SomaticSignatures
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Hi there, > I am a Post-doc student started analyzing human genome data few days > back. My aim is to find UVA signature mutations. i have done variant > calling by GATK and was wondering how i can extract signatures using > these call without using much programming (as I am a biologist working > in Bioinformatics field). while doing search on web i came > across Package ???SomaticSignatures???. i have some questions > can you please suggest what can help me in handling this package? > My first aim is to use my data and find sequence context of these variants > please suggest me any easy guide to start with > -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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@steve-lianoglou-2771
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Hi, On Sat, Mar 22, 2014 at 2:13 PM, hasif [guest] <guest at="" bioconductor.org=""> wrote: > > Hi there, >> I am a Post-doc student started analyzing human genome data few days >> back. My aim is to find UVA signature mutations. i have done variant >> calling by GATK and was wondering how i can extract signatures using >> these call without using much programming (as I am a biologist working >> in Bioinformatics field). while doing search on web i came >> across Package ? EURO ~SomaticSignatures? EURO (tm). i have some questions >> can you please suggest what can help me in handling this package? >> My first aim is to use my data and find sequence context of these variants >> please suggest me any easy guide to start with Have you read through the rather extensive looking vignette? http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSigna tures/inst/doc/SomaticSignatures-vignette.pdf -- Steve Lianoglou Computational Biologist Genentech
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Hi Hasif, For this, the 'mutationContext' should be all you need. As Steve mentioned, the vignette of the package covers a real-life example with all the relevant steps. Best wishes Julian On 22/03/14 23:52, Steve Lianoglou wrote: > Hi, > > On Sat, Mar 22, 2014 at 2:13 PM, hasif [guest] <guest at="" bioconductor.org=""> wrote: >> >> Hi there, >>> I am a Post-doc student started analyzing human genome data few days >>> back. My aim is to find UVA signature mutations. i have done variant >>> calling by GATK and was wondering how i can extract signatures using >>> these call without using much programming (as I am a biologist working >>> in Bioinformatics field). while doing search on web i came >>> across Package ? EURO ~SomaticSignatures? EURO (tm). i have some questions >>> can you please suggest what can help me in handling this package? >>> My first aim is to use my data and find sequence context of these variants >>> please suggest me any easy guide to start with > > Have you read through the rather extensive looking vignette? > > http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSig natures/inst/doc/SomaticSignatures-vignette.pdf >
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@steve-lianoglou-2771
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Hi Huma, First: please keep all correspondence on-list (by replying with "Reply-All") so that other can help as well as benefit from discussion. Other comments inline: On 24 Mar 2014, at 6:32, Huma Asif wrote: > hi, > i have read that just but i have to get my machine ready first so i > can apply the instruction in that? > i am doing this and got this message > Warning messages: > 1: package ?SomaticSignatures? is not available (for R version > 3.0.3)? It looks like this package is only available in bioc-devel, which has not been released yet. How would you have known? It will be released sometime in April (I believe) after R-3.1.x is released. In order for you to install SomaticSignatures via biocLite, you have to first install the current development version of R-3.1. > 2: installed directory not writable, cannot update packages 'foreign', > ? 'KernSmooth', 'rpart', 'spatial' It also looks like you are running R as a user who does not have rights to install into the default package directory. You can either run R as administrator account, or setup a package directory in your home directory that R can use "on top of" the default install. To figure out how to do that, google "r_libs_user" HTH, -steve
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Woops, meant to expand on the "how would you have known" (that this package is only available in bioc-devel) bit before hitting send. There are two things that would have clued you into that fact: First, on the package page, under the "Details" section, there is a row that says "In Bioconductor since", with a value of "BioC 2.14 (R-3.1)" btw, the current version of bioconductor is bioc 2.13 (which is tied to R-3.0.x (the "announcement" message you get when you load the "BiocInstaller" package should tell you the version of bioconductor it thinks you are using)). Also, the URL for the package only works with "devel" in it, instead of "release". This works: http://www.bioconductor.org/packages/devel/bioc/html/SomaticSignatures .html This doesn't: http://www.bioconductor.org/packages/release/bioc/html/SomaticSignatur es.html HTH, -steve On Mon, Mar 24, 2014 at 9:22 AM, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > Hi Huma, > > First: please keep all correspondence on-list (by replying with "Reply-All") > so that other can help as well as benefit from discussion. > > Other comments inline: > > On 24 Mar 2014, at 6:32, Huma Asif wrote: > >> hi, >> i have read that just but i have to get my machine ready first so i can >> apply the instruction in that >> i am doing this and got this message >> Warning messages: >> 1: package 'SomaticSignatures' is not available (for R version 3.0.3) > > > It looks like this package is only available in bioc-devel, which has not > been released yet. > > How would you have known? > > It will be released sometime in April (I believe) after R-3.1.x is released. > In order for you to install SomaticSignatures via biocLite, you have to > first install the current development version of R-3.1. > >> 2: installed directory not writable, cannot update packages 'foreign', >> 'KernSmooth', 'rpart', 'spatial' > > > It also looks like you are running R as a user who does not have rights to > install into the default package directory. You can either run R as > administrator account, or setup a package directory in your home directory > that R can use "on top of" the default install. To figure out how to do > that, google "r_libs_user" > > HTH, > > -steve > > > _______________________________________________ > 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 Genentech
