linux vs. Windows
On 10/02/2008 1:07 PM, Erin Hodgess wrote: Hi R People: I sure that this is a really easy question, but here goes: I'm trying to build a package that will run on both Linux and Windows. However, there are several commands in a section that will be different in Linux than they are in Windows. Would I be better off just to build two separate packages, please? If just one is needed, how could I determine which system is running in order to use the correct command, please? You will find it much easier to build just one package. You can use .Platform or (for more detail) Sys.info() to find out what kind of system you're running on. Remember that R doesn't just run on Linux and Windows: there's also MacOSX, and other Unix and Unix-like systems (Solaris, etc.). Duncan Murdoch __ R-help@r-project.org mailing list 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] building packages for Linux vs. Windows
Hi R People: I sure that this is a really easy question, but here goes: I'm trying to build a package that will run on both Linux and Windows. However, there are several commands in a section that will be different in Linux than they are in Windows. Would I be better off just to build two separate packages, please? If just one is needed, how could I determine which system is running in order to use the correct command, please? Thanks in advance, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@r-project.org mailing list 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] building packages for Linux vs. Windows
On my widows XP computer, W
From my windows XP system running R 2.6.1:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 6.1
year 2007
month 11
day26
svn rev43537
language R
version.string R version 2.6.1 (2007-11-26)
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Ted Harding [EMAIL PROTECTED] 2/10/2008 1:39 PM
On 10-Feb-08 18:07:56, Erin Hodgess wrote:
Hi R People:
I sure that this is a really easy question, but here goes:
I'm trying to build a package that will run on both Linux and Windows.
However, there are several commands in a section that will be
different in Linux than they are in Windows.
Would I be better off just to build two separate packages, please?
If just one is needed, how could I determine which system is running
in order to use the correct command, please?
Thanks in advance,
Erin
There is the version (a list) variable:
version
# platform i486-pc-linux-gnu
# arch i486
# os linux-gnu
# system i486, linux-gnu
# status Patched
# major 2
# minor 4.0
# year 2006
# month 11
# day25
# svn rev39997
# language R
from which you can extract the os component:
version$os
# [1] linux-gnu
I don;t know what this says on a Windows system,
but it surely won't mention Linux!
So testing this wil enable you to set a flag, e.g.
Linux-ifelse(length(grep(linux,version$os))0, TRUE, FALSE)
if(Linux){window-function(...) X11(...)} else
{window-function(...) windows(...)}
Hoping this helps,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 10-Feb-08 Time: 18:39:29
-- XFMail --
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Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
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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] building packages for Linux vs. Windows
On 10-Feb-08 18:07:56, Erin Hodgess wrote:
Hi R People:
I sure that this is a really easy question, but here goes:
I'm trying to build a package that will run on both Linux and Windows.
However, there are several commands in a section that will be
different in Linux than they are in Windows.
Would I be better off just to build two separate packages, please?
If just one is needed, how could I determine which system is running
in order to use the correct command, please?
Thanks in advance,
Erin
There is the version (a list) variable:
version
# platform i486-pc-linux-gnu
# arch i486
# os linux-gnu
# system i486, linux-gnu
# status Patched
# major 2
# minor 4.0
# year 2006
# month 11
# day25
# svn rev39997
# language R
from which you can extract the os component:
version$os
# [1] linux-gnu
I don;t know what this says on a Windows system,
but it surely won't mention Linux!
So testing this wil enable you to set a flag, e.g.
Linux-ifelse(length(grep(linux,version$os))0, TRUE, FALSE)
if(Linux){window-function(...) X11(...)} else
{window-function(...) windows(...)}
Hoping this helps,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 10-Feb-08 Time: 18:39:29
-- XFMail --
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] building packages: hhc.exe not found using xp
On Mon, 19 Nov 2007, Nicodemus, Kristin (NIH/NIMH) [C] wrote: Hello, Apologies in advance if this should be in R-devel, not Rhelp. I did read through the R-devel thread started by Gabor Grothendieck in September of this year - I am getting the exact same error using a new computer that has XP installed, not vista, complaining that the file hhc.exe is not found. It works for many careful people, including on Vista. I have downloaded the hhc.exe to HTML Help Workshop dir in Program Files but it says that there is a newer version (apparently not called hhc.exe) and seems to refuse to see the hhc.exe. On my old computer, also running XP, I was able to compile the CHM files. Is it on your path? There are two parts to HTML Help Workshop, and it is the second that is not installed on recent systems. I can successfully build the package with the appropriate non-html help files and I had resigned myself to leaving it as-is for the windows version, until I noticed that when calling up help in windows, instead of simply bringing up the non-html help files it actually prints an error message: Warning message: In print.help_files_with_topic(C:/PROGRA~1/R/R-26~1.0/library/package1/chm/package1) : No CHM help for 'package1' in package 'package1' is available: the CHM file for the package is missing If nothing else, is there a way to turn off this warning in windows? Yes, choose a different default help type, either when you install R or by editing etc/Rprofile.site. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list 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] building packages on Windows
On 01/10/2007 11:45 PM, Edna Bell wrote: Hi again. I'm sure that this is really simple. I'm trying to build a package on a Windows Vista machine. I use Rcmd build --binary test but I get the Please set TMPDIR to a valid temporary directory I tried TMPDIR=c:\temp but to no avail. I suspect you don't have write permission on c:\temp. Windows systems typically have TEMP set to a writeable directory, and recent builds of R 2.6.0 will use that directory; in older versions you should be able to manually set TMPDIR to the same directory. Duncan Murdoch __ R-help@r-project.org mailing list 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] building packages on Windows
Hi again. I'm sure that this is really simple. I'm trying to build a package on a Windows Vista machine. I use Rcmd build --binary test but I get the Please set TMPDIR to a valid temporary directory I tried TMPDIR=c:\temp but to no avail. Please help. thanks __ R-help@r-project.org mailing list 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] building packages on Windows
This happened with older versions of R but its fixed in the more recent R 2.6.0 versions. On 10/1/07, Edna Bell [EMAIL PROTECTED] wrote: Hi again. I'm sure that this is really simple. I'm trying to build a package on a Windows Vista machine. I use Rcmd build --binary test but I get the Please set TMPDIR to a valid temporary directory I tried TMPDIR=c:\temp but to no avail. Please help. thanks __ R-help@r-project.org mailing list 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 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] Building packages including Java files
Hello all, Can someone please point me in the right direction to find the documentation that explains how to build packages that include java code. Thank you. I'm sorry if this is entirely obvious! Best regards, Mark -- Mark Collins [EMAIL PROTECTED] __ R-help@r-project.org mailing list 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] Building packages including Java files
I think you have to visit the following website to get information about java packages: http://www.rforge.net/rJava/ http://www.rforge.net/rJava/ Then of course the official R documentation which describes how to build packages for R. With kind regards Marcel -- View this message in context: http://www.nabble.com/Building-packages-including-Java-files-tf4492509.html#a12814486 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
