Re: [Bioc-devel] BiocManager::install() downgrade installed packages
If it were me I might update version
BiocManager::install(version="3.10")
...
Update xxx packages [y/n]: n
Confirm I've got the right version
BiocManager::version()
and then recover the URLs
BiocManager::repositories()
as arguments to install.packages(). It doesn't make sense to ask for
repositories(version="...") if that's not the version BiocManager knows about...
Martin
On 10/31/19, 3:54 PM, "Bioc-devel on behalf of Henrik Bengtsson"
wrote:
On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald wrote:
>
> The main goal for BiocManager is to help end users ensure that their
R/BioC installation is consistent for the version of R that they are using. So
by definition, any packages that are outside the versions for a given R/BioC
installation should be up or down-graded to make the installation valid. There
are those of us who are l33t enough to mix'n'match packages and debug errors
that may then occur. But it's probably not a good idea to make it easily hacked
by naive users, allowing them to do things that might cause problems.
>
> Anyway, I believe doing
>
> options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)
>
> will stop BiocManager::install from changing any installed CRAN packages.
And it's suitably obscure to limit that to the cool kids who can find it.
Unfortunately, this doesn't seem to make a difference. By searching
the GitHub code base it doesn't look like this option is used
anywhere:
https://github.com/search?q=org%3ABioconductor+BIOCMANAGER_CRANCHECK_BEHAVIOR=Code
My current workaround it to not use BiocManager and roll my own
'repos' settings;
> unname(getOption("repos"))
[1] "https://cloud.r-project.org;
[2] "https://bioconductor.org/packages/3.10/bioc;
[3] "https://bioconductor.org/packages/3.10/data/annotation;
[4] "https://bioconductor.org/packages/3.10/data/experiment;
[5] "https://bioconductor.org/packages/3.10/workflows;
and use good old update.packages().
Alternative wish: It would be handy if there was a
BiocManager::repositories(version = "3.10") for finding these,
especially since some of them come and go depending on Bioc version.
/Henrik
PS. I also tried setting ditto env var because it looked more like an
env var than R option name to me.
>
> On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
wrote:
>>
>> (posting this here since I think it's not a support question per se)
>>
>> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
setup:
>>
>> > BiocManager::install(version = "3.10")
>> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
>> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched
(2019-09-12
>> r77183)
>> Installing package(s) 'BiocVersion'
>> ...
>> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
>> 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck',
'scales',
>> 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
>> 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase',
'BiocCheck',
>> 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion',
'biocViews',
>> 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib',
'DelayedArray',
>> 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter',
'GenomeInfoDb',
>> 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db',
'graph',
>> 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
>> 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
>> 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
'QDNAseq.mm10',
>> 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib',
'Rsamtools',
>> 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4',
'SummarizedExperiment',
>> 'XVector', 'zlibbioc'
>> trying URL
'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz'
>> Content type 'application/x-gzip' length 7833 bytes
>> ==
>> downloaded 7833 bytes
>>
>> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
>> Content type 'application/x-gzip' length 294967 bytes (288 KB)
>> ==
>> downloaded 288 KB
>> ...
>>
>> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
>> package versions, even if you have newer versions installed. For
>> instance, I've got base64enc 0.1.4 from
>> http://www.rforge.net/base64enc/, my own development version of future
>> 1.14.0-9000, and so on. Note that the prompt says nothing about
>> downgrading. Is this really wanted and is there a way to avoid this?
>>
>> (*) Will this also downgrade Bioc developers' Bioc
Re: [Bioc-devel] BiocManager::install() downgrade installed packages
On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald wrote:
>
> The main goal for BiocManager is to help end users ensure that their R/BioC
> installation is consistent for the version of R that they are using. So by
> definition, any packages that are outside the versions for a given R/BioC
> installation should be up or down-graded to make the installation valid.
> There are those of us who are l33t enough to mix'n'match packages and debug
> errors that may then occur. But it's probably not a good idea to make it
> easily hacked by naive users, allowing them to do things that might cause
> problems.
>
> Anyway, I believe doing
>
> options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)
>
> will stop BiocManager::install from changing any installed CRAN packages. And
> it's suitably obscure to limit that to the cool kids who can find it.
Unfortunately, this doesn't seem to make a difference. By searching
the GitHub code base it doesn't look like this option is used
anywhere:
https://github.com/search?q=org%3ABioconductor+BIOCMANAGER_CRANCHECK_BEHAVIOR=Code
My current workaround it to not use BiocManager and roll my own
'repos' settings;
> unname(getOption("repos"))
[1] "https://cloud.r-project.org;
[2] "https://bioconductor.org/packages/3.10/bioc;
[3] "https://bioconductor.org/packages/3.10/data/annotation;
[4] "https://bioconductor.org/packages/3.10/data/experiment;
[5] "https://bioconductor.org/packages/3.10/workflows;
and use good old update.packages().
