On 04/26/2017 10:34 AM, James W. MacDonald wrote:
On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@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
and
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";
> 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.
> 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
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