VariantTools installation problem: dependencies not available
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heyi xiao ▴ 360
@heyi-xiao-3308
Last seen 8.1 years ago
United States
I tried to install VariantTools under R version 3.0.1 on my Linux machine. It failed due to dependencies not available (error message below). Any suggestion or help would be appreciated. > biocLite("VariantTools", type="source") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R version 3.0.1. Installing package(s) 'VariantTools' also installing the dependencies XVector, IRanges, GenomicRanges, gmapR, BiocParallel trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/XVe ctor_0.1.4.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/cont rib/XVector_0.1.4.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package XVector failed trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/IRa nges_1.19.38.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/cont rib/IRanges_1.19.38.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package IRanges failed ?
IRanges GenomicRanges VariantTools XVector IRanges GenomicRanges VariantTools XVector • 2.4k views
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@michael-lawrence-3846
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Looks like some sort of cache or something is stale. It's trying to install the old devel versions of the Bioc 2.13 packages. Michael On Mon, Nov 11, 2013 at 9:32 AM, heyi xiao <xiaoheyiyh@yahoo.com> wrote: > I tried to install VariantTools under R version 3.0.1 on my Linux machine. > It failed due to dependencies not available (error message below). Any > suggestion or help would be appreciated. > > > > biocLite("VariantTools", type="source") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R version 3.0.1. > Installing package(s) 'VariantTools' > also installing the dependencies XVector, IRanges, GenomicRanges, gmapR, > BiocParallel > > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4 .tar.gz > ' > Error in download.file(url, destfile, method, mode = "wb", ...) : > cannot open URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4 .tar.gz > ' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb", ...) : > cannot open: HTTP status was '404 Not Found' > Warning in download.packages(pkgs, destdir = tmpd, available = available, > : > download of package XVector failed > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19. 38.tar.gz > ' > Error in download.file(url, destfile, method, mode = "wb", ...) : > cannot open URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19. 38.tar.gz > ' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb", ...) : > cannot open: HTTP status was '404 Not Found' > Warning in download.packages(pkgs, destdir = tmpd, available = available, > : > download of package IRanges failed > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Hi Michael, You mean that URL ?http://bioconductor.org/packages/2.13/bioc/src/contrib/? points to the old devel versions? But it looks like the 2.13 branch, or is it the same thing? I didn?t specify anything in the installation as you see in my code, with or without type="source" gives the same problem. What shall I do now? Thanks! Heyi -------------------------------------------- On Mon, 11/11/13, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: Subject: Re: [BioC] VariantTools installation problem: dependencies not available Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Date: Monday, November 11, 2013, 12:46 PM Looks like some sort of cache or something is stale. It's trying to install the old devel versions of the Bioc 2.13 packages. Michael wrote: I tried to install VariantTools under R version 3.0.1 on my Linux machine. It failed due to dependencies not available (error message below). Any suggestion or help would be appreciated. > biocLite("VariantTools", type="source") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R version 3.0.1. Installing package(s) 'VariantTools' also installing the dependencies XVector, IRanges, GenomicRanges, gmapR, BiocParallel trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/XV ector_0.1.4.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : ? cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/con trib/XVector_0.1.4.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : ? cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, ?: ? download of package XVector failed trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/IR anges_1.19.38.