[Bioc-devel] Windows binaries for the new release?
Martin Morgan
martin.morgan at roswellpark.org
Wed Apr 26 17:26:29 CEST 2017
On 04/26/2017 11:23 AM, James W. MacDonald wrote:
>
>
> On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan
> <martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>
> wrote:
>
> On 04/26/2017 10:34 AM, James W. MacDonald wrote:
>
>
>
> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan
> <martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>
> <mailto:martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>>>
>
> wrote:
>
> On 04/26/2017 10:00 AM, James W. MacDonald wrote:
>
> I see the binaries on the respective web pages, but biocLite
> seems not to:
>
>
> I'm not 100% sure but can you try again in a new R session?
> I think
> you have a cached version of the repository index.
>
>
> At a command prompt, using --vanilla:
>
> C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla
>
> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> library(BiocInstaller)
>
> Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
>
> biocLite()
>
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
> installation path not writeable, unable to update packages: foreign
> Old packages: 'Biobase', 'IRanges', 'S4Vectors'
> Update all/some/none? [a/s/n]: a
>
> There are binary versions available but the source versions
> are later:
> binary source needs_compilation
> Biobase 2.35.1 2.36.0 TRUE
> IRanges 2.9.19 2.10.0 TRUE
> S4Vectors 0.13.17 0.14.0 TRUE
>
> Do you want to install from sources the packages which need
> compilation?
> y/n:
>
> Is there a way to remove the cache manually? I have already
> uninstalled
> and re-installed BiocInstaller.
>
>
> contrib.url(BiocInstaller::biocinstallRepos())
>
> should be pointing to
>
> https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
> <https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib>
>
> and
>
> https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
> <https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib>
> /3.4/PACKAGES
>
> has the current information
>
> Package: Biobase
> Version: 2.36.0
> Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
> Imports: methods
> Suggests: tools, tkWidgets, ALL, RUnit, golubEsets
> License: Artistic-2.0
> Archs: i386, x64
>
> as well as in R
>
> > fl =
> "https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/PACKAGES.rds
> <https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/PACKAGES.rds>"
> > xx = readRDS(url(fl))
> > xx['Biobase', , drop=FALSE] Package Version Priority
> Biobase "Biobase" "2.36.0" NA
> Depends Imports
> LinkingTo
> Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" "methods" NA
> Suggests Enhances License
> Biobase "tools, tkWidgets, ALL, RUnit, golubEsets" NA
> "Artistic-2.0"
> License_is_FOSS License_restricts_use OS_type Archs MD5sum
> Biobase NA NA NA "i386, x64" NA
>
> should be pointing to the current .zip files.
>
> biocLite() delegates to available.packages(), which should be
> checking the session temporary directory and, since you're in a new
> session, retrieving the rds file above. You could
>
> debug(available.packages)
>
> and try and figure out where the issue is?
>
> FWIW with a new R installation I could not reproduce your problem.
>
>
> OK. If it's just weirdness on my end I don't really care. I was just
> concerned that this would be a problem for regular end users.
If you're having a problem then it would be great to have your expert
insight into what is going wrong...
Martin
>
> Thanks,
>
> Jim
>
>
>
>
>
> > sessionInfo()
> R version 3.4.0 (2017-04-21)
> Platform: i386-w64-mingw32/i386 (32-bit)
> Running under: Windows Server 2012 R2 x64 (build 9600)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.26.0
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0 tools_3.4.0
>
> Martin
>
>
>
> Jim
>
>
>
>
> Martin
>
>
> biocLite()
>
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0
> (2017-04-21).
> installation path not writeable, unable to update
> packages: foreign
> Old packages: 'AnnotationDbi', 'Biobase',
> 'BiocGenerics', 'biomaRt',
> 'IRanges',
> 'S4Vectors'
> Update all/some/none? [a/s/n]: a
>
> There are binary versions available but the source
> versions
> are later:
> binary source needs_compilation
> AnnotationDbi 1.37.4 1.38.0 FALSE
> Biobase 2.35.1 2.36.0 TRUE
> BiocGenerics 0.21.3 0.22.0 FALSE
> biomaRt 2.31.10 2.32.0 FALSE
> IRanges 2.9.19 2.10.0 TRUE
> S4Vectors 0.13.17 0.14.0 TRUE
>
> Do you want to install from sources the packages which need
> compilation?
> y/n:
>
> sessionInfo()
>
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 14393)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] BiocInstaller_1.26.0
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0 tools_3.4.0
>
>
>
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>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
> This email message may contain legally privileged and/or
> confidential information. If you are not the intended recipient(s),
> or the employee or agent responsible for the delivery of this
> message to the intended recipient(s), you are hereby notified that
> any disclosure, copying, distribution, or use of this email message
> is prohibited. If you have received this message in error, please
> notify the sender immediately by e-mail and delete this email
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>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
This email message may contain legally privileged and/or...{{dropped:2}}
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