Re: [Rd] improving the performance of install.packages
Joshua, Doing this well "horizontally" (across different OSs even though for just one domain, like CRAN and R) is difficult. We have decent "vertical" solutions (with one OS / distro) for (at least some) use / deployment cases as I show in a brief blog post and video here http://dirk.eddelbuettel.com/blog/2019/06/09#022_rocker_and_ppas https://www.youtube.com/watch?v=qIjWirNma-8&t=19s Installing either 'tidyverse' or 'rstan' reduces to a single 'apt-get install' command invocation which installs everything needed in a minute or two. In a vertical stack, we can control for other OS-specific dependencies which is powerful. But it doesn't span across OSs. Covering installations both "horizontally" and "vertically" is hard. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] improving the performance of install.packages
If this is the behaviour you are looking for, you might like to try
pak (https://pak.r-lib.org)
# Create a temporary library
path <- tempfile()
dir.create(path)
.libPaths(path)
pak::pkg_install("scales")
#> → Will install 8 packages:
#> colorspace (1.4-1), labeling (0.3), munsell (0.5.0), R6 (2.4.0),
RColorBrewer
#> (1.1-2), Rcpp (1.0.2), scales (1.0.0), viridisLite (0.3.0)
#>
#> → Will download 2 CRAN packages (4.7 MB), cached: 6 (3.69 MB).
#>
#> ✔ Installed colorspace 1.4-1 [139ms]
#> ✔ Installed labeling 0.3 [206ms]
#> ✔ Installed munsell 0.5.0 [288ms]
#> ✔ Installed R6 2.4.0 [375ms]
#> ✔ Installed RColorBrewer 1.1-2 [423ms]
#> ✔ Installed Rcpp 1.0.2 [472ms]
#> ✔ Installed scales 1.0.0 [511ms]
#> ✔ Installed viridisLite 0.3.0 [569ms]
#> ✔ 1 + 7 pkgs | kept 0, updated 0, new 8 | downloaded 2 (4.7 MB) [2.8s]
pak::pkg_install("scales")
#> ✔ No changes needed
#> ✔ 1 + 7 pkgs | kept 7, updated 0, new 0 | downloaded 0 (0 B) [855ms]
remove.packages(c("Rcpp", "munsell"))
pak::pkg_install("scales")
#> → Will install 2 packages:
#> munsell (0.5.0), Rcpp (1.0.2)
#>
#> → All 2 packages (4.88 MB) are cached.
#>
#> ✔ Installed munsell 0.5.0 [75ms]
#> ✔ Installed Rcpp 1.0.2 [242ms]
#> ✔ 1 + 7 pkgs | kept 6, updated 0, new 2 | downloaded 0 (0 B) [1.5s]
On Fri, Nov 8, 2019 at 1:07 AM Joshua Bradley wrote:
>
> Hello,
>
> Currently if you install a package twice:
>
> install.packages("testit")
> install.packages("testit")
>
> R will build the package from source (depending on what OS you're using)
> twice by default. This becomes especially burdensome when people are using
> big packages (i.e. lots of depends) and someone has a script with:
>
> install.packages("tidyverse")
> ...
> ... later on down the script
> ...
> install.packages("dplyr")
>
> In this case, "dplyr" is part of the tidyverse and will install twice. As
> the primary "package manager" for R, it should not install a package twice
> (by default) when it can be so easily checked. Indeed, many people resort
> to writing a few lines of code to filter out already-installed packages An
> r-help post from 2010 proposed a solution to improving the default
> behavior, by adding "force=FALSE" as a api addition to install.packages.(
> https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
>
> Would the R-core devs still consider this proposal?
>
> Josh Bradley
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
http://hadley.nz
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] improving the performance of install.packages
Just to clarify the expected behavior I had in mind when proposing the
force argument.
force = T would mean you will "force" an install no matter what (aligns
with the current behavior of the command)
force = F means install a package if it is not found in the local R library
on your system. If it is already installed, do nothing and return as if a
successfull install occurred.
On Fri, Nov 8, 2019, 7:27 PM Duncan Murdoch
wrote:
> On 08/11/2019 6:17 p.m., Henrik Bengtsson wrote:
> > I believe introducing a backward compatible force=TRUE is a good
> > start, even if we're not ready for making force=FALSE the default at
> > this point. It would help simplify quite-common instructions like
> >
> > if (requireNamespace("BiocManager"))
> >install.packages("BiocManager")
> > BiocManager::install(...)
> >
> > to
> >
> > install.packages("BiocManager", force=FALSE)
> > BiocManager::install(...)
>
> If simplifying instructions is the goal, it would be even simpler to
> just install it unconditionally:
>
> install.packages("BiocManager")
>
> Unlike dplyr (the original example in this thread), BiocManager is a
> tiny package with no compiling needed, so it hardly needs any time to
> install.
>
> And as previously mentioned, the backward compatible force=TRUE wouldn't
> help with the bad script at all. In fact, the bad script could be fixed
> simply by realizing that
>
> install.packages("tidyverse")
>
> means it's actually a bad idea to also include
>
> install.packages("dplyr")
>
> because the former would install dplyr if and only if it was not already
> installed. So it seems to me that fixing the bad script (by deleting
> one line) is the solution to the problem, not fixing R with a multistage
> series of revisions, tests, etc.
>
> Duncan Murdoch
>
> >
> > and more so when installing lots of packages conditionally, e.g.
> >
> > if (requireNamespace("foo")) install.packages("foo")
> > if (requireNamespace("bar")) install.packages("bar")
> > ...
> >
> > to
> >
> > install.packages(c("foo", "bar", ...), force = FALSE)
> >
> > Before deciding on making force=FALSE the new default, I think it
> > would be valuable to play the devil's advocate and explore and
> > identify all possible downsides of such a default, e.g. breaking
> > existing instructions, downstream package code that uses
> > install.packages() internally, and so on.
> >
> > /Henrik
> >
> > PS. Although the idea of having update.packages() install missing
> > packages is not bad, I don't think I'm a not a fan for the sole
> > purpose of risking installation instructions starting using
> > update.packages() instead, which will certainly confuse those who
> > don't know the history (think require() vs library()).
> >
> > On Fri, Nov 8, 2019 at 3:11 PM Pages, Herve
> wrote:
> >>
> >> Hi Gabe,
> >>
> >> Keeping track of where a package was installed from would be a nice
> >> feature. However it wouldn't be as reliable as comparing hashes to
> >> decide whether a package needs re-installation or not.
> >>
> >> H.