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Hi Is there any other way to install Somatic signature if not via biocLite Do you  means i have to wait till April to use this Package. Though i have downloaded and unzip the package but dont know how to proceed next. in document it says The starting point of the analysis is a VRanges object which describes the somatic variants in terms of their genomic locations as well as reference and alternative alleles so do i need to install VariantAnnotation  also Sorry if it sounds stupid Huma >________________________________ > From: Steve Lianoglou <lianoglou.steve@gene.com> >To: Huma Asif <humaasif79@yahoo.com> >Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> >Sent: Monday, March 24, 2014 1:33 PM >Subject: Re: [BioC] SomaticSignatures > > >Woops, meant to expand on the "how would you have known" (that this >package is only available in bioc-devel) bit before hitting send. > >There are two things that would have clued you into that fact: > >First, on the package page, under the "Details" section, there is a >row that says "In Bioconductor since", with a value of "BioC 2.14 >(R-3.1)" > >btw, the current version of bioconductor is bioc 2.13 (which is tied >to R-3.0.x (the "announcement" message you get when  you load the >"BiocInstaller" package should tell you the version of bioconductor it >thinks you are using)). > >Also, the URL for the package only works with "devel" in it, instead >of "release". > >This works: > >http://www.bioconductor.org/packages/devel/bioc/html/SomaticSignature s.html > >This doesn't: > >http://www.bioconductor.org/packages/release/bioc/html/SomaticSignatu res.html > > >HTH, > >-steve > > > >On Mon, Mar 24, 2014 at 9:22 AM, Steve Lianoglou ><lianoglou.steve@gene.com> wrote: >> Hi Huma, >> >> First: please keep all correspondence on-list (by replying with "Reply-All") >> so that other can help as well as benefit from discussion. >> >> Other comments inline: >> >> On 24 Mar 2014, at 6:32, Huma Asif wrote: >> >>> hi, >>> i have read that just but i have to get my machine ready first so i can >>> apply the instruction in that >>> i am doing this and got this message >>> Warning messages: >>> 1: package 'SomaticSignatures' is not available (for R version 3.0.3) >> >> >> It looks like this package is only available in bioc-devel, which has not >> been released yet. >> >> How would you have known? >> >> It will be released sometime in April (I believe) after R-3.1.x is released. >> In order for you to install SomaticSignatures via biocLite, you have to >> first install the current development version of R-3.1. >> >>> 2: installed directory not writable, cannot update packages 'foreign', >>>  'KernSmooth', 'rpart', 'spatial' >> >> >> It also looks like you are running R as a user who does not have rights to >> install into the default package directory. You can either run R as >> administrator account, or setup a package directory in your home directory >> that R can use "on top of" the default install. To figure out how to do >> that, google "r_libs_user" >> >> HTH, >> >> -steve >> >> >> _______________________________________________ >> 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 > > > >-- >Steve Lianoglou >Computational Biologist >Genentech > > > > [[alternative HTML version deleted]]
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Hi, On 24 Mar 2014, at 12:02, Huma Asif wrote: > Hi > Is there any other way to install Somatic signature if not via > biocLite > Do you ?means i have to wait till April to use this Package. You could always install the current working version of 3.1-dev -- this is very easy to do on OSX and probably equally easy on other platforms (except windows, of course ;-) if you are comfortable doing some basic sys-admin type of tasks. What system are you on? > Though i have downloaded and unzip the package but dont know how to > proceed next. you downloaded the source package? > in document it says > The starting point of the analysis is a VRanges object which describes > the somatic variants in terms of their genomic?locations as well as > reference and alternative alleles > > so do i need to install VariantAnnotation? also? > Sorry if it sounds stupid? You will have to install every package listed in the Imports and Depends fields that you see on the package's home page. All of those can be installed in your current version of R easily via biocLite If you insist on installing this package into your current working version of R (after you installed the dependent packages), you may be able to do so if it doesn't depend on functionality coming in bioc2.14 that's not in bioc2.13 -- I have no idea of knowing the answer to that. If I were you, I'd install a working version of R-devel and all of the packages from bioc2.14 -- which will happen automatically when you use biocLite. If you search the mailing lists, the question of how to do this (with answers) appears often here -- read through several of these threads in their entirety so you avoid tripping over some gotcha's that may bite you in the process. Having multiple working versions of R (current and devel) is ultimately pretty easy (assuming you know how to do it ;-). Depending on your level of sys-admin savvy it can be anywhere from a 30 minute "thing" to a multiple day endeavor. HTH, -steve
