[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") [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=e4cRnI7RwkBDHiDNJodfgLbk-BNKmO6OZsD1MoUHxLc&e= >> >> 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&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc&e= >> >> > > > This email message may contain legally privileged and/or...{{dropped:2}} > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc&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 [[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
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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=e4cRnI7RwkBDHiDNJodfgLbk-BNKmO6OZsD1MoUHxLc&e= >> >> 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&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc&e= >> >> > > > This email message may contain legally privileged and/or...{{dropped:2}} > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc&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 This email message may contain legally privileged and/or...{{dropped:2}} ___ 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'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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Date for the next release
Hi I am the developer of the packages DAPAR and Prostar. I have to plan in advance some work and I would like to synchronise this with the next release of Bioconductor. I know it is a bit early but do you know the date of the next release ? Will it be the 31th of Octobre as last year ? Thanks in advance Sam [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel