Re: [Bioc-devel] using BiocLite() on Ubuntu Xenial with its default R 3.2.3 release
On 07/20/2017 08:36 AM, Jack Howarth wrote:
I am trying to use the BiocLite() feature of Bioconductor to install
the R modules required by MetaboAnalyst 3.0 under Ubuntu Xenial
16.04LTS with its system R 3.2.3 release. I have added the repo for
Micheal Rutter's cran2deb4ubuntu to provide the missing cran R modules
but have avoided installing any of the r-bioc ones to keep the
installation purely using those installed in /usr/local/lib/R by
BiocLite(). Unfortunately, this is failing on
$ sudo R
source("https://bioconductor.org/biocLite.R;)
biocLite("‘AnnotationDbi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) ‘‘AnnotationDbi’
Warning message:
package ‘‘AnnotationDbi’ is not available (for R version 3.2.3)
Certainly there must be a way to redirect BiocLite to a legacy release
which fully supports the older R 3.2.3 in the current Ubuntu LTS
release?
Unfortunately (?) this 'works for me' (the .5 Patched moniker should
really be of no consequence)
> biocLite("AnnotationDbi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.5 Patched (2016-05-05
r72327).
Installing package(s) ‘AnnotationDbi’
trying URL
'https://bioconductor.org/packages/3.2/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz'
Content type 'application/x-gzip' length 4268480 bytes (4.1 MB)
==
downloaded 4.1 MB
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in
package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package
‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package
‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package
‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package
‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationDbi)
The downloaded source packages are in
‘/tmp/Rtmpbyzs5c/downloaded_packages’
The message about 'package not available' could have a number of
interpretations; it's R's way of saying that it doesn't know where to
find the package, but that could be, e.g., because R can't access the
web site where the package is. To trouble shoot, you could try
> BiocInstaller::biocinstallRepos()
BioCsoft
"https://bioconductor.org/packages/3.2/bioc;
BioCann
"https://bioconductor.org/packages/3.2/data/annotation;
BioCexp
"https://bioconductor.org/packages/3.2/data/experiment;
BioCextra
"https://bioconductor.org/packages/3.2/extra;
CRAN
"https://cran.rstudio.com;
AnnotationDbi should be listed in
> url = paste0(contrib.url(BiocInstaller::biocinstallRepos())[1],
"/PACKAGES")
> url
[1] "https://bioconductor.org/packages/3.2/bioc/src/contrib/PACKAGES;
and you should be able read that file, e.g.,
> txt = readLines(url)
> length(txt)
[1] 10581
> grep("Package: AnnotationDbi", txt)
[1] 390
You should also be able to download the package
> download.packages("AnnotationDbi", tempdir(), repos=biocinstallRepos())
trying URL
'https://bioconductor.org/packages/3.2/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz'
Content type 'application/x-gzip' length 4268480 bytes (4.1 MB)
==
downloaded 4.1 MB
[,1][,2]
[1,] "AnnotationDbi" "/tmp/Rtmpbyzs5c/AnnotationDbi_1.32.3.tar.gz"
I'm not sure if that helps...
Martin
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Re: [Bioc-devel] strand<- method for 'GPos' doesn't work
hi Hervé, i had not imagine this could require so much code refactoring, so thanks a lot for the quick and extensive fix. i'll have a close look and let you know if i encounter any problem. thanks again!!! robert. On 07/20/2017 11:23 AM, Hervé Pagès wrote: Hi Robert, This should work in GenomicRanges 1.29.10. Note that working on this revealed some minor shortcomings of the GPos internal representation so I decided to change it. The new one relies on IPos, a new class in IRanges 2.11.10. IPos is analog to GPos but for "integer positions" instead of "genomic positions". See ?IPos for the details. The new GPos objects behave exactly like the old ones except for 2 things: - the strand() setter now works - ranges() now returns an IPos instead of an IRanges object Update any old GPos object 'x' with x <- updateObject(x, verbose=TRUE) Let me know if you run into any issue with this. Cheers, H. On 07/18/2017 03:00 PM, Robert Castelo wrote: great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: Hi Robert, I'm working on this. Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote: hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1) <- "-" Error in methods::slot(object, name) : no slot of name "call" for this object of class "GPos" traceback() 10: methods::slot(object, name) 9: getElement(x, "call") 8: getCall.default(object) 7: getCall(object) 6: update.default(x, strand = value, check = FALSE) 5: update(x, strand = value, check = FALSE) 4: update(x, strand = value, check = FALSE) 3: .local(x, ..., value) 2: `strand<-`(`*tmp*`, value = "-") 1: `strand<-`(`*tmp*`, value = "-") this kind of operation works perfectly on 'GRanges' objects, so i guess it should also work also with 'GPos' objects: example(GRanges) gr1 GRanges object with 1 range and 0 metadata columns: seqnamesranges strand [1] chr2 [56, 125] * --- seqinfo: 1 sequence from an unspecified genome; no seqlength strand(gr1) <- "-" gr1 GRanges object with 1 range and 0 metadata columns: seqnamesranges strand [1] chr2 [56, 125] - --- seqinfo: 1 sequence from an unspecified genome; no seqlengths below my session info. thanks! robert. ps: sessionInfo() sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8 [7] LC_PAPER=en_US.UTF8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 IRanges_2.10.2 [4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2 loaded via a namespace (and not attached): [1] zlibbioc_1.22.0 compiler_3.4.0 tools_3.4.0 [4] XVector_0.16.0 GenomeInfoDbData_0.99.0 RCurl_1.95-4.8 [7] bitops_1.0-6 ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw= -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] using BiocLite() on Ubuntu Xenial with its default R 3.2.3 release
I am trying to use the BiocLite() feature of Bioconductor to install
the R modules required by MetaboAnalyst 3.0 under Ubuntu Xenial
16.04LTS with its system R 3.2.3 release. I have added the repo for
Micheal Rutter's cran2deb4ubuntu to provide the missing cran R modules
but have avoided installing any of the r-bioc ones to keep the
installation purely using those installed in /usr/local/lib/R by
BiocLite(). Unfortunately, this is failing on
$ sudo R
> source("https://bioconductor.org/biocLite.R;)
> biocLite("‘AnnotationDbi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) ‘‘AnnotationDbi’
Warning message:
package ‘‘AnnotationDbi’ is not available (for R version 3.2.3)
>
Certainly there must be a way to redirect BiocLite to a legacy release
which fully supports the older R 3.2.3 in the current Ubuntu LTS
release?
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Re: [Bioc-devel] strand<- method for 'GPos' doesn't work
Hi Robert, This should work in GenomicRanges 1.29.10. Note that working on this revealed some minor shortcomings of the GPos internal representation so I decided to change it. The new one relies on IPos, a new class in IRanges 2.11.10. IPos is analog to GPos but for "integer positions" instead of "genomic positions". See ?IPos for the details. The new GPos objects behave exactly like the old ones except for 2 things: - the strand() setter now works - ranges() now returns an IPos instead of an IRanges object Update any old GPos object 'x' with x <- updateObject(x, verbose=TRUE) Let me know if you run into any issue with this. Cheers, H. On 07/18/2017 03:00 PM, Robert Castelo wrote: great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: Hi Robert, I'm working on this. Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote: hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1) <- "-" Error in methods::slot(object, name) : no slot of name "call" for this object of class "GPos" traceback() 10: methods::slot(object, name) 9: getElement(x, "call") 8: getCall.default(object) 7: getCall(object) 6: update.default(x, strand = value, check = FALSE) 5: update(x, strand = value, check = FALSE) 4: update(x, strand = value, check = FALSE) 3: .local(x, ..., value) 2: `strand<-`(`*tmp*`, value = "-") 1: `strand<-`(`*tmp*`, value = "-") this kind of operation works perfectly on 'GRanges' objects, so i guess it should also work also with 'GPos' objects: example(GRanges) gr1 GRanges object with 1 range and 0 metadata columns: seqnamesranges strand [1] chr2 [56, 125] * --- seqinfo: 1 sequence from an unspecified genome; no seqlength strand(gr1) <- "-" gr1 GRanges object with 1 range and 0 metadata columns: seqnamesranges strand [1] chr2 [56, 125] - --- seqinfo: 1 sequence from an unspecified genome; no seqlengths below my session info. thanks! robert. ps: sessionInfo() sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8 [7] LC_PAPER=en_US.UTF8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 IRanges_2.10.2 [4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2 loaded via a namespace (and not attached): [1] zlibbioc_1.22.0 compiler_3.4.0 tools_3.4.0 [4] XVector_0.16.0 GenomeInfoDbData_0.99.0 RCurl_1.95-4.8 [7] bitops_1.0-6 ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw= -- 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