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On 03/24/2014 12:12 PM, Steve Lianoglou wrote: > If you insist on installing this package into your current working version of R > (after you installed the dependent packages), you may be able to do so if it > doesn't depend on functionality coming in bioc2.14 that's not in bioc2.13 -- I > have no idea of knowing the answer to that. Do not try to install a 'devel' version into your current R version. > > If I were you, I'd install a working version of R-devel and all of the packages > from bioc2.14 -- which will happen automatically when you use biocLite. > Not R-devel, but R-3.1.0 alpha, followed by the installation instructions on the SomaticSignatures developer landing page. Do not attempt anything more elaborate. Martin -- 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, i am using Ubuntu 12.04 on VM wareplayer XXXXXXXXXXXXXXXXXXXXXXXXXXX yes i downloaded source package XXXXXXXXXXXXXXXXXXXXXX  i have installed some of the packages that are required for Somaticsignature however i need  help with these error during variantannotation installation source("http://bioconductor.org/biocLite.R") > biocLite() Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies ‘BiocGenerics’, ‘DBI’, ‘RSQLite’ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ERRORS during varriant annotation XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ........................................................ ERROR: configuration failed for package ‘XML’  removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/XML’ Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/RCurl’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/biomaRt’ samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory compilation terminated. make: *** [R_init_Rsamtools.o] Error 1 ERROR: compilation failed for package ‘Rsamtools’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/Rsamtools’ ERROR: dependencies ‘XML’, ‘RCurl’, ‘Rsamtools’ are not available for package ‘rtracklayer’ * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/rtracklayer’ ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’ * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/GenomicFeatures’ ERROR: dependencies ‘Rsamtools’, ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘VariantAnnotation’ * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/VariantAnnotation’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘RCurl’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘biomaRt’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘Rsamtools’ had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘rtracklayer’ had non-zero exit status 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘GenomicFeatures’ had non-zero exit status 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘VariantAnnotation’ had non-zero exit status i am planning to install  R-3.1.0 alpha and removing the current R version please give me the link for this R version Do you think the packages installed will work with R-3.1.0 alpha confused Regards Huma >________________________________ > From: Martin Morgan <mtmorgan@fhcrc.org> >To: Steve Lianoglou <lianoglou.steve@gene.com>; Huma Asif <humaasif79@yahoo.com> >Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> >Sent: Monday, March 24, 2014 4:44 PM >Subject: Re: [BioC] SomaticSignatures > > >On 03/24/2014 12:12 PM, Steve Lianoglou wrote: >> If you insist on installing this package into your current working version of R >> (after you installed the dependent packages), you may be able to do so if it >> doesn't depend on functionality coming in bioc2.14 that's not in bioc2.13 -- I >> have no idea of knowing the answer to that. > >Do not try to install a 'devel' version into your current R version. > > >> >> If I were you, I'd install a working version of R-devel and all of the packages >> from bioc2.14 -- which will happen automatically when  you use biocLite. >> > >Not R-devel, but R-3.1.0 alpha, followed by the installation instructions on the >SomaticSignatures developer landing page. Do not attempt anything more elaborate. > >Martin > >-- >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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On 03/25/2014 01:08 PM, Huma Asif wrote: > Hi, > i am using Ubuntu 12.04 on VM wareplayer > XXXXXXXXXXXXXXXXXXXXXXXXXXX > yes i downloaded source package > XXXXXXXXXXXXXXXXXXXXXX > > i have installed some of the packages that are required for Somaticsignature > however i need help with these error during variantannotation installation > > source("http://bioconductor.org/biocLite.R") > > biocLite() > Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies > ?BiocGenerics?, ?DBI?, ?RSQLite? > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > ERRORS during varriant annotation > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > ........................................................ > ERROR: configuration failed for package ?XML? > removing ?/home/asif/R/i686-pc-linux-gnu-library/3.0/XML? > > > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/asif/R/i686-pc-linux-gnu-library/3.0/RCurl? > > ERROR: dependencies ?XML?, ?RCurl? are not available for package ?biomaRt? > * removing ?/home/asif/R/i686-pc-linux-gnu-library/3.0/biomaRt? These are missing system (instead of R) dependencies; you'll need (be sure to get the 'dev' versions) sudo apt-get install libxml2-dev sudo apt-get install libcurl4-openssl-dev > > samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory This is surprising, suggesting that you have a very minimal system. You'll need sudo apt-get install zlib1g-dev I am not sure of the precise library versions. Martin > compilation terminated. > make: *** [R_init_Rsamtools.o] Error 1 > ERROR: compilation failed for package ?Rsamtools? > * removing ?/home/asif/R/i686-pc-linux-gnu-library/3.0/Rsamtools? > > ERROR: dependencies ?XML?, ?RCurl?, ?Rsamtools? are not available for package > ?rtracklayer? > * removing ?/home/asif/R/i686-pc-linux-gnu-library/3.0/rtracklayer? > ERROR: dependencies ?rtracklayer?, ?biomaRt?, ?RCurl? are not available for > package ?GenomicFeatures? > * removing ?/home/asif/R/i686-pc-linux-gnu- library/3.0/GenomicFeatures? > ERROR: dependencies ?Rsamtools?, ?GenomicFeatures?, ?rtracklayer? are not > available for package > > ?VariantAnnotation? > * removing ?/home/asif/R/i686-pc-linux-gnu- library/3.0/VariantAnnotation? > > > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?XML? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?biomaRt? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?Rsamtools? had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?rtracklayer? had non-zero exit status > 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?GenomicFeatures? had non-zero exit status > 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ?VariantAnnotation? had non-zero exit status > > > i am planning to install R-3.1.0 alpha and removing the current R version > please give me the link for this R version > > > Do you think the packages installed will work with R-3.1.0 alpha > confused > > > > > > > > > Regards > Huma > > ---------------------------------------------------------------- ---------------- > *From:* Martin Morgan <mtmorgan at="" fhcrc.org=""> > *To:* Steve Lianoglou <lianoglou.steve at="" gene.com="">; Huma Asif > <humaasif79 at="" yahoo.com=""> > *Cc:* "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > *Sent:* Monday, March 24, 2014 4:44 PM > *Subject:* Re: [BioC] SomaticSignatures > > On 03/24/2014 12:12 PM, Steve Lianoglou wrote: > > If you insist on installing this package into your current working > version of R > > (after you installed the dependent packages), you may be able to do so if it > > doesn't depend on functionality coming in bioc2.14 that's not in bioc2.13 > -- I > > have no idea of knowing the answer to that. > > Do not try to install a 'devel' version into your current R version. > > > > > > If I were you, I'd install a working version of R-devel and all of the > packages > > from bioc2.14 -- which will happen automatically when you use biocLite. > > > > > Not R-devel, but R-3.1.0 alpha, followed by the installation instructions on > the > SomaticSignatures developer landing page. Do not attempt anything more > elaborate. > > Martin > > -- > 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 > > > -- 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 Though i installed variant annotation and R vesion as suggested. every package seems dependent on other like somatic signature....mutationcontext..... variantannotation......GRanges....h5vc package. It seems impossible I need  to know is there any other package that can help in signatures extraction from vcf files with out being dependent on R. Regards >________________________________ > From: Martin Morgan <mtmorgan@fhcrc.org> >To: Huma Asif <humaasif79@yahoo.com>; Steve Lianoglou <lianoglou.steve@gene.com> >Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> >Sent: Tuesday, March 25, 2014 5:24 PM >Subject: Re: [BioC] SomaticSignatures > > >On 03/25/2014 01:08 PM, Huma Asif wrote: >> Hi, >> i am using Ubuntu 12.04 on VM wareplayer >> XXXXXXXXXXXXXXXXXXXXXXXXXXX >> yes i downloaded source package >> XXXXXXXXXXXXXXXXXXXXXX >> >>  i have installed some of the packages that are required for Somaticsignature >> however i need help with these error during variantannotation installation >> >> source("http://bioconductor.org/biocLite.R") >>  > biocLite() >> Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies >> ‘BiocGenerics’, ‘DBI’, ‘RSQLite’ >> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX >> ERRORS during varriant annotation >> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX >> ........................................................ >> ERROR: configuration failed for package ‘XML’ >>  removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/XML’ >> >> >> Cannot find curl-config >> ERROR: configuration failed for package ‘RCurl’ >> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/RCurl’ >> >> ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’ >> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/biomaRt’ > >These are missing system (instead of R) dependencies; you'll need (be sure to >get the 'dev' versions) > >  sudo apt-get install libxml2-dev >  sudo apt-get install libcurl4-openssl-dev > >> >> samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory > >This is surprising, suggesting that you have a very minimal system. You'll need > >  sudo apt-get install zlib1g-dev > >I am not sure of the precise library versions. > >Martin > >> compilation terminated. >> make: *** [R_init_Rsamtools.o] Error 1 >> ERROR: compilation failed for package ‘Rsamtools’ >> * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/Rsamtools’ >> >> ERROR: dependencies ‘XML’, ‘RCurl’, ‘Rsamtools’ are not available for package >> ‘rtracklayer’ >> * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/rtracklayer’ >> ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for >> package ‘GenomicFeatures’ >> * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/GenomicFeatures’ >> ERROR: dependencies ‘Rsamtools’, ‘GenomicFeatures’, ‘rtracklayer’ are not >> available for package >> >> ‘VariantAnnotation’ >> * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.0/VariantAnnotation’ >> >> >> Warning messages: >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘XML’ had non-zero exit status >> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘RCurl’ had non-zero exit status >> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘biomaRt’ had non-zero exit status >> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘Rsamtools’ had non-zero exit status >> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘rtracklayer’ had non-zero exit status >> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘GenomicFeatures’ had non-zero exit status >> 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>    installation of package ‘VariantAnnotation’ had non-zero exit status >> >> >> i am planning to install  R-3.1.0 alpha and removing the current R version >> please give me the link for this R version >> >> >> Do you think the packages installed will work with R-3.1.0 alpha >> confused >> >> >> >> >> >> >> >> >> Regards >> Huma >> >>    ------------------------------------------------------------- ------------------- >>    *From:* Martin Morgan <mtmorgan@fhcrc.org> >>    *To:* Steve Lianoglou <lianoglou.steve@gene.com>; Huma Asif >>    <humaasif79@yahoo.com> >>    *Cc:* "bioconductor@r-project.org