> >>
> >> On 11/8/19 12:37, Gabriel Becker wrote:
> >>> Hi Josh,
> >>>
> >>> There are a few issues I can think of with this. The primary one is
> that
> >>> CRAN(/Bioconductor) is not the only place one can install packages
> from. I
> >>> might have version x.y.z of a package installed that was, at the time,
> a
> >>> development version I got from github, or installed locally, etc. Hell
> I
> >>> might have a later devel version but want the CRAN version. Not common,
> >>> sure, but wiill likely happen often enough that install.packages not
> doing
> >>> that for me when I tell it to is probably bad.
> >>>
> >>> Currently (though there has been some discussion of changing this)
> packages
> >>> do not remember where they were installed from, so R wouldn't know if
> the
> >>> version you have is actually fully the same one on the repository you
> >>> pointed install.packages to or not. If that were changed and we knew
> that
> >>> we were getting the byte identical package from the actual same
> source, I
> >>> think this would be a nice addition, though without it I think it
> would be
> >>> right a high but not high enough proportion of the time.
> >>>
> >>> R will build the package from source (depending on what OS you're
> using)
> twice by default. This becomes especially burdensome when people are
> using
> big packages (i.e. lots of depends) and someone has a script with:
>
> >>>
> >>>
> >>> install.packages("tidyverse")
> ...
> ... later on down the script
> ...
> install.packages("dplyr")
>
> >>>
> >>> I mean, IMHO and as I think Duncan was alluding to, that's straight up
> an
> >>> error by the script author. I think its a few of them, actually, but
> its at
> >>> least one. An understandable one, sure, but thats still what it is.
> Scripts
> >>> (which are meant to be run more than once, generally) usually shouldn't
> >>> really be calling install.packages in the first place, but if
Re: [Rd] improving the performance of install.packages
On 08/11/2019 6:17 p.m., Henrik Bengtsson wrote:
I believe introducing a backward compatible force=TRUE is a good
start, even if we're not ready for making force=FALSE the default at
this point. It would help simplify quite-common instructions like
if (requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install(...)
to
install.packages("BiocManager", force=FALSE)
BiocManager::install(...)
If simplifying instructions is the goal, it would be even simpler to
just install it unconditionally:
install.packages("BiocManager")
Unlike dplyr (the original example in this thread), BiocManager is a
tiny package with no compiling needed, so it hardly needs any time to
install.
And as previously mentioned, the backward compatible force=TRUE wouldn't
help with the bad script at all. In fact, the bad script could be fixed
simply by realizing that
install.packages("tidyverse")
means it's actually a bad idea to also include
install.packages("dplyr")
because the former would install dplyr if and only if it was not already
installed. So it seems to me that fixing the bad script (by deleting
one line) is the solution to the problem, not fixing R with a multistage
series of revisions, tests, etc.
Duncan Murdoch
and more so when installing lots of packages conditionally, e.g.
if (requireNamespace("foo")) install.packages("foo")
if (requireNamespace("bar")) install.packages("bar")
...
to
install.packages(c("foo", "bar", ...), force = FALSE)
Before deciding on making force=FALSE the new default, I think it
would be valuable to play the devil's advocate and explore and
identify all possible downsides of such a default, e.g. breaking
existing instructions, downstream package code that uses
install.packages() internally, and so on.
/Henrik
PS. Although the idea of having update.packages() install missing
packages is not bad, I don't think I'm a not a fan for the sole
purpose of risking installation instructions starting using
update.packages() instead, which will certainly confuse those who
don't know the history (think require() vs library()).
On Fri, Nov 8, 2019 at 3:11 PM Pages, Herve wrote:
Hi Gabe,
Keeping track of where a package was installed from would be a nice
feature. However it wouldn't be as reliable as comparing hashes to
decide whether a package needs re-installation or not.
H.
On 11/8/19 12:37, Gabriel Becker wrote:
Hi Josh,
There are a few issues I can think of with this. The primary one is that
CRAN(/Bioconductor) is not the only place one can install packages from. I
might have version x.y.z of a package installed that was, at the time, a
development version I got from github, or installed locally, etc. Hell I
might have a later devel version but want the CRAN version. Not common,
sure, but wiill likely happen often enough that install.packages not doing
that for me when I tell it to is probably bad.
Currently (though there has been some discussion of changing this) packages
do not remember where they were installed from, so R wouldn't know if the
version you have is actually fully the same one on the repository you
pointed install.packages to or not. If that were changed and we knew that
we were getting the byte identical package from the actual same source, I
think this would be a nice addition, though without it I think it would be
right a high but not high enough proportion of the time.
R will build the package from source (depending on what OS you're using)
twice by default. This becomes especially burdensome when people are using
big packages (i.e. lots of depends) and someone has a script with:
install.packages("tidyverse")
...
... later on down the script
...
install.packages("dplyr")
I mean, IMHO and as I think Duncan was alluding to, that's straight up an
error by the script author. I think its a few of them, actually, but its at
least one. An understandable one, sure, but thats still what it is. Scripts
(which are meant to be run more than once, generally) usually shouldn't
really be calling install.packages in the first place, but if they do, they
should certainly not be installing umbrella packages and the packages they
bring with them separately.
Even having one vectorized call to install.packages where all the packages
are installed would prevent this issue, including in the case where the
user doesn't understand the purpose of the tidyverse package. Though the
installation would still occur every time the script was run.
The last thing to note is that there are at least 2 packages which provide
a function which does this already (install.load and remotes), so people
can get this functionality if they need it.
On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
I assumed this list is used to discuss proposals like this to the R
codebase. If I'm on the wrong list, please let me know.
This is the right place to discuss things like this. Thanks for starting
the conversation.
Best,
~G
[
Re: [Rd] improving the performance of install.packages
Sounds a very reasonable approach to me.
H.
On 11/8/19 15:17, Henrik Bengtsson wrote:
> I believe introducing a backward compatible force=TRUE is a good
> start, even if we're not ready for making force=FALSE the default at
> this point. It would help simplify quite-common instructions like:
>
> if (requireNamespace("BiocManager"))
>install.packages("BiocManager")
> BiocManager::install(...)
>
> to
>
> install.packages("BiocManager", force=FALSE)
> BiocManager::install(...)
>
> and more so when installing lots of packages conditionally, e.g.
>
> if (requireNamespace("foo")) install.packages("foo")
> if (requireNamespace("bar")) install.packages("bar")
> ...
>
> to
>
> install.packages(c("foo", "bar", ...), force = FALSE)
>
> Before deciding on making force=FALSE the new default, I think it
> would be valuable to play the devil's advocate and explore and
> identify all possible downsides of such a default, e.g. breaking
> existing instructions, downstream package code that uses
> install.packages() internally, and so on.
>
> /Henrik
>
> PS. Although the idea of having update.packages() install missing
> packages is not bad, I don't think I'm a not a fan for the sole
> purpose of risking installation instructions starting using
> update.packages() instead, which will certainly confuse those who
> don't know the history (think require() vs library()).
>
> On Fri, Nov 8, 2019 at 3:11 PM Pages, Herve wrote:
>>
>> Hi Gabe,
>>
>> Keeping track of where a package was installed from would be a nice
>> feature. However it wouldn't be as reliable as comparing hashes to
>> decide whether a package needs re-installation or not.
>>
>> H.
>>
>> On 11/8/19 12:37, Gabriel Becker wrote:
>>> Hi Josh,
>>>
>>> There are a few issues I can think of with this. The primary one is that
>>> CRAN(/Bioconductor) is not the only place one can install packages from. I
>>> might have version x.y.z of a package installed that was, at the time, a
>>> development version I got from github, or installed locally, etc. Hell I
>>> might have a later devel version but want the CRAN version. Not common,
>>> sure, but wiill likely happen often enough that install.packages not doing
>>> that for me when I tell it to is probably bad.
>>>
>>> Currently (though there has been some discussion of changing this) packages
>>> do not remember where they were installed from, so R wouldn't know if the
>>> version you have is actually fully the same one on the repository you
>>> pointed install.packages to or not. If that were changed and we knew that
>>> we were getting the byte identical package from the actual same source, I
>>> think this would be a nice addition, though without it I think it would be
>>> right a high but not high enough proportion of the time.
>>>
>>> R will build the package from source (depending on what OS you're using)
twice by default. This becomes especially burdensome when people are using
big packages (i.e. lots of depends) and someone has a script with:
>>>
>>>
>>> install.packages("tidyverse")
...
... later on down the script
...
install.packages("dplyr")
>>>
>>> I mean, IMHO and as I think Duncan was alluding to, that's straight up an
>>> error by the script author. I think its a few of them, actually, but its at
>>> least one. An understandable one, sure, but thats still what it is. Scripts
>>> (which are meant to be run more than once, generally) usually shouldn't
>>> really be calling install.packages in the first place, but if they do, they
>>> should certainly not be installing umbrella packages and the packages they
>>> bring with them separately.
>>>
>>> Even having one vectorized call to install.packages where all the packages
>>> are installed would prevent this issue, including in the case where the
>>> user doesn't understand the purpose of the tidyverse package. Though the
>>> installation would still occur every time the script was run.
>>>
>>>
>>> The last thing to note is that there are at least 2 packages which provide
>>> a function which does this already (install.load and remotes), so people
>>> can get this functionality if they need it.
>>>
>>>
>>> On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
>>>
I assumed this list is used to discuss proposals like this to the R
codebase. If I'm on the wrong list, please let me know.
>>>
>>> This is the right place to discuss things like this. Thanks for starting
>>> the conversation.
>>>
>>> Best,
>>> ~G
>>>
>>>
>>>[[alternative HTML version deleted]]
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XG4gVQKZam41YLfI3w8XRAu8s7f2I5jCppA45q6NBu0&s=cOXQGMA9Va3o9x1USGggzF82D1LtFQb2ALpLRLQs2k4&e=
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Com
Re: [Rd] improving the performance of install.packages
Actually there is one gotcha here: even if a package has not changed
(i.e. same exact hash), there are situations where you want to reinstall
it because one package it depends on has changed. This is because some
of the stuff that gets cached at installation time (e.g. method table)
can become stale and needs to be resynced.
We sometimes have to deal with this kind of situation in Bioconductor
when we make changes to some infrastructure packages. To avoid package
caches to become out-of-sync on the user machine after the user gets the
new version of the infrastructure package, we also bump the versions of
all the reverse deps for which the cache needs to be resynced. A side
effect of the version bumps is to also trigger build and propagation of
new Windows and Mac binaries for the reverse deps affected by the
change, which is good, because they also need to be rebuilt and
reinstalled. This is an ugly situation but luckily a rare one and it
generally happens in BioC devel only.
H.
On 11/8/19 15:05, Hervé Pagès wrote:
> Hi Gabe,
>
> Keeping track of where a package was installed from would be a nice
> feature. However it wouldn't be as reliable as comparing hashes to
> decide whether a package needs re-installation or not.
>
> H.
>
> On 11/8/19 12:37, Gabriel Becker wrote:
>> Hi Josh,
>>
>> There are a few issues I can think of with this. The primary one is that
>> CRAN(/Bioconductor) is not the only place one can install packages
>> from. I
>> might have version x.y.z of a package installed that was, at the time, a
>> development version I got from github, or installed locally, etc. Hell I
>> might have a later devel version but want the CRAN version. Not common,
>> sure, but wiill likely happen often enough that install.packages not
>> doing
>> that for me when I tell it to is probably bad.
>>
>> Currently (though there has been some discussion of changing this)
>> packages
>> do not remember where they were installed from, so R wouldn't know if the
>> version you have is actually fully the same one on the repository you
>> pointed install.packages to or not. If that were changed and we knew
>> that
>> we were getting the byte identical package from the actual same source, I
>> think this would be a nice addition, though without it I think it
>> would be
>> right a high but not high enough proportion of the time.
>>
>> R will build the package from source (depending on what OS you're using)
>>> twice by default. This becomes especially burdensome when people are
>>> using
>>> big packages (i.e. lots of depends) and someone has a script with:
>>>
>>
>>
>> install.packages("tidyverse")
>>> ...
>>> ... later on down the script
>>> ...
>>> install.packages("dplyr")
>>>
>>
>> I mean, IMHO and as I think Duncan was alluding to, that's straight up an
>> error by the script author. I think its a few of them, actually, but
>> its at
>> least one. An understandable one, sure, but thats still what it is.
>> Scripts
>> (which are meant to be run more than once, generally) usually shouldn't
>> really be calling install.packages in the first place, but if they do,
>> they
>> should certainly not be installing umbrella packages and the packages
>> they
>> bring with them separately.
>>
>> Even having one vectorized call to install.packages where all the
>> packages
>> are installed would prevent this issue, including in the case where the
>> user doesn't understand the purpose of the tidyverse package. Though the
>> installation would still occur every time the script was run.
>>
>>
>> The last thing to note is that there are at least 2 packages which
>> provide
>> a function which does this already (install.load and remotes), so people
>> can get this functionality if they need it.
>>
>>
>> On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley
>> wrote:
>>
>>>
>>>
>>> I assumed this list is used to discuss proposals like this to the R
>>> codebase. If I'm on the wrong list, please let me know.
>>>
>>
>> This is the right place to discuss things like this. Thanks for starting
>> the conversation.