Alternative wish: It would be handy if there was a
BiocManager::repositories(version = "3.10") for finding these,
especially since some of them come and go depending on Bioc version.
/Henrik
PS. I also tried setting ditto env var because it looked more like an
env var than R option name to me.
>
> On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
> wrote:
>>
>> (posting this here since I think it's not a support question per se)
>>
>> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
>> setup:
>>
>> > BiocManager::install(version = "3.10")
>> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
>> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12
>> r77183)
>> Installing package(s) 'BiocVersion'
>> ...
>> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
>> 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck', 'scales',
>> 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
>> 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase', 'BiocCheck',
>> 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews',
>> 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib', 'DelayedArray',
>> 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb',
>> 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db', 'graph',
>> 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
>> 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
>> 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
>> 'QDNAseq.mm10',
>> 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools',
>> 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4', 'SummarizedExperiment',
>> 'XVector', 'zlibbioc'
>> trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz'
>> Content type 'application/x-gzip' length 7833 bytes
>> ==
>> downloaded 7833 bytes
>>
>> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
>> Content type 'application/x-gzip' length 294967 bytes (288 KB)
>> ==
>> downloaded 288 KB
>> ...
>>
>> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
>> package versions, even if you have newer versions installed. For
>> instance, I've got base64enc 0.1.4 from
>> http://www.rforge.net/base64enc/, my own development version of future
>> 1.14.0-9000, and so on. Note that the prompt says nothing about
>> downgrading. Is this really wanted and is there a way to avoid this?
>>
>> (*) Will this also downgrade Bioc developers' Bioc packages?
>>
>> Thanks,
>>
>> Henrik
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager::install() downgrade installed packages
The main goal for BiocManager is to help end users ensure that their R/BioC
installation is consistent for the version of R that they are using. So by
definition, any packages that are outside the versions for a given R/BioC
installation should be up or down-graded to make the installation valid.
There are those of us who are l33t enough to mix'n'match packages and debug
errors that may then occur. But it's probably not a good idea to make it
easily hacked by naive users, allowing them to do things that might cause
problems.
Anyway, I believe doing
options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)
will stop BiocManager::install from changing any installed CRAN packages.
And it's suitably obscure to limit that to the cool kids who can find it.
On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
wrote:
> (posting this here since I think it's not a support question per se)
>
> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
> setup:
>
> > BiocManager::install(version = "3.10")
> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12
> r77183)
> Installing package(s) 'BiocVersion'
> ...
> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
> 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck',
> 'scales',
> 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
> 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase',
> 'BiocCheck',
> 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews',
> 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib',
> 'DelayedArray',
> 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb',
> 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db',
> 'graph',
> 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
> 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
> 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
> 'QDNAseq.mm10',
> 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools',
> 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4',
> 'SummarizedExperiment',
> 'XVector', 'zlibbioc'
> trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz
> '
> Content type 'application/x-gzip' length 7833 bytes
> ==
> downloaded 7833 bytes
>
> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
> Content type 'application/x-gzip' length 294967 bytes (288 KB)
> ==
> downloaded 288 KB
> ...
>
> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
> package versions, even if you have newer versions installed. For
> instance, I've got base64enc 0.1.4 from
> http://www.rforge.net/base64enc/, my own development version of future
> 1.14.0-9000, and so on. Note that the prompt says nothing about
> downgrading. Is this really wanted and is there a way to avoid this?
>
> (*) Will this also downgrade Bioc developers' Bioc packages?
>
> Thanks,
>
> Henrik
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocManager::install() downgrade installed packages
(posting this here since I think it's not a support question per se) Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1 setup: > BiocManager::install(version = "3.10") Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12 r77183) Installing package(s) 'BiocVersion' ... Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv', 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck', 'scales', 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate', 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase', 'BiocCheck', 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews', 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib', 'DelayedArray', 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb', 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db', 'graph', 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges', 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db', 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19', 'QDNAseq.mm10', 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools', 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4', 'SummarizedExperiment', 'XVector', 'zlibbioc' trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz' Content type 'application/x-gzip' length 7833 bytes == downloaded 7833 bytes trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz' Content type 'application/x-gzip' length 294967 bytes (288 KB) == downloaded 288 KB ... It surprised me that BiocManager::install() will _downgrade_ to CRAN(*) package versions, even if you have newer versions installed. For instance, I've got base64enc 0.1.4 from http://www.rforge.net/base64enc/, my own development version of future 1.14.0-9000, and so on. Note that the prompt says nothing about downgrading. Is this really wanted and is there a way to avoid this? (*) Will this also downgrade Bioc developers' Bioc packages? Thanks, Henrik ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
