Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
Dear all,
we recently observed a similar behavior due to a bug
in the remotes package which has been fixed in the github
version of the package:
https://github.com/r-lib/remotes/commit/d3a6766c0bcb456b82a0b06608f6149
fe4f5d83e
essentially, internally, somewhere, it would do something like:
if (identical(type, "both")) {
type <- "binary"
}
which makes annotation packages install fail on Mac
(Windows as well I think). The fix for this is in the github
version of remotes but not on CRAN.
Best wishes,
Bernd
On Di, 2018-07-24 at 09:36 -0400, Levi Waldron wrote:
> On Fri, Jul 20, 2018 at 10:26 AM Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
> >
> > I think it's a Mac thing, and it's decided to install binary (tgz),
> > and
> > the annotation packages are source (tar.gz).
> >
> > Have you set options(pkgType = "both") ?
> >
> Thanks Martin, and sorry for the slow reply. You're right, I don't
> see the
> same behavior on GNU/Linux (not sure about Windows). But
> options(pkgType =
> "both") does not alter this behavior.
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
On Fri, Jul 20, 2018 at 10:26 AM Martin Morgan < martin.mor...@roswellpark.org> wrote: > I think it's a Mac thing, and it's decided to install binary (tgz), and > the annotation packages are source (tar.gz). > > Have you set options(pkgType = "both") ? > Thanks Martin, and sorry for the slow reply. You're right, I don't see the same behavior on GNU/Linux (not sure about Windows). But options(pkgType = "both") does not alter this behavior. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
I think it's a Mac thing, and it's decided to install binary (tgz), and
the annotation packages are source (tar.gz).
Have you set options(pkgType = "both") ?
On 07/20/2018 08:40 AM, Levi Waldron wrote:
I think the problem I was actually having was that
BiocManager::install("githubuser/repo") will not install annotation or
experimental data packages that are among the repo's dependencies. It is
the same for devtools::install_github("githubuser/repo", repos =
BiocManager::repositories(), dependencies = TRUE). Here is a minimal
example from github.com/lwaldron/nothing
, which depends on one software, one
annotation, and one experimental data package - the software package
will be installed, but the annotation and data packages are not available:
> remove.packages(c("TCGAutils", "mirbase.db", "curatedTCGAData"))
Removing packages from
‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
(as ‘lib’ is unspecified)
> BiocManager::install("lwaldron/nothing")
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing github package(s) 'lwaldron/nothing'
Downloading GitHub repo lwaldron/nothing@master
Skipping 3 packages not available: curatedTCGAData, GenomeInfoDbData,
mirbase.db
Installing 1 packages: TCGAutils
ERROR: dependencies *_‘mirbase.db’, ‘curatedTCGAData’_* are not
available for package ‘nothing’
On Mon, Jul 9, 2018 at 12:48 PM Levi Waldron
mailto:lwaldron.resea...@gmail.com>> wrote:
Thanks Pariksheet and Martin! It seems that in fact both of these
approaches work, e.g. (I made a simpler test case to figure this out):
devtools::install_github("lwaldron/nothing", repos =
BiocManager::repositories(), dependencies = TRUE)
remove.packages(c("nothing", "ABCp2"))
BiocManager::install("lwaldron/nothing", dependencies = TRUE)
It's the dependencies of the Remotes: in Bioconductor/BiocWorkshops
that get skipped, but at this point it seems like trying to do
dependency management through GitHub and asking for trouble. I think
the thing to do is to copy all the dependencies of the Remotes:
directly into the DESCRIPTION file to streamline installation.
--
Levi Waldron http://www.waldronlab.io
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616Skype: levi.waldron
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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
I think the problem I was actually having was that
BiocManager::install("githubuser/repo")
will not install annotation or experimental data packages that are among
the repo's dependencies. It is the same
for devtools::install_github("githubuser/repo", repos =
BiocManager::repositories(), dependencies = TRUE). Here is a minimal
example from github.com/lwaldron/nothing, which depends on one software,
one annotation, and one experimental data package - the software package
will be installed, but the annotation and data packages are not available:
> remove.packages(c("TCGAutils", "mirbase.db", "curatedTCGAData"))
Removing packages from
‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
(as ‘lib’ is unspecified)
> BiocManager::install("lwaldron/nothing")
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing github package(s) 'lwaldron/nothing'
Downloading GitHub repo lwaldron/nothing@master
Skipping 3 packages not available: curatedTCGAData, GenomeInfoDbData,
mirbase.db
Installing 1 packages: TCGAutils
ERROR: dependencies *‘mirbase.db’, ‘curatedTCGAData’* are not available for
package ‘nothing’
On Mon, Jul 9, 2018 at 12:48 PM Levi Waldron
wrote:
> Thanks Pariksheet and Martin! It seems that in fact both of these
> approaches work, e.g. (I made a simpler test case to figure this out):
>
> devtools::install_github("lwaldron/nothing", repos =
> BiocManager::repositories(), dependencies = TRUE)
> remove.packages(c("nothing", "ABCp2"))
> BiocManager::install("lwaldron/nothing", dependencies = TRUE)
>
> It's the dependencies of the Remotes: in Bioconductor/BiocWorkshops that
> get skipped, but at this point it seems like trying to do dependency
> management through GitHub and asking for trouble. I think the thing to do
> is to copy all the dependencies of the Remotes: directly into the
> DESCRIPTION file to streamline installation.