>>
>> Best,
>> ~G
>>
>>>
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XG4gVQKZam41YLfI3w8XRAu8s7f2I5jCppA45q6NBu0&s=cOXQGMA9Va3o9x1USGggzF82D1LtFQb2ALpLRLQs2k4&e=
>>
>>
>>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] improving the performance of install.packages
I believe introducing a backward compatible force=TRUE is a good
start, even if we're not ready for making force=FALSE the default at
this point. It would help simplify quite-common instructions like:
if (requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install(...)
to
install.packages("BiocManager", force=FALSE)
BiocManager::install(...)
and more so when installing lots of packages conditionally, e.g.
if (requireNamespace("foo")) install.packages("foo")
if (requireNamespace("bar")) install.packages("bar")
...
to
install.packages(c("foo", "bar", ...), force = FALSE)
Before deciding on making force=FALSE the new default, I think it
would be valuable to play the devil's advocate and explore and
identify all possible downsides of such a default, e.g. breaking
existing instructions, downstream package code that uses
install.packages() internally, and so on.
/Henrik
PS. Although the idea of having update.packages() install missing
packages is not bad, I don't think I'm a not a fan for the sole
purpose of risking installation instructions starting using
update.packages() instead, which will certainly confuse those who
don't know the history (think require() vs library()).
On Fri, Nov 8, 2019 at 3:11 PM Pages, Herve wrote:
>
> Hi Gabe,
>
> Keeping track of where a package was installed from would be a nice
> feature. However it wouldn't be as reliable as comparing hashes to
> decide whether a package needs re-installation or not.
>
> H.
>
> On 11/8/19 12:37, Gabriel Becker wrote:
> > Hi Josh,
> >
> > There are a few issues I can think of with this. The primary one is that
> > CRAN(/Bioconductor) is not the only place one can install packages from. I
> > might have version x.y.z of a package installed that was, at the time, a
> > development version I got from github, or installed locally, etc. Hell I
> > might have a later devel version but want the CRAN version. Not common,
> > sure, but wiill likely happen often enough that install.packages not doing
> > that for me when I tell it to is probably bad.
> >
> > Currently (though there has been some discussion of changing this) packages
> > do not remember where they were installed from, so R wouldn't know if the
> > version you have is actually fully the same one on the repository you
> > pointed install.packages to or not. If that were changed and we knew that
> > we were getting the byte identical package from the actual same source, I
> > think this would be a nice addition, though without it I think it would be
> > right a high but not high enough proportion of the time.
> >
> > R will build the package from source (depending on what OS you're using)
> >> twice by default. This becomes especially burdensome when people are using
> >> big packages (i.e. lots of depends) and someone has a script with:
> >>
> >
> >
> > install.packages("tidyverse")
> >> ...
> >> ... later on down the script
> >> ...
> >> install.packages("dplyr")
> >>
> >
> > I mean, IMHO and as I think Duncan was alluding to, that's straight up an
> > error by the script author. I think its a few of them, actually, but its at
> > least one. An understandable one, sure, but thats still what it is. Scripts
> > (which are meant to be run more than once, generally) usually shouldn't
> > really be calling install.packages in the first place, but if they do, they
> > should certainly not be installing umbrella packages and the packages they
> > bring with them separately.
> >
> > Even having one vectorized call to install.packages where all the packages
> > are installed would prevent this issue, including in the case where the
> > user doesn't understand the purpose of the tidyverse package. Though the
> > installation would still occur every time the script was run.
> >
> >
> > The last thing to note is that there are at least 2 packages which provide
> > a function which does this already (install.load and remotes), so people
> > can get this functionality if they need it.
> >
> >
> > On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
> >
> >>
> >>
> >> I assumed this list is used to discuss proposals like this to the R
> >> codebase. If I'm on the wrong list, please let me know.
> >>
> >
> > This is the right place to discuss things like this. Thanks for starting
> > the conversation.
> >
> > Best,
> > ~G
> >
> >>
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XG4gVQKZam41YLfI3w8XRAu8s7f2I5jCppA45q6NBu0&s=cOXQGMA9Va3o9x1USGggzF82D1LtFQb2ALpLRLQs2k4&e=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail
Re: [Rd] improving the performance of install.packages
On 08/11/2019 6:02 p.m., William Dunlap wrote:
Suppose update.packages("pkg") installed "pkg" if it were not already
installed, in addition to its current behavior of installing "pkg" if
"pkg" is installed but a newer version is available. The OP could then
use update.packages() all the time instead of install.packages() the
first time and update.packages() subsequent times.
That makes more sense to me than the "force = FALSE" proposal.
Duncan Murdoch
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Nov 8, 2019 at 2:51 PM Duncan Murdoch > wrote:
On 08/11/2019 2:55 p.m., Joshua Bradley wrote:
> I could do this...and I have before. This brings up a more
fundamental
> question though. You're asking me to write code that changes the
logic of
> the installation process (i.e. writing my own package installer).
Instead
> of doing that, I would rather integrate that logic into R itself
to improve
> the baseline installation process. This api proposal change would be
> additive and would not break legacy code.
That's not true. The current behaviour is equivalent to force=TRUE; I
believe the proposal was to change the default to force=FALSE.
If you didn't change the default, it wouldn't help your example: the
badly written script would run with force=TRUE, and wouldn't benefit
at all.
Duncan Murdoch
>
> Package managers like pip (python), conda (python), yum (CentOS), apt
> (Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
> defaults) when to not download a package again. By proposing this
change,
> I'm essentially asking that R follow some of the same conventions
and best
> practices that other package managers have adopted over the decades.
>
> I assumed this list is used to discuss proposals like this to the R
> codebase. If I'm on the wrong list, please let me know.
>
> P.S. if this change happened, it would be interesting to study
the effect
> it has on the bandwidth across all CRAN mirrors. A significant
drop would
> turn into actual $$ saved
>
> Josh Bradley
>
>
> On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
mailto:murdoch.dun...@gmail.com>>
> wrote:
>
>> On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
>>> Hello,
>>>
>>> Currently if you install a package twice:
>>>
>>> install.packages("testit")
>>> install.packages("testit")
>>>
>>> R will build the package from source (depending on what OS
you're using)
>>> twice by default. This becomes especially burdensome when
people are
>> using
>>> big packages (i.e. lots of depends) and someone has a script with:
>>>
>>> install.packages("tidyverse")
>>> ...
>>> ... later on down the script
>>> ...
>>> install.packages("dplyr")
>>>
>>> In this case, "dplyr" is part of the tidyverse and will install
twice. As
>>> the primary "package manager" for R, it should not install a
package
>> twice
>>> (by default) when it can be so easily checked. Indeed, many
people resort
>>> to writing a few lines of code to filter out already-installed
packages
>> An
>>> r-help post from 2010 proposed a solution to improving the default
>>> behavior, by adding "force=FALSE" as a api addition to
install.packages.(
>>> https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
>>>
>>> Would the R-core devs still consider this proposal?