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : ? cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/con trib/IRanges_1.19.38.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : ? cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, ?: ? download of package IRanges failed ? _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, Can you please provide the output of sessionInfo()? Also, you are running R-3.0.1 when bioc2.13 is "tied' to R-3.0.2. Instead of diagnosing your current setup, I suspect if you "simply" upgrade to R-3.0.2, then: R> source("http://bioconductor.org/biocLite.R") R> biocLite("VariantTools") Will probably work. Could you try to upgrade R first then reinstall your bioconductor universe via biocLite? HTH, -steve On Mon, Nov 11, 2013 at 10:10 AM, heyi xiao <xiaoheyiyh at="" yahoo.com=""> wrote: > Hi Michael, > You mean that URL ?http://bioconductor.org/packages/2.13/bioc/src/contrib/? points to the old devel versions? But it looks like the 2.13 branch, or is it the same thing? I didn?t specify anything in the installation as you see in my code, with or without type="source" gives the same problem. > What shall I do now? Thanks! > Heyi > > -------------------------------------------- > On Mon, 11/11/13, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > > Subject: Re: [BioC] VariantTools installation problem: dependencies not available > > Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Date: Monday, November 11, 2013, 12:46 PM > > Looks like some sort of > cache or something is stale. It's trying to install the > old devel versions of the Bioc 2.13 packages. > > Michael > > > > > wrote: > > I tried to install VariantTools under R version 3.0.1 on my > Linux machine. It failed due to dependencies not available > (error message below). Any suggestion or help would be > appreciated. > > > > > > > biocLite("VariantTools", > type="source") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R > version 3.0.1. > > Installing package(s) 'VariantTools' > > also installing the dependencies XVector, IRanges, > GenomicRanges, gmapR, BiocParallel > > > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/ XVector_0.1.4.tar.gz' > > Error in download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/c ontrib/XVector_0.1.4.tar.gz' > > In addition: Warning message: > > In download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open: HTTP status was '404 Not Found' > > Warning in download.packages(pkgs, destdir = tmpd, available > = available, : > > download of package XVector failed > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/ IRanges_1.19.38.tar.gz' > > Error in download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/c ontrib/IRanges_1.19.38.tar.gz' > > In addition: Warning message: > > In download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open: HTTP status was '404 Not Found' > > Warning in download.packages(pkgs, destdir = tmpd, available > = available, : > > download of package IRanges failed > > ? > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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On 11/11/2013 10:10 AM, heyi xiao wrote: > Hi Michael, > You mean that URL ?http://bioconductor.org/packages/2.13/bioc/src/contrib/? points to the old devel versions? But it looks like the 2.13 branch, or is it the same thing? I didn?t specify anything in the installation as you see in my code, with or without type="source" gives the same problem. > What shall I do now? Thanks! I can't really understand what's going wrong, but I'd start by R --vanilla and then source("http://bioconductor.org/biocLite.R") biocLite("BiocInstaller") which should end up with BiocInstaller v. 1.12.0 Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help If there are still problems, it might be helpful to try installing XVector itself biocLite("XVector") and visiting via a browser http://bioconductor.org/packages/2.13/bioc/src/contrib/PACKAGES which should have lines like Package: XVector Version: 0.2.0 to indicate that XVector_0.2.0.tar.gz should be returned. If this file reports something different in the web browser, e.g., Version: 0.1.4, then my guess is that your institution has some kind of proxy mechanism in place, and this is stale -- you'd need to speak with your system administrator. The output