>
--
Levi Waldron
http://www.waldronlab.io
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
Thanks Pariksheet and Martin! It seems that in fact both of these
approaches work, e.g. (I made a simpler test case to figure this out):
devtools::install_github("lwaldron/nothing", repos =
BiocManager::repositories(), dependencies = TRUE)
remove.packages(c("nothing", "ABCp2"))
BiocManager::install("lwaldron/nothing", dependencies = TRUE)
It's the dependencies of the Remotes: in Bioconductor/BiocWorkshops that
get skipped, but at this point it seems like trying to do dependency
management through GitHub and asking for trouble. I think the thing to do
is to copy all the dependencies of the Remotes: directly into the
DESCRIPTION file to streamline installation.
[[alternative HTML version deleted]]
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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
I'm not able to confirm this, but since BiocManager::install() uses
remotes::install_github() when it sees a pattern "foo/bar", I think
BiocManager::install("foo/bar", dependencies = TRUE) will behave as
desired.
For local installs, I think we end up at utils::install.packages(),
where the docs say
dependencies: logical indicating whether to also install uninstalled
packages which these packages depend on/link
to/import/suggest (and so on recursively). Not used if
'repos = NULL'.
where I think the repos has to be NULL for the local installation... I
don't want BiocManager::install() to deviate from base R behavior in
this case.
Martin
On 07/09/2018 11:39 AM, Pariksheet Nanda wrote:
Hi Levi,
Why not use devtools which already does this? Setting `dependencies =
TRUE` installs the packages listed in Imports and Suggests, and
BiocManager::repositories() like BiocInstaller::biocinstallRepos() returns
a list of repositories. See inline below:
On Mon, Jul 9, 2018 at 4:51 AM, Levi Waldron
wrote:
It would be useful to be able to use BiocManager to install
the Depends/Imports/Suggests of a source package not on Bioconductor, e.g.:
BiocManager::install("Bioconductor/BiocWorkshops") #works but only if all
Depends/Imports are already installed
devtools::install("Bioconductor/BiocWorkshops", repos =
BiocManager::repositories(), dependencies = TRUE)
Also from a local package, e.g.:
BiocManager::install("mypackage_0.1.tar.gz") # or,
BiocManager::install("mypackage")
devtools::install("mypackage_0.1.tar.gz", repos =
BiocManager::repositories(), dependencies = TRUE)
devtools::install("mypackage", repos = BiocManager::repositories(),
dependencies = TRUE)
devtools::install(".", repos = BiocManager::repositories(), dependencies =
TRUE)
Pariksheet
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Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests
Hi Levi,
Why not use devtools which already does this? Setting `dependencies =
TRUE` installs the packages listed in Imports and Suggests, and
BiocManager::repositories() like BiocInstaller::biocinstallRepos() returns
a list of repositories. See inline below:
On Mon, Jul 9, 2018 at 4:51 AM, Levi Waldron
wrote:
> It would be useful to be able to use BiocManager to install
> the Depends/Imports/Suggests of a source package not on Bioconductor, e.g.:
>
> BiocManager::install("Bioconductor/BiocWorkshops") #works but only if all
> Depends/Imports are already installed
>
devtools::install("Bioconductor/BiocWorkshops", repos =
BiocManager::repositories(), dependencies = TRUE)
> Also from a local package, e.g.:
>
> BiocManager::install("mypackage_0.1.tar.gz") # or,
> BiocManager::install("mypackage")
>
devtools::install("mypackage_0.1.tar.gz", repos =
BiocManager::repositories(), dependencies = TRUE)
devtools::install("mypackage", repos = BiocManager::repositories(),
dependencies = TRUE)
devtools::install(".", repos = BiocManager::repositories(), dependencies =
TRUE)
Pariksheet
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[Bioc-devel] BiocManager to install Depends/Imports/Suggests
It would be useful to be able to use BiocManager to install
the Depends/Imports/Suggests of a source package not on Bioconductor, e.g.:
BiocManager::install("Bioconductor/BiocWorkshops") #works but only if all
Depends/Imports are already installed
or:
BiocManager::install_deps("Bioconductor/BiocWorkshops") #to avoid any
change to BiocManager::install()
BiocManager::install("Bioconductor/BiocWorkshops") #recommends the above
if not all deps are available
Also from a local package, e.g.:
BiocManager::install("mypackage_0.1.tar.gz") # or,
BiocManager::install("mypackage")
BiocManager::install_deps("mypackage_0.1.tar.gz") # or,
BiocManager::install_deps("mypackage")
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