>>
>> Whether or not they'd do it, it's easy for you to do it.
>>
>> install.packages <- function(pkgs, ..., force = FALSE) {
>> if (!force) {
>> pkgs <- Filter(Negate(requireNamespace), pkgs
>>
>> utils::install.packages(pkgs, ...)
>> }
>>
>> You might want to make this more elaborate, e.g. doing
update.packages()
>> on the ones that exist. But really, isn't the problem with the
script
>> you're using, which could have done a simple test before forcing
a slow
>> install?
>>
>> Duncan Murdoch
>>
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] improving the performance of install.packages
Hi Gabe,
Keeping track of where a package was installed from would be a nice
feature. However it wouldn't be as reliable as comparing hashes to
decide whether a package needs re-installation or not.
H.
On 11/8/19 12:37, Gabriel Becker wrote:
> Hi Josh,
>
> There are a few issues I can think of with this. The primary one is that
> CRAN(/Bioconductor) is not the only place one can install packages from. I
> might have version x.y.z of a package installed that was, at the time, a
> development version I got from github, or installed locally, etc. Hell I
> might have a later devel version but want the CRAN version. Not common,
> sure, but wiill likely happen often enough that install.packages not doing
> that for me when I tell it to is probably bad.
>
> Currently (though there has been some discussion of changing this) packages
> do not remember where they were installed from, so R wouldn't know if the
> version you have is actually fully the same one on the repository you
> pointed install.packages to or not. If that were changed and we knew that
> we were getting the byte identical package from the actual same source, I
> think this would be a nice addition, though without it I think it would be
> right a high but not high enough proportion of the time.
>
> R will build the package from source (depending on what OS you're using)
>> twice by default. This becomes especially burdensome when people are using
>> big packages (i.e. lots of depends) and someone has a script with:
>>
>
>
> install.packages("tidyverse")
>> ...
>> ... later on down the script
>> ...
>> install.packages("dplyr")
>>
>
> I mean, IMHO and as I think Duncan was alluding to, that's straight up an
> error by the script author. I think its a few of them, actually, but its at
> least one. An understandable one, sure, but thats still what it is. Scripts
> (which are meant to be run more than once, generally) usually shouldn't
> really be calling install.packages in the first place, but if they do, they
> should certainly not be installing umbrella packages and the packages they
> bring with them separately.
>
> Even having one vectorized call to install.packages where all the packages
> are installed would prevent this issue, including in the case where the
> user doesn't understand the purpose of the tidyverse package. Though the
> installation would still occur every time the script was run.
>
>
> The last thing to note is that there are at least 2 packages which provide
> a function which does this already (install.load and remotes), so people
> can get this functionality if they need it.
>
>
> On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
>
>>
>>
>> I assumed this list is used to discuss proposals like this to the R
>> codebase. If I'm on the wrong list, please let me know.
>>
>
> This is the right place to discuss things like this. Thanks for starting
> the conversation.
>
> Best,
> ~G
>
>>
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XG4gVQKZam41YLfI3w8XRAu8s7f2I5jCppA45q6NBu0&s=cOXQGMA9Va3o9x1USGggzF82D1LtFQb2ALpLRLQs2k4&e=
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Rd] improving the performance of install.packages
Suppose update.packages("pkg") installed "pkg" if it were not already
installed, in addition to its current behavior of installing "pkg" if "pkg"
is installed but a newer version is available. The OP could then use
update.packages() all the time instead of install.packages() the first time
and update.packages() subsequent times.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Nov 8, 2019 at 2:51 PM Duncan Murdoch
wrote:
> On 08/11/2019 2:55 p.m., Joshua Bradley wrote:
> > I could do this...and I have before. This brings up a more fundamental
> > question though. You're asking me to write code that changes the logic of
> > the installation process (i.e. writing my own package installer). Instead
> > of doing that, I would rather integrate that logic into R itself to
> improve
> > the baseline installation process. This api proposal change would be
> > additive and would not break legacy code.
>
> That's not true. The current behaviour is equivalent to force=TRUE; I
> believe the proposal was to change the default to force=FALSE.
>
> If you didn't change the default, it wouldn't help your example: the
> badly written script would run with force=TRUE, and wouldn't benefit at
> all.
>
> Duncan Murdoch
>
> >
> > Package managers like pip (python), conda (python), yum (CentOS), apt
> > (Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
> > defaults) when to not download a package again. By proposing this change,
> > I'm essentially asking that R follow some of the same conventions and
> best
> > practices that other package managers have adopted over the decades.
> >
> > I assumed this list is used to discuss proposals like this to the R
> > codebase. If I'm on the wrong list, please let me know.
> >
> > P.S. if this change happened, it would be interesting to study the effect
> > it has on the bandwidth across all CRAN mirrors. A significant drop would
> > turn into actual $$ saved
> >
> > Josh Bradley
> >
> >
> > On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
> > wrote:
> >
> >> On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
> >>> Hello,
> >>>
> >>> Currently if you install a package twice:
> >>>
> >>> install.packages("testit")
> >>> install.packages("testit")
> >>>
> >>> R will build the package from source (depending on what OS you're
> using)
> >>> twice by default. This becomes especially burdensome when people are
> >> using
> >>> big packages (i.e. lots of depends) and someone has a script with:
> >>>
> >>> install.packages("tidyverse")
> >>> ...
> >>> ... later on down the script
> >>> ...
> >>> install.packages("dplyr")
> >>>
> >>> In this case, "dplyr" is part of the tidyverse and will install twice.
> As
> >>> the primary "package manager" for R, it should not install a package
> >> twice
> >>> (by default) when it can be so easily checked. Indeed, many people
> resort
> >>> to writing a few lines of code to filter out already-installed packages
> >> An
> >>> r-help post from 2010 proposed a solution to improving the default
> >>> behavior, by adding "force=FALSE" as a api addition to
> install.packages.(
> >>> https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
> >>>
> >>> Would the R-core devs still consider this proposal?
> >>
> >> Whether or not they'd do it, it's easy for you to do it.
> >>
> >> install.packages <- function(pkgs, ..., force = FALSE) {
> >> if (!force) {
> >> pkgs <- Filter(Negate(requireNamespace), pkgs
> >>
> >> utils::install.packages(pkgs, ...)
> >> }
> >>
> >> You might want to make this more elaborate, e.g. doing update.packages()
> >> on the ones that exist. But really, isn't the problem with the script
> >> you're using, which could have done a simple test before forcing a slow
> >> install?
> >>
> >> Duncan Murdoch
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] improving the performance of install.packages
On 08/11/2019 2:55 p.m., Joshua Bradley wrote:
I could do this...and I have before. This brings up a more fundamental
question though. You're asking me to write code that changes the logic of
the installation process (i.e. writing my own package installer). Instead
of doing that, I would rather integrate that logic into R itself to improve
the baseline installation process. This api proposal change would be
additive and would not break legacy code.