of biocinstallRepos() might be helpful. Martin > Heyi > > -------------------------------------------- > On Mon, 11/11/13, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > > Subject: Re: [BioC] VariantTools installation problem: dependencies not available > > Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Date: Monday, November 11, 2013, 12:46 PM > > Looks like some sort of > cache or something is stale. It's trying to install the > old devel versions of the Bioc 2.13 packages. > > Michael > > > > > wrote: > > I tried to install VariantTools under R version 3.0.1 on my > Linux machine. It failed due to dependencies not available > (error message below). Any suggestion or help would be > appreciated. > > > > > > > biocLite("VariantTools", > type="source") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R > version 3.0.1. > > Installing package(s) 'VariantTools' > > also installing the dependencies XVector, IRanges, > GenomicRanges, gmapR, BiocParallel > > > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib /XVector_0.1.4.tar.gz' > > Error in download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/ contrib/XVector_0.1.4.tar.gz' > > In addition: Warning message: > > In download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open: HTTP status was '404 Not Found' > > Warning in download.packages(pkgs, destdir = tmpd, available > = available, : > > download of package XVector failed > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib /IRanges_1.19.38.tar.gz' > > Error in download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src/ contrib/IRanges_1.19.38.tar.gz' > > In addition: Warning message: > > In download.file(url, destfile, method, mode = > "wb", ...) : > > cannot open: HTTP status was '404 Not Found' > > Warning in download.packages(pkgs, destdir = tmpd, available > = available, : > > download of package IRanges failed > > ? > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Steve and Martin, Thanks for all the suggestions. Following Martin?s suggestion, I started a new session using: R ?vanilla Then, source("http://bioconductor.org/biocLite.R") biocLite("VariantTools") Now VariantTools and dependencies are installed fine. BTW, one question here: Is there any special advantage of using GSNAP (besides calling within R through gmapR) over BWA in reads mapping? GSNAP should be slower. Heyi -------------------------------------------- On Mon, 11/11/13, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: Subject: Re: [BioC] VariantTools installation problem: dependencies not available el at gene.com> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Date: Monday, November 11, 2013, 1:32 PM On 11/11/2013 10:10 AM, heyi xiao wrote: > Hi Michael, > You mean that URL ?http://bioconductor.org/packages/2.13/bioc/src/contrib/? points to the old devel versions? But it looks like the 2.13 branch, or is it the same thing? I didn?t specify anything in the installation as you see in my code, with or without type="source" gives the same problem. [[elided Yahoo spam]] I can't really understand what's going wrong, but I'd start by ???R --vanilla and then ???source("http://bioconductor.org/biocLite.R") ???biocLite("BiocInstaller") which should end up with BiocInstaller v. 1.12.0 ???Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help If there are still problems, it might be helpful to try installing XVector itself ???biocLite("XVector") and visiting via a browser ???http://bioconductor.org/packages/2.13/bioc/src/contrib/PACKAGES which should have lines like ???Package: XVector ???Version: 0.2.0 to indicate that XVector_0.2.0.tar.gz should be returned. If this file reports something different in the web browser, e.g., Version: 0.1.4, then my guess is that your institution has some kind of proxy mechanism in place, and this is stale -- you'd need to speak with your system administrator. The output of ???biocinstallRepos() might be helpful. Martin > Heyi > > -------------------------------------------- > On Mon, 11/11/13, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > >???Subject: Re: [BioC] VariantTools installation problem: dependencies not available > >???Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> >???Date: Monday, November 11, 2013, 12:46 PM > >???Looks like some sort of >???cache or something is stale. It's trying to install the >???old devel versions of the Bioc 2.13 packages. > >???Michael > > > > >???wrote: > >???I tried to install VariantTools under R version 3.0.1 on my >???Linux machine. It failed due to dependencies not available >???