[Bioc-devel] Windows binaries for the new release?
James W. MacDonald
jmacdon at uw.edu
Wed Apr 26 17:40:29 CEST 2017
On Wed, Apr 26, 2017 at 11:26 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
> 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/cont
>> rib/3.4/PACKAGES.rds
>> <https://bioconductor.org/packages/3.5/bioc/bin/windows/cont
>> rib/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...
Well, getOption("pkgType") on my Windows box returns 'both' rather than
'win.binary', so this is what I get:
> contrib.url(biocinstallRepos())
[1] "https://bioconductor.org/packages/3.5/bioc/src/contrib"
[2] "https://bioconductor.org/packages/3.5/data/annotation/src/contrib"
[3] "https://bioconductor.org/packages/3.5/data/experiment/src/contrib"
[4] "https://bioconductor.org/packages/3.5/extra/src/contrib"
[5] "https://cran.rstudio.com/src/contrib"
[6] "https://www.stats.ox.ac.uk/pub/RWin/src/contrib"
and if I set that to win.binary, I get what you get. I don't remember ever
changing that option, but maybe it gets changed when you install the Rtools
toolset? I don't see any documentation to that effect, and I just
re-installed Rtools just to check. Regardless, that's what the deal was.
Jim
>
> 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
>> message from your computer. Thank you.
>>
>>
>>
>>
>> --
>> 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 message from your computer. Thank you.
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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