That's not true. The current behaviour is equivalent to force=TRUE; I
believe the proposal was to change the default to force=FALSE.
If you didn't change the default, it wouldn't help your example: the
badly written script would run with force=TRUE, and wouldn't benefit at all.
Duncan Murdoch
Package managers like pip (python), conda (python), yum (CentOS), apt
(Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
defaults) when to not download a package again. By proposing this change,
I'm essentially asking that R follow some of the same conventions and best
practices that other package managers have adopted over the decades.
I assumed this list is used to discuss proposals like this to the R
codebase. If I'm on the wrong list, please let me know.
P.S. if this change happened, it would be interesting to study the effect
it has on the bandwidth across all CRAN mirrors. A significant drop would
turn into actual $$ saved
Josh Bradley
On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
wrote:
On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
Hello,
Currently if you install a package twice:
install.packages("testit")
install.packages("testit")
R will build the package from source (depending on what OS you're using)
twice by default. This becomes especially burdensome when people are
using
big packages (i.e. lots of depends) and someone has a script with:
install.packages("tidyverse")
...
... later on down the script
...
install.packages("dplyr")
In this case, "dplyr" is part of the tidyverse and will install twice. As
the primary "package manager" for R, it should not install a package
twice
(by default) when it can be so easily checked. Indeed, many people resort
to writing a few lines of code to filter out already-installed packages
An
r-help post from 2010 proposed a solution to improving the default
behavior, by adding "force=FALSE" as a api addition to install.packages.(
https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
Would the R-core devs still consider this proposal?
Whether or not they'd do it, it's easy for you to do it.
install.packages <- function(pkgs, ..., force = FALSE) {
if (!force) {
pkgs <- Filter(Negate(requireNamespace), pkgs
utils::install.packages(pkgs, ...)
}
You might want to make this more elaborate, e.g. doing update.packages()
on the ones that exist. But really, isn't the problem with the script
you're using, which could have done a simple test before forcing a slow
install?
Duncan Murdoch
[[alternative HTML version deleted]]
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Re: [Rd] improving the performance of install.packages
Hi Josh,
There are a few issues I can think of with this. The primary one is that
CRAN(/Bioconductor) is not the only place one can install packages from. I
might have version x.y.z of a package installed that was, at the time, a
development version I got from github, or installed locally, etc. Hell I
might have a later devel version but want the CRAN version. Not common,
sure, but wiill likely happen often enough that install.packages not doing
that for me when I tell it to is probably bad.
Currently (though there has been some discussion of changing this) packages
do not remember where they were installed from, so R wouldn't know if the
version you have is actually fully the same one on the repository you
pointed install.packages to or not. If that were changed and we knew that
we were getting the byte identical package from the actual same source, I
think this would be a nice addition, though without it I think it would be
right a high but not high enough proportion of the time.
R will build the package from source (depending on what OS you're using)
> twice by default. This becomes especially burdensome when people are using
> big packages (i.e. lots of depends) and someone has a script with:
>
install.packages("tidyverse")
> ...
> ... later on down the script
> ...
> install.packages("dplyr")
>
I mean, IMHO and as I think Duncan was alluding to, that's straight up an
error by the script author. I think its a few of them, actually, but its at
least one. An understandable one, sure, but thats still what it is. Scripts
(which are meant to be run more than once, generally) usually shouldn't
really be calling install.packages in the first place, but if they do, they
should certainly not be installing umbrella packages and the packages they
bring with them separately.
Even having one vectorized call to install.packages where all the packages
are installed would prevent this issue, including in the case where the
user doesn't understand the purpose of the tidyverse package. Though the
installation would still occur every time the script was run.
The last thing to note is that there are at least 2 packages which provide
a function which does this already (install.load and remotes), so people
can get this functionality if they need it.
On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
>
>
> I assumed this list is used to discuss proposals like this to the R
> codebase. If I'm on the wrong list, please let me know.
>
This is the right place to discuss things like this. Thanks for starting
the conversation.
Best,
~G
>
>
[[alternative HTML version deleted]]
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Re: [Rd] improving the performance of install.packages
Exactly. Every major commit isn’t want to check that the package works.
Also, besides package development, there are other reasons why one would
install packages over themselves. For example, rebuilding from source after
changing options in Makevars[.win]. The package hasn’t been updated but
recompilation is desired.
Avi
On Fri, Nov 8, 2019 at 3:07 PM William Dunlap via R-devel <
r-devel@r-project.org> wrote:
> While developing a package, I often run install.packages() on it many times
> in a session without updating its version number. How would your proposed
> change affect this workflow?
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley
> wrote:
>
> > I could do this...and I have before. This brings up a more fundamental
> > question though. You're asking me to write code that changes the logic of
> > the installation process (i.e. writing my own package installer). Instead
> > of doing that, I would rather integrate that logic into R itself to
> improve
> > the baseline installation process. This api proposal change would be
> > additive and would not break legacy code.
> >
> > Package managers like pip (python), conda (python), yum (CentOS), apt
> > (Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
> > defaults) when to not download a package again. By proposing this change,
> > I'm essentially asking that R follow some of the same conventions and
> best
> > practices that other package managers have adopted over the decades.
> >
> > I assumed this list is used to discuss proposals like this to the R
> > codebase. If I'm on the wrong list, please let me know.
> >
> > P.S. if this change happened, it would be interesting to study the effect
> > it has on the bandwidth across all CRAN mirrors. A significant drop would
> > turn into actual $$ saved
> >
> > Josh Bradley
> >
> >
> > On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
> > wrote:
> >
> > > On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
> > > > Hello,
> > > >
> > > > Currently if you install a package twice:
> > > >
> > > > install.packages("testit")
> > > > install.packages("testit")
> > > >
> > > > R will build the package from source (depending on what OS you're
> > using)
> > > > twice by default. This becomes especially burdensome when people are
> > > using
> > > > big packages (i.e. lots of depends) and someone has a script with:
> > > >
> > > > install.packages("tidyverse")
> > > > ...
> > > > ... later on down the script
> > > > ...
> > > > install.packages("dplyr")
> > > >
> > > > In this case, "dplyr" is part of the tidyverse and will install
> twice.
> > As
> > > > the primary "package manager" for R, it should not install a package
> > > twice
> > > > (by default) when it can be so easily checked. Indeed, many people
> > resort
> > > > to writing a few lines of code to filter out already-installed
> packages
> > > An
> > > > r-help post from 2010 proposed a solution to improving the default
> > > > behavior, by adding "force=FALSE" as a api addition to
> > install.packages.(
> > > > https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
> > > >
> > > > Would the R-core devs still consider this proposal?