(error message below). Any suggestion or help would be >???appreciated. > > > > > >???> biocLite("VariantTools", >???type="source") > >???BioC_mirror: http://bioconductor.org > >???Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R >???version 3.0.1. > >???Installing package(s) 'VariantTools' > >???also installing the dependencies XVector, IRanges, >???GenomicRanges, gmapR, BiocParallel > > > >???trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contri b/XVector_0.1.4.tar.gz' > >???Error in download.file(url, destfile, method, mode = >???"wb", ...) : > >? ???cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src /contrib/XVector_0.1.4.tar.gz' > >???In addition: Warning message: > >???In download.file(url, destfile, method, mode = >???"wb", ...) : > >? ???cannot open: HTTP status was '404 Not Found' > >???Warning in download.packages(pkgs, destdir = tmpd, available >???= available,? : > >? ???download of package XVector failed > >???trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contri b/IRanges_1.19.38.tar.gz' > >???Error in download.file(url, destfile, method, mode = >???"wb", ...) : > >? ???cannot open URL 'http://bioconductor.org/packages/2.13/bioc/src /contrib/IRanges_1.19.38.tar.gz' > >???In addition: Warning message: > >???In download.file(url, destfile, method, mode = >???"wb", ...) : > >? ???cannot open: HTTP status was '404 Not Found' > >???Warning in download.packages(pkgs, destdir = tmpd, available >???= available,? : > >? ???download of package IRanges failed > >???? > > > >???_______________________________________________ > >???Bioconductor mailing list > >???Bioconductor at r-project.org > >???https://stat.ethz.ch/mailman/listinfo/bioconductor > >???Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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I would recommend to use GSNAP for RNA-seq data. For Exome/WGS, it makes little difference. GSNAP has recently undergone an optimization spree that improves performance by an order of magnitude, but those changes are not yet reflected in the version embedded within gmapR. If you do use GSNAP with paired end data, we recommend setting clip_overlaps to TRUE, so that overlapping ends are hard clipped and variants in the overlap are not double counted by bam_tally. On Mon, Nov 11, 2013 at 12:24 PM, heyi xiao <xiaoheyiyh@yahoo.com> wrote: > Hi Steve and Martin, > Thanks for all the suggestions. Following Martin’s suggestion, I started a > new session using: > R –vanilla > Then, > source("http://bioconductor.org/biocLite.R") > biocLite("VariantTools") > Now VariantTools and dependencies are installed fine. > > BTW, one question here: Is there any special advantage of using GSNAP > (besides calling within R through gmapR) over BWA in reads mapping? GSNAP > should be slower. > Heyi > > -------------------------------------------- > On Mon, 11/11/13, Martin Morgan <mtmorgan@fhcrc.org> wrote: > > Subject: Re: [BioC] VariantTools installation problem: dependencies not > available > To: "heyi xiao" <xiaoheyiyh@yahoo.com>, "Michael Lawrence" < > lawrence.michael@gene.com> > Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> > Date: Monday, November 11, 2013, 1:32 PM > > On 11/11/2013 10:10 AM, heyi xiao > wrote: > > Hi Michael, > > You mean that URL “ > http://bioconductor.org/packages/2.13/bioc/src/contrib/” > points to the old devel versions? But it looks like the 2.13 > branch, or is it the same thing? I didn’t specify anything > in the installation as you see in my code, with or without > type="source" gives the same problem. > > What shall I do now? Thanks! > > I can't really understand what's going wrong, but I'd start > by > > R --vanilla > > and then > > source("http://bioconductor.org/biocLite.R") > biocLite("BiocInstaller") > > which should end up with BiocInstaller v. 1.12.0 > > Bioconductor version 2.13 (BiocInstaller > 1.12.0), ?biocLite for help > > If there are still problems, it might be helpful to try > installing XVector itself > > biocLite("XVector") > > and visiting via a browser > > http://bioconductor.org/packages/2.13/bioc/src/contrib/PACKAGES > > which should have lines like > > Package: XVector > Version: 0.2.0 > > to indicate that XVector_0.2.0.tar.gz should be returned. If > this