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.
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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] Build error in tokay2: cannot reserve space for vector
On 07/09/2018 11:00 AM, Sergio Picart Armada wrote:
Thank you Morgan,
I already fixed this by skipping the offending test on win32.
I fixed the devel version, but the release version has not noticed the
version bump (from 1.0.0 to 1.0.1).
Did I forget anything?
builds are nightly, not on commit. You made your change on
commit 71e725742eafa45a71e49d76441383dda26621c3
Author: Sergi Picart
Date: Mon Jul 9 12:53:04 2018 +0200
Version number bump
so the build system has not had a chance to build. Look at the
'snapshot' date on the build report page for the date that the most
recent build started.
Martin
Thank you again,
On Monday, May 21, 2018 18:58 CEST, Hervé Pagès
wrote:
On 05/21/2018 05:50 AM, Martin Morgan wrote:
> Remember that 32-bit Windows can only address vectors that are less than
> 2^32 - 1 elements long -- it looks like your example is trying to do
> more than this, and the solution is to implement a more modest example.
32-bit Windows limits the amount of memory used by a single process to
a little bit less than 3GB. So I think you can actually create vectors
that have more than 2^32 elements as long as the total memory used by
R doesn't exceeds 3GB.
One more thing: since this is a 32-bit Windows issue, you should be able
to reproduce this locally by starting R in 32-bit mode:
R --arch i386
Hope this helps,
H.
>
> Martin
>
> On 05/18/2018 04:05 AM, Sergio Picart Armada wrote:
>>
>> Dear Bioconductor team,
>>
>> I'm the maintainer of the FELLA package.
>> Lately the check in tokay2 has failed, see
>>
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_FELLA_tokay2-2Dchecksrc.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk=e4cRnI7RwkBDHiDNJodfgLbk-BNKmO6OZsD1MoUHxLc=
>>
>> Specifically: Message: At vector.pmt:442 : cannot reserve space for
>> vector, Out of memory
>> Class: simpleError/error/conditionIt only happens in tokay2 and I
>> cannot reproduce this locally.
>> Is this something on the server side or should I take action?
>>
>> Thank you,
>> Sergi
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>>
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
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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: [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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Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector
Thank you Morgan,
I already fixed this by skipping the offending test on win32.
I fixed the devel version, but the release version has not noticed the version
bump (from 1.0.0 to 1.0.1).
Did I forget anything?
Thank you again,
On Monday, May 21, 2018 18:58 CEST, Hervé Pagès wrote:
On 05/21/2018 05:50 AM, Martin Morgan wrote:
> Remember that 32-bit Windows can only address vectors that are less than
> 2^32 - 1 elements long -- it looks like your example is trying to do
> more than this, and the solution is to implement a more modest example.
32-bit Windows limits the amount of memory used by a single process to
a little bit less than 3GB. So I think you can actually create vectors
that have more than 2^32 elements as long as the total memory used by
R doesn't exceeds 3GB.
One more thing: since this is a 32-bit Windows issue, you should be able
to reproduce this locally by starting R in 32-bit mode:
R --arch i386
Hope this helps,
H.
>
> Martin
>
> On 05/18/2018 04:05 AM, Sergio Picart Armada wrote:
>>
>> Dear Bioconductor team,
>>
>> I'm the maintainer of the FELLA package.
>> Lately the check in tokay2 has failed, see
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_FELLA_tokay2-2Dchecksrc.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk=e4cRnI7RwkBDHiDNJodfgLbk-BNKmO6OZsD1MoUHxLc=
>>
>> Specifically: Message: At vector.pmt:442 : cannot reserve space for
>> vector, Out of memory
>> Class: simpleError/error/conditionIt only happens in tokay2 and I
>> cannot reproduce this locally.
>> Is this something on the server side or should I take action?
>>
>> Thank you,
>> Sergi
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc=
>>
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
> ___
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> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc=
>
--
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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[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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