list" <bioconductor@r-project.org> >>    *Sent:* Monday, March 24, 2014 4:44 PM >>    *Subject:* Re: [BioC] SomaticSignatures >> >>    On 03/24/2014 12:12 PM, Steve Lianoglou wrote: >>      > If you insist on installing this package into your current working >>    version of R >>      > (after you installed the dependent packages), you may be able to do so if it >>      > doesn't depend on functionality coming in bioc2.14 that's not in bioc2.13 >>    -- I >>      > have no idea of knowing the answer to that. >> >>    Do not try to install a 'devel' version into your current R version. >> >> >>      > >>      > If I were you, I'd install a working version of R-devel and all of the >>    packages >>      > from bioc2.14 -- which will happen automatically when you use biocLite. >> >>      > >> >>    Not R-devel, but R-3.1.0 alpha, followed by the installation instructions on >>    the >>    SomaticSignatures developer landing page. Do not attempt anything more >>    elaborate. >> >>    Martin >> >>    -- >>    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 > >> >> >> > > >-- >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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Hi, On 27 Mar 2014, at 13:01, Huma Asif wrote: > Hi > Though i installed variant annotation and R vesion as suggested. every > package seems dependent on other like somatic signature > ....mutationcontext..... variantannotation......GRanges....h5vc > package. That's why installation functions (like biocLite) are made available. They handle the dependency chasing for you. > It seems impossible It's not impossible, you just need to do a lot of book keeping regarding the dependency structure of the packages SomaticSignatures depends on (and the packages those packages depend on) if you insist on installing this manually. Why is installing it via `biocLite('SomaticSignatures')` out of the question here? You obviously have access to an internet connection -- you are sending email and downloading the dependent packages by hand -- so, why don't you just install it that way? > I need ?to know is there any other package that can help in > signatures extraction from vcf files with out being dependent on R. It looks like they are "just" creating a variant-by-sample matrix and performing some matrix decomposition on that (SVD, NMF), so if you know how to do each one of these things individually that does not involve R, then you're in business. -steve -- Steve Lianoglou Computational Biologist Genentech
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----- Original Message ----- > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > To: "Huma Asif" <humaasif79 at="" yahoo.com=""> > Cc: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > Sent: Thursday, March 27, 2014 1:34:01 PM > Subject: Re: [BioC] SomaticSignatures > > Hi, > > On 27 Mar 2014, at 13:01, Huma Asif wrote: > > > Hi > > Though i installed variant annotation and R vesion as suggested. > > every > > package seems dependent on other like somatic signature > > ....mutationcontext..... variantannotation......GRanges....h5vc > > package. > > That's why installation functions (like biocLite) are made available. > They handle the dependency chasing for you. > > > It seems impossible > > It's not impossible, you just need to do a lot of book keeping > regarding > the dependency structure of the packages SomaticSignatures depends on > (and the packages those packages depend on) if you insist on > installing > this manually. > > Why is installing it via `biocLite('SomaticSignatures')` out of the > question here? You obviously have access to an internet connection -- > you are sending email and downloading the dependent packages by hand > -- > so, why don't you just install it that way? I think the machine in question (a cluster?) has no direct access to the internet, so packages must be downloaded to some other machine and then copied there. Though usually we direct people in the opposite direction, this StackOverflow post may help: https://stackoverflow.com/questions/19268515/installing-bioconductor- without-internet/19269962#19269962 If the machine that has internet and the machine that doesn't are similar enough and have the same libraries installed, this could work. You could also create your own internal CRAN and BioC mirrors though this may be overkill, but our mirror page will provide more info: http://www.bioconductor.org/about/mirrors/mirror-how-to/ Dan > > > I need ?to know is there any other package that can help in > > signatures extraction from vcf files with out being dependent on R. > > It looks like they are "just" creating a variant-by-sample matrix and > performing some matrix decomposition on that (SVD, NMF), so if you > know > how to do each one of these things individually that does not involve > R, > then you're in business. > > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech > > _______________________________________________ > 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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On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: [snip] >> >> Why is installing it via `biocLite('SomaticSignatures')` out of the >> question here? You obviously have access to an internet connection -- >> you are sending email and downloading the dependent packages by hand >> -- >> so, why don't you just install it that way? > > I think the machine in question (a cluster?) has no direct access to the internet, so packages > must be downloaded to some other machine and then copied there. I see. > > Though usually we direct people in the opposite direction, this StackOverflow post may help: > > https://stackoverflow.com/questions/19268515/installing- bioconductor-without-internet/19269962#19269962 > > If the machine that has internet and the machine that doesn't are similar enough and have the same libraries installed, this could work. You could also create your own internal CRAN and BioC mirrors though this may be overkill, but our mirror page will provide more info: > > http://www.bioconductor.org/about/mirrors/mirror-how-to/ An altertnative would be to "cheat" and follow along