file reports > something different in the web browser, e.g., Version: > 0.1.4, then my guess is > that your institution has some kind of proxy mechanism in > place, and this is > stale -- you'd need to speak with your system > administrator. > > The output of > > biocinstallRepos() > > might be helpful. > > Martin > > > Heyi > > > > -------------------------------------------- > > On Mon, 11/11/13, Michael Lawrence <lawrence.michael@gene.com> > wrote: > > > > Subject: Re: [BioC] VariantTools > installation problem: dependencies not available > > > > Cc: "bioconductor@r-project.org" > <bioconductor@r-project.org> > > Date: Monday, November 11, 2013, 12:46 > PM > > > > Looks like some sort of > > cache or something is stale. It's > trying to install the > > old devel versions of the Bioc 2.13 > packages. > > > > Michael > > > > > > > > > > wrote: > > > > I tried to install VariantTools under > R version 3.0.1 on my > > Linux machine. It failed due to > dependencies not available > > (error message below). Any suggestion > or help would be > > appreciated. > > > > > > > > > > > > > biocLite("VariantTools", > > type="source") > > > > BioC_mirror: http://bioconductor.org > > > > Using Bioconductor version 2.13 > (BiocInstaller 1.11.4), R > > version 3.0.1. > > > > Installing package(s) 'VariantTools' > > > > also installing the dependencies > XVector, IRanges, > > GenomicRanges, gmapR, BiocParallel > > > > > > > > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4 .tar.gz > ' > > > > Error in download.file(url, destfile, > method, mode = > > "wb", ...) : > > > > cannot open URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4 .tar.gz > ' > > > > In addition: Warning message: > > > > In download.file(url, destfile, > method, mode = > > "wb", ...) : > > > > cannot open: HTTP status was > '404 Not Found' > > > > Warning in download.packages(pkgs, > destdir = tmpd, available > > = available, : > > > > download of package XVector > failed > > > > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19. 38.tar.gz > ' > > > > Error in download.file(url, destfile, > method, mode = > > "wb", ...) : > > > > cannot open URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19. 38.tar.gz > ' > > > > In addition: Warning message: > > > > In download.file(url, destfile, > method, mode = > > "wb", ...) : > > > > cannot open: HTTP status was > '404 Not Found' > > > > Warning in download.packages(pkgs, > destdir = tmpd, available > > = available, : > > > > download of package IRanges > failed > > > > > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@r-project.org > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research > Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > [[alternative HTML version deleted]]
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Thanks Michael, for all the info! -------------------------------------------- On Tue, 11/12/13, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: Subject: Re: [BioC] VariantTools installation problem: dependencies not available Cc: "Michael Lawrence" <lawrence.michael at="" gene.com="">, "Martin Morgan" <mtmorgan at="" fhcrc.org="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Date: Tuesday, November 12, 2013, 12:24 AM I would recommend to use GSNAP for RNA-seq data. For Exome/WGS, it makes little difference. GSNAP has recently undergone an optimization spree that improves performance by an order of magnitude, but those changes are not yet reflected in the version embedded within gmapR. If you do use GSNAP with paired end data, we recommend setting clip_overlaps to TRUE, so that overlapping ends are hard clipped and variants in the overlap are not double counted by bam_tally. On Mon, Nov 11, 2013 wrote: Hi Steve and Martin, Thanks for all the suggestions. Following Martin?s suggestion, I started a new session using: R ?vanilla Then, source("http://bioconductor.org/biocLite.R") biocLite("VariantTools") Now VariantTools and dependencies are installed fine. BTW, one question here: Is there any special advantage of using GSNAP (besides calling within R through gmapR) over BWA in reads mapping? GSNAP should be slower. Heyi -------------------------------------------- On Mon, 11/11/13, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: ?Subject: Re: [BioC] VariantTools installation problem: dependencies not available "Michael Lawrence" <lawrence.michael at="" gene.com=""> ?Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> ?Date: Monday, November 11, 2013, 1:32 PM ?On 11/11/2013 10:10 AM, heyi xiao ?wrote: ?> Hi Michael, ?> You mean that URL ?http://bioconductor.org/packages/2.13/bioc/src/contrib/? ?points to the old devel versions? But it looks like the 2.13 ?branch, or is it the same thing? I didn?t specify anything ?in the installation as you see in my code, with or without ?type="source" gives the same problem. [[elided Yahoo spam]] ?I can't really understand what's going wrong, but I'd start ?by ????R --vanilla ?and then ????source("http://bioconductor.org/biocLite.R") ????biocLite("BiocInstaller") ?which should end up with BiocInstaller v. 1.12.0 ????Bioconductor version 2.13 (BiocInstaller ?1.12.0), ?biocLite for help ?If there are still problems, it might be helpful to try ?installing XVector itself ????biocLite("XVector") ?and visiting via a browser ????http://bioconductor.org/packages/2.13/bioc/src/contrib/PACKAGES ?which should have lines like ????Package: XVector ????Version: 0.2.0 ?to indicate that XVector_0.2.0.tar.gz should be returned. If ?this file reports ?something different in the web browser, e.g., Version: ?0.1.4, then my guess is ?that your institution has some kind of proxy mechanism in ?place, and this is ?stale -- you'd need to speak with your system ?administrator. ?The output of ????biocinstallRepos() ?might be helpful. ?Martin ?> Heyi ?> ?> -------------------------------------------- ?> On Mon, 11/11/13, Michael Lawrence <lawrence.michael at="" gene.com=""> ?wrote: ?> ?>???Subject: Re: [BioC] VariantTools ?installation problem: dependencies not available ?> ?>???Cc: "bioconductor at r-project.org" ?<bioconductor at="" r-project.org=""> ?>???Date: Monday, November 11, 2013, 12:46 ?PM ?> ?>???Looks like some sort of ?>???cache or something is stale. It's ?trying to install the ?>???old devel versions of the Bioc 2.13 ?packages. ?> ?>???Michael ?> ?> ?> ?> ?>???wrote: ?> ?>???I tried to install VariantTools under ?R version 3.0.1 on my ?>???Linux machine. It failed due to ?dependencies not available ?>???(error message below). Any suggestion ?or help would be ?>???appreciated. ?> ?> ?> ?> ?> ?>???> biocLite("VariantTools", ?>???type="source") ?> ?>???BioC_mirror: http://bioconductor.org ?> ?>???Using Bioconductor version 2.13 ?(BiocInstaller 1.11.4), R ?>???version 3.0.1. ?> ?>???Installing package(s) 'VariantTools' ?> ?>???also installing the dependencies ?XVector, IRanges, ?>???GenomicRanges, gmapR, BiocParallel ?> ?> ?> ?>???trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contr ib/XVector_0.1.4.tar.gz' ?> ?>???Error in download.file(url, destfile, ?method, mode = ?>???"wb", ...) : ?> ?>? ???cannot open URL 'http://bioconductor.org/packages/2.13/bioc/sr c/contrib/XVector_0.1.4.tar.gz' ?> ?>???In addition: Warning message: ?> ?>???In download.file(url, destfile, ?method, mode = ?>???"wb", ...) : ?> ?>? ???cannot open: HTTP status was ?'404 Not Found' ?> ?>???Warning in download.packages(pkgs, ?destdir = tmpd, available ?>???= available,? : ?> ?>? ???download of package XVector ?failed ?> ?>???trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contr ib/IRanges_1.19.38.tar.gz' ?> ?>???Error in download.file(url, destfile, ?method, mode = ?>???"wb", ...) : ?> ?>? ???cannot open URL 'http://bioconductor.org/packages/2.13/bioc/sr c/contrib/IRanges_1.19.38.tar.gz' ?> ?>???In addition: Warning message: ?> ?>???In download.file(url, destfile, ?method, mode = ?>???"wb", ...) : ?> ?>? ???cannot open: HTTP status was ?'404 Not Found' ?> ?>???Warning in download.packages(pkgs, ?destdir = tmpd, available ?>???= available,? : ?> ?>? ???download of package IRanges ?failed ?> ?>???? ?> ?> ?> ?>???_______________________________________________ ?> ?>???Bioconductor mailing list ?> ?>???Bioconductor at r-project.org ?> ?>???https://stat.ethz.ch/mailman/listinfo/bioconductor ?> ?>???Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ?> ?> _______________________________________________ ?> Bioconductor mailing list ?> Bioconductor at r-project.org ?> https://stat.ethz.ch/mailman/listinfo/bioconductor ?> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ?> ?-- ?Computational Biology / Fred Hutchinson Cancer Research ?Center ?1100 Fairview Ave. N. ?PO Box 19024 Seattle, WA 98109 ?Location: Arnold Building M1 B861 ?Phone: (206) 667-2793
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