> > >
> > > Whether or not they'd do it, it's easy for you to do it.
> > >
> > > install.packages <- function(pkgs, ..., force = FALSE) {
> > >if (!force) {
> > > pkgs <- Filter(Negate(requireNamespace), pkgs
> > >
> > >utils::install.packages(pkgs, ...)
> > > }
> > >
> > > You might want to make this more elaborate, e.g. doing
> update.packages()
> > > on the ones that exist. But really, isn't the problem with the script
> > > you're using, which could have done a simple test before forcing a slow
> > > install?
> > >
> > > Duncan Murdoch
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> [[alternative HTML version deleted]]
>
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>
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Re: [Rd] improving the performance of install.packages
Since we are on this topic, another area of improvement is when
install.packages() downloads hundreds of packages only to realize later
that many of them actually fail to install because one of the packages
they depend on (directly or indirectly) failed to install.
Cheers,
H.
On 11/8/19 11:55, Joshua Bradley wrote:
> I could do this...and I have before. This brings up a more fundamental
> question though. You're asking me to write code that changes the logic of
> the installation process (i.e. writing my own package installer). Instead
> of doing that, I would rather integrate that logic into R itself to improve
> the baseline installation process. This api proposal change would be
> additive and would not break legacy code.
>
> Package managers like pip (python), conda (python), yum (CentOS), apt
> (Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
> defaults) when to not download a package again. By proposing this change,
> I'm essentially asking that R follow some of the same conventions and best
> practices that other package managers have adopted over the decades.
>
> I assumed this list is used to discuss proposals like this to the R
> codebase. If I'm on the wrong list, please let me know.
>
> P.S. if this change happened, it would be interesting to study the effect
> it has on the bandwidth across all CRAN mirrors. A significant drop would
> turn into actual $$ saved
>
> Josh Bradley
>
>
> On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
> wrote:
>
>> On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
>>> Hello,
>>>
>>> Currently if you install a package twice:
>>>
>>> install.packages("testit")
>>> install.packages("testit")
>>>
>>> R will build the package from source (depending on what OS you're using)
>>> twice by default. This becomes especially burdensome when people are
>> using
>>> big packages (i.e. lots of depends) and someone has a script with:
>>>
>>> install.packages("tidyverse")
>>> ...
>>> ... later on down the script
>>> ...
>>> install.packages("dplyr")
>>>
>>> In this case, "dplyr" is part of the tidyverse and will install twice. As
>>> the primary "package manager" for R, it should not install a package
>> twice
>>> (by default) when it can be so easily checked. Indeed, many people resort
>>> to writing a few lines of code to filter out already-installed packages
>> An
>>> r-help post from 2010 proposed a solution to improving the default
>>> behavior, by adding "force=FALSE" as a api addition to install.packages.(
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_r-2Dhelp_2010-2DMay_239492.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UA8pThQCyQOMZf_tiAAnzSPckXg-h9-262Eu2WCyGHs&s=qtl85Oi2X2-U4rTQW-78pu9_Jb2vhBo1VZZN9pm6M8U&e=
>>> )
>>>
>>> Would the R-core devs still consider this proposal?
>>
>> Whether or not they'd do it, it's easy for you to do it.
>>
>> install.packages <- function(pkgs, ..., force = FALSE) {
>> if (!force) {
>> pkgs <- Filter(Negate(requireNamespace), pkgs
>>
>> utils::install.packages(pkgs, ...)
>> }
>>
>> You might want to make this more elaborate, e.g. doing update.packages()
>> on the ones that exist. But really, isn't the problem with the script
>> you're using, which could have done a simple test before forcing a slow
>> install?
>>
>> Duncan Murdoch
>>
>
> [[alternative HTML version deleted]]
>
> __
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>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Rd] improving the performance of install.packages
I guess you would just use force=TRUE
H.
On 11/8/19 12:06, William Dunlap via R-devel wrote:
> While developing a package, I often run install.packages() on it many times
> in a session without updating its version number. How would your proposed
> change affect this workflow?
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
>
>> I could do this...and I have before. This brings up a more fundamental
>> question though. You're asking me to write code that changes the logic of
>> the installation process (i.e. writing my own package installer). Instead
>> of doing that, I would rather integrate that logic into R itself to improve
>> the baseline installation process. This api proposal change would be
>> additive and would not break legacy code.
>>
>> Package managers like pip (python), conda (python), yum (CentOS), apt
>> (Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
>> defaults) when to not download a package again. By proposing this change,
>> I'm essentially asking that R follow some of the same conventions and best
>> practices that other package managers have adopted over the decades.
>>
>> I assumed this list is used to discuss proposals like this to the R
>> codebase. If I'm on the wrong list, please let me know.
>>
>> P.S. if this change happened, it would be interesting to study the effect
>> it has on the bandwidth across all CRAN mirrors. A significant drop would
>> turn into actual $$ saved
>>
>> Josh Bradley
>>
>>
>> On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
>> wrote:
>>
>>> On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
Hello,
Currently if you install a package twice:
install.packages("testit")
install.packages("testit")
R will build the package from source (depending on what OS you're
>> using)
twice by default. This becomes especially burdensome when people are
>>> using
big packages (i.e. lots of depends) and someone has a script with:
install.packages("tidyverse")
...
... later on down the script
...
install.packages("dplyr")
In this case, "dplyr" is part of the tidyverse and will install twice.
>> As
the primary "package manager" for R, it should not install a package
>>> twice
(by default) when it can be so easily checked. Indeed, many people
>> resort
to writing a few lines of code to filter out already-installed packages
>>> An
r-help post from 2010 proposed a solution to improving the default
behavior, by adding "force=FALSE" as a api addition to
>> install.packages.(
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_r-2Dhelp_2010-2DMay_239492.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iJofJNzrnbF8idVP_KjXyi-Pt9e0cAgor0UEiDJPPro&s=R1s-MHqzxEbvj-KerylYVqz-IkWatde6QREua4MPqmU&e=
)
Would the R-core devs still consider this proposal?
>>>
>>> Whether or not they'd do it, it's easy for you to do it.
>>>
>>> install.packages <- function(pkgs, ..., force = FALSE) {
>>> if (!force) {
>>> pkgs <- Filter(Negate(requireNamespace), pkgs
>>>
>>> utils::install.packages(pkgs, ...)
>>> }
>>>
>>> You might want to make this more elaborate, e.g. doing update.packages()
>>> on the ones that exist. But really, isn't the problem with the script
>>> you're using, which could have done a simple test before forcing a slow
>>> install?
>>>
>>> Duncan Murdoch
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iJofJNzrnbF8idVP_KjXyi-Pt9e0cAgor0UEiDJPPro&s=mIZ0fcjSg7KaJAY4wgLlKOaWwcD2uv9lI-GQNvcj4cg&e=
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iJofJNzrnbF8idVP_KjXyi-Pt9e0cAgor0UEiDJPPro&s=mIZ0fcjSg7KaJAY4wgLlKOaWwcD2uv9lI-GQNvcj4cg&e=
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
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Re: [Rd] improving the performance of install.packages
While developing a package, I often run install.packages() on it many times
in a session without updating its version number. How would your proposed
change affect this workflow?
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley wrote:
> I could do this...and I have before. This brings up a more fundamental
> question though. You're asking me to write code that changes the logic of
> the installation process (i.e. writing my own package installer). Instead
> of doing that, I would rather integrate that logic into R itself to improve
> the baseline installation process. This api proposal change would be
> additive and would not break legacy code.
>
> Package managers like pip (python), conda (python), yum (CentOS), apt
> (Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
> defaults) when to not download a package again. By proposing this change,
> I'm essentially asking that R follow some of the same conventions and best
> practices that other package managers have adopted over the decades.
>
> I assumed this list is used to discuss proposals like this to the R
> codebase. If I'm on the wrong list, please let me know.
>
> P.S. if this change happened, it would be interesting to study the effect
> it has on the bandwidth across all CRAN mirrors. A significant drop would
> turn into actual $$ saved
>
> Josh Bradley
>
>
> On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
> wrote:
>
> > On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
> > > Hello,
> > >
> > > Currently if you install a package twice:
> > >
> > > install.packages("testit")
> > > install.packages("testit")
> > >
> > > R will build the package from source (depending on what OS you're
> using)
> > > twice by default. This becomes especially burdensome when people are
> > using
> > > big packages (i.e. lots of depends) and someone has a script with:
> > >
> > > install.packages("tidyverse")
> > > ...
> > > ... later on down the script
> > > ...
> > > install.packages("dplyr")
> > >
> > > In this case, "dplyr" is part of the tidyverse and will install twice.
> As
> > > the primary "package manager" for R, it should not install a package
> > twice
> > > (by default) when it can be so easily checked. Indeed, many people
> resort
> > > to writing a few lines of code to filter out already-installed packages
> > An
> > > r-help post from 2010 proposed a solution to improving the default
> > > behavior, by adding "force=FALSE" as a api addition to
> install.packages.(
> > > https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
> > >
> > > Would the R-core devs still consider this proposal?
> >
> > Whether or not they'd do it, it's easy for you to do it.
> >
> > install.packages <- function(pkgs, ..., force = FALSE) {
> >if (!force) {
> > pkgs <- Filter(Negate(requireNamespace), pkgs
> >
> >utils::install.packages(pkgs, ...)
> > }
> >
> > You might want to make this more elaborate, e.g. doing update.packages()
> > on the ones that exist. But really, isn't the problem with the script
> > you're using, which could have done a simple test before forcing a slow
> > install?
> >
> > Duncan Murdoch
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
[[alternative HTML version deleted]]
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Re: [Rd] improving the performance of install.packages
I could do this...and I have before. This brings up a more fundamental
question though. You're asking me to write code that changes the logic of
the installation process (i.e. writing my own package installer). Instead
of doing that, I would rather integrate that logic into R itself to improve
the baseline installation process. This api proposal change would be
additive and would not break legacy code.
Package managers like pip (python), conda (python), yum (CentOS), apt
(Ubuntu), and apk (Alpine) are all "smart" enough to know (by their
defaults) when to not download a package again. By proposing this change,
I'm essentially asking that R follow some of the same conventions and best
practices that other package managers have adopted over the decades.
I assumed this list is used to discuss proposals like this to the R
codebase. If I'm on the wrong list, please let me know.
P.S. if this change happened, it would be interesting to study the effect
it has on the bandwidth across all CRAN mirrors. A significant drop would
turn into actual $$ saved
Josh Bradley
On Fri, Nov 8, 2019 at 5:00 AM Duncan Murdoch
wrote:
> On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
> > Hello,
> >
> > Currently if you install a package twice:
> >
> > install.packages("testit")
> > install.packages("testit")
> >
> > R will build the package from source (depending on what OS you're using)
> > twice by default. This becomes especially burdensome when people are
> using
> > big packages (i.e. lots of depends) and someone has a script with:
> >
> > install.packages("tidyverse")
> > ...
> > ... later on down the script
> > ...
> > install.packages("dplyr")
> >
> > In this case, "dplyr" is part of the tidyverse and will install twice. As
> > the primary "package manager" for R, it should not install a package
> twice
> > (by default) when it can be so easily checked. Indeed, many people resort
> > to writing a few lines of code to filter out already-installed packages
> An
> > r-help post from 2010 proposed a solution to improving the default
> > behavior, by adding "force=FALSE" as a api addition to install.packages.(
> > https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
> >
> > Would the R-core devs still consider this proposal?
>
> Whether or not they'd do it, it's easy for you to do it.
>
> install.packages <- function(pkgs, ..., force = FALSE) {
>if (!force) {
> pkgs <- Filter(Negate(requireNamespace), pkgs
>
>utils::install.packages(pkgs, ...)
> }
>
> You might want to make this more elaborate, e.g. doing update.packages()
> on the ones that exist. But really, isn't the problem with the script
> you're using, which could have done a simple test before forcing a slow
> install?
>
> Duncan Murdoch
>
[[alternative HTML version deleted]]
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Re: [Rd] improving the performance of install.packages
On 08/11/2019 2:06 a.m., Joshua Bradley wrote:
Hello,
Currently if you install a package twice:
install.packages("testit")
install.packages("testit")
R will build the package from source (depending on what OS you're using)
twice by default. This becomes especially burdensome when people are using
big packages (i.e. lots of depends) and someone has a script with:
install.packages("tidyverse")
...
... later on down the script
...
install.packages("dplyr")
In this case, "dplyr" is part of the tidyverse and will install twice. As
the primary "package manager" for R, it should not install a package twice
(by default) when it can be so easily checked. Indeed, many people resort
to writing a few lines of code to filter out already-installed packages An
r-help post from 2010 proposed a solution to improving the default
behavior, by adding "force=FALSE" as a api addition to install.packages.(
https://stat.ethz.ch/pipermail/r-help/2010-May/239492.html)
Would the R-core devs still consider this proposal?
Whether or not they'd do it, it's easy for you to do it.
install.packages <- function(pkgs, ..., force = FALSE) {
if (!force) {
pkgs <- Filter(Negate(requireNamespace), pkgs
utils::install.packages(pkgs, ...)
}
You might want to make this more elaborate, e.g. doing update.packages()
on the ones that exist. But really, isn't the problem with the script
you're using, which could have done a simple test before forcing a slow
install?
Duncan Murdoch
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