with what Vincent did. You could start on your own machine w/ a brand new empty R-3.1-alpha install. Then do: R> source('http://bioconductor.org/biocLite.R') R> biocLite('SomaticSignatures') You will then see all of the packages that were downloaded to satisfy the dependency tree required for the installation (here are just three of them that Vincent required): """ trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' Content type 'application/x-gzip' length 153373 bytes (149 Kb) opened URL ================================================== downloaded 149 Kb trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb trying URL ' http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1.53 .4.tar.gz ' """ Now you have the packages required (here he needed gridBase, NMF and pcaMethods) *as well as* the URLs required to download them. Go back and pull out all of the URLs Download the packages. Move them over to your cluster. Then install by the command line as you like *into R-3.1-alpha* HTH, -steve -- Steve Lianoglou Computational Biologist Genentech
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----- Original Message ----- > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > Sent: Thursday, March 27, 2014 1:45:18 PM > Subject: Re: [BioC] SomaticSignatures > > On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > wrote: > [snip] > >> > >> Why is installing it via `biocLite('SomaticSignatures')` out of > >> the > >> question here? You obviously have access to an internet connection > >> -- > >> you are sending email and downloading the dependent packages by > >> hand > >> -- > >> so, why don't you just install it that way? > > > > I think the machine in question (a cluster?) has no direct access > > to the internet, so packages > > must be downloaded to some other machine and then copied there. > > I see. > > > > > Though usually we direct people in the opposite direction, this > > StackOverflow post may help: > > > > https://stackoverflow.com/questions/19268515/installing- bioconductor-without-internet/19269962#19269962 > > > > If the machine that has internet and the machine that doesn't are > > similar enough and have the same libraries installed, this could > > work. You could also create your own internal CRAN and BioC > > mirrors though this may be overkill, but our mirror page will > > provide more info: > > > > http://www.bioconductor.org/about/mirrors/mirror-how-to/ > > An altertnative would be to "cheat" and follow along with what > Vincent did. > > You could start on your own machine w/ a brand new empty R-3.1-alpha > install. > > Then do: > > R> source('http://bioconductor.org/biocLite.R') > R> biocLite('SomaticSignatures') > > You will then see all of the packages that were downloaded to satisfy > the dependency tree required for the installation (here are just > three > of them that Vincent required): > > """ > trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' > Content type 'application/x-gzip' length 153373 bytes (149 Kb) > opened URL > ================================================== > downloaded 149 Kb > > trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' > Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) > opened URL > ================================================== > downloaded 1.7 Mb > > trying URL ' > http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1. 53.4.tar.gz > ' > """ > > Now you have the packages required (here he needed gridBase, NMF and > pcaMethods) *as well as* the URLs required to download them. > > Go back and pull out all of the URLs > > Download the packages. > A trick I learned from Martin yesterday may help with this step (eliminating the need to know URLs): library(BiocInstaller) download.packages(c("SomaticSignatures", "gridBase", "NMF", "pcaMethods"), repos=biocinstallRepos(), type="source") This will download all the source package tarballs to your current directory. As Steve and Vince point out, your actual list of packages that you'd need to download would be longer. I think there is another trick to tell you the recursive dependencies of a package, but I don't know if off the top of my head. Dan > Move them over to your cluster. > > Then install by the command line as you like *into R-3.1-alpha* > > HTH, > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech >
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----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > Sent: Thursday, March 27, 2014 1:49:13 PM > Subject: Re: [BioC] SomaticSignatures > > > > ----- Original Message ----- > > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org > > list" <bioconductor at="" r-project.org=""> > > Sent: Thursday, March 27, 2014 1:45:18 PM > > Subject: Re: [BioC] SomaticSignatures > > > > On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > > wrote: > > [snip] > > >> > > >> Why is installing it via `biocLite('SomaticSignatures')` out of > > >> the > > >> question here? You obviously have access to an internet > > >> connection > > >> -- > > >> you are sending email and downloading the dependent packages by > > >> hand > > >> -- > > >> so, why don't you just install it that way? > > > > > > I think the machine in question (a cluster?) has no direct access > > > to the internet, so packages > > > must be downloaded to some other machine and then copied there. > > > > I see. > > > > > > > > Though usually we direct people in the opposite direction, this > > > StackOverflow post may help: > > > > > > https://stackoverflow.com/questions/19268515/installing- bioconductor-without-internet/19269962#19269962 > > > > > > If the machine that has internet and the machine that doesn't are > > > similar enough and have the same libraries installed, this could > > > work. You could also create your own internal CRAN and BioC > > > mirrors though this may be overkill, but our mirror page will > > > provide more info: > > > > > > http://www.bioconductor.org/about/mirrors/mirror-how-to/ > > > > An altertnative would be to "cheat" and follow along with what > > Vincent did. > > > > You could start on your own machine w/ a brand new empty > > R-3.1-alpha > > install. > > > > Then do: > > > > R> source('http://bioconductor.org/biocLite.R') > > R> biocLite('SomaticSignatures') > > > > You will then see all of the packages that were downloaded to > > satisfy > > the dependency tree required for the installation (here are just > > three > > of them that Vincent required): > > > > """ > > trying URL > > 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' > > Content type 'application/x-gzip' length 153373 bytes (149 Kb) > > opened URL > > ================================================== > > downloaded 149 Kb > > > > trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' > > Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) > > opened URL > > ================================================== > > downloaded 1.7 Mb > > > > trying URL ' > > http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_ 1.53.4.tar.gz > > ' > > """ > > > > Now you have the packages required (here he needed gridBase, NMF > > and > > pcaMethods) *as well as* the URLs required to download them. > > > > Go back and pull out all of the URLs > > > > Download the packages. > > > > A trick I learned from Martin yesterday may help with this step > (eliminating the need to know URLs): > > library(BiocInstaller) > download.packages(c("SomaticSignatures", "gridBase", "NMF", > "pcaMethods"), > repos=biocinstallRepos(), type="source") > > This will download all the source package tarballs to your current > directory. > > As Steve and Vince point out, your actual list of packages that you'd > need to download would be longer. > > I think there is another trick to tell you the recursive dependencies > of a package, but I don't know if off the top of my head. Here it is: library(BiocInstaller) pdb <- available.packages(contrib.url(biocinstallRepos())) pkgs <- unlist(unname(package_dependencies("SomaticSignatures", db=pdb))) Then use pkgs as the first argument to download.packages() above. Dan > > Dan > > > > Move them over to your cluster. > > > > Then install by the command line as you like *into R-3.1-alpha* > > > > HTH, > > -steve > > > > -- > > Steve Lianoglou > > Computational Biologist > > Genentech > > > > _______________________________________________ > 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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----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > Sent: Thursday, March 27, 2014 1:59:27 PM > Subject: Re: [BioC] SomaticSignatures > > > > ----- Original Message ----- > > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > > To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org > > list" <bioconductor at="" r-project.org=""> > > Sent: Thursday, March 27, 2014 1:49:13 PM > > Subject: Re: [BioC] SomaticSignatures > > > > > > > > ----- Original Message ----- > > > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > > > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, > > > "bioconductor at r-project.org > > > list" <bioconductor at="" r-project.org=""> > > > Sent: Thursday, March 27, 2014 1:45:18 PM > > > Subject: Re: [BioC] SomaticSignatures > > > > > > On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum > > > <dtenenba at="" fhcrc.org=""> > > > wrote: > > > [snip] > > > >> > > > >> Why is installing it via `biocLite('SomaticSignatures')` out > > > >> of > > > >> the > > > >> question here? You obviously have access to an internet > > > >> connection > > > >> -- > > > >> you are sending email and downloading the dependent packages > > > >> by > > > >> hand > > > >> -- > > > >> so, why don't you just install it that way? > > > > > > > > I think the machine in question (a cluster?) has no direct > > > > access > > > > to the internet, so packages > > > > must be downloaded to some other machine and then copied there. > > > > > > I see. > > > > > > > > > > > Though usually we direct people in the opposite direction, this > > > > StackOverflow post may help: > > > > > > > > https://stackoverflow.com/questions/19268515/installing- bioconductor-without-internet/19269962#19269962 > > > > > > > > If the machine that has internet and the machine that doesn't > > > > are > > > > similar enough and have the same libraries installed, this > > > > could > > > > work. You could also create your own internal CRAN and BioC > > > > mirrors though this may be overkill, but our mirror page will > > > > provide more info: > > > > > > > > http://www.bioconductor.org/about/mirrors/mirror-how-to/ > > > > > > An altertnative would be to "cheat" and follow along with what > > > Vincent did. > > > > > > You could start on your own machine w/ a brand new empty > > > R-3.1-alpha > > > install. > > > > > > Then do: > > > > > > R> source('http://bioconductor.org/biocLite.R') > > > R> biocLite('SomaticSignatures') > > > > > > You will then see all of the packages that were downloaded to > > > satisfy > > > the dependency tree required for the installation (here are just > > > three > > > of them that Vincent required): > > > > > > """ > > > trying URL > > > 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' > > > Content type 'application/x-gzip' length 153373 bytes (149 Kb) > > > opened URL > > > ================================================== > > > downloaded 149 Kb > > > > > > trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' > > > Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) > > > opened URL > > > ================================================== > > > downloaded 1.7 Mb > > > > > > trying URL ' > > > http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethod s_1.53.4.tar.gz > > > ' > > > """ > > > > > > Now you have the packages required (here he needed gridBase, NMF > > > and > > > pcaMethods) *as well as* the URLs required to download them. > > > > > > Go back and pull out all of the URLs > > > > > > Download the packages. > > > > > > > A trick I learned from Martin yesterday may help with this step > > (eliminating the need to know URLs): > > > > library(BiocInstaller) > > download.packages(c("SomaticSignatures", "gridBase", "NMF", > > "pcaMethods"), > > repos=biocinstallRepos(), type="source") > > > > This will download all the source package tarballs to your current > > directory. > > > > As Steve and Vince point out, your actual list of packages that > > you'd > > need to download would be longer. > > > > I think there is another trick to tell you the recursive > > dependencies > > of a package, but I don't know if off the top of my head. > > Here it is: > > library(BiocInstaller) #oops, you need to do this here: library(tools) library(utils) Dan > pdb <- available.packages(contrib.url(biocinstallRepos())) > pkgs <- unlist(unname(package_dependencies("SomaticSignatures", > db=pdb))) > > Then use pkgs as the first argument to download.packages() above. > Dan > > > > > > Dan > > > > > > > Move them over to your cluster. > > > > > > Then install by the command line as you like *into R-3.1-alpha* > > > > > > HTH, > > > -steve > > > > > > -- > > > Steve Lianoglou > > > Computational Biologist > > > Genentech > > > > > > > _______________________________________________ > > 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 >
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So, to wrap this all up for the OP. To identify the packages needed for installation of SomaticSignatures, you will need to be running R-3.1-alpha on an internet connected machine and enter these commands: library(tools) library(utils) library(BiocInstaller) pdb <- available.packages(contrib.url(biocinstallRepos())) pkgs <- unlist(unname(package_dependencies("SomaticSignatures", db=pdb))) Then to download the packages into the *current working directory* that R is executing in, he would then do: download.packages(pkgs, '.', repos=biocinstallRepos(), type="source") These copies could then be copied to the cluster and will have to be installed individually (ensuring that the cluster already has R-3.1-alpha already installed!). The OP will have to be careful to install them in the correct order, which might require some trial and error, but at least all of the packages will be available on the filesystem to do so. OP: let us know how that goes. On a side note: that's pretty cool! Perhaps parts of this would make handy utility functions in the BiocInstaller package ... I could imagine a function to "identify dependent packages" being useful. -steve On Thu, Mar 27, 2014 at 2:01 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > > > ----- Original Message ----- >> From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> >> Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> >> Sent: Thursday, March 27, 2014 1:59:27 PM >> Subject: Re: [BioC] SomaticSignatures >> >> >> >> ----- Original Message ----- >> > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> > To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> >> > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org >> > list" <bioconductor at="" r-project.org=""> >> > Sent: Thursday, March 27, 2014 1:49:13 PM >> > Subject: Re: [BioC] SomaticSignatures >> > >> > >> > >> > ----- Original Message ----- >> > > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> >> > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> > > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, >> > > "bioconductor at r-project.org >> > > list" <bioconductor at="" r-project.org=""> >> > > Sent: Thursday, March 27, 2014 1:45:18 PM >> > > Subject: Re: [BioC] SomaticSignatures >> > > >> > > On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum >> > > <dtenenba at="" fhcrc.org=""> >> > > wrote: >> > > [snip] >> > > >> >> > > >> Why is installing it via `biocLite('SomaticSignatures')` out >> > > >> of >> > > >> the >> > > >> question here? You obviously have access to an internet >> > > >> connection >> > > >> -- >> > > >> you are sending email and downloading the dependent packages >> > > >> by >> > > >> hand >> > > >> -- >> > > >> so, why don't you just install it that way? >> > > > >> > > > I think the machine in question (a cluster?) has no direct >> > > > access >> > > > to the internet, so packages >> > > > must be downloaded to some other machine and then copied there. >> > > >> > > I see. >> > > >> > > > >> > > > Though usually we direct people in the opposite direction, this >> > > > StackOverflow post may help: >> > > > >> > > > https://stackoverflow.com/questions/19268515/installing- bioconductor-without-internet/19269962#19269962 >> > > > >> > > > If the machine that has internet and the machine that doesn't >> > > > are >> > > > similar enough and have the same libraries installed, this >> > > > could >> > > > work. You could also create your own internal CRAN and BioC >> > > > mirrors though this may be overkill, but our mirror page will >> > > > provide more info: >> > > > >> > > > http://www.bioconductor.org/about/mirrors/mirror-how-to/ >> > > >> > > An altertnative would be to "cheat" and follow along with what >> > > Vincent did. >> > > >> > > You could start on your own machine w/ a brand new empty >> > > R-3.1-alpha >> > > install. >> > > >> > > Then do: >> > > >> > > R> source('http://bioconductor.org/biocLite.R') >> > > R> biocLite('SomaticSignatures') >> > > >> > > You will then see all of the packages that were downloaded to >> > > satisfy >> > > the dependency tree required for the installation (here are just >> > > three >> > > of them that Vincent required): >> > > >> > > """ >> > > trying URL >> > > 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' >> > > Content type 'application/x-gzip' length 153373 bytes (149 Kb) >> > > opened URL >> > > ================================================== >> > > downloaded 149 Kb >> > > >> > > trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' >> > > Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) >> > > opened URL >> > > ================================================== >> > > downloaded 1.7 Mb >> > > >> > > trying URL ' >> > > http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMetho ds_1.53.4.tar.gz >> > > ' >> > > """ >> > > >> > > Now you have the packages required (here he needed gridBase, NMF >> > > and >> > > pcaMethods) *as well as* the URLs required to download them. >> > > >> > > Go back and pull out all of the URLs >> > > >> > > Download the packages. >> > > >> > >> > A trick I learned from Martin yesterday may help with this step >> > (eliminating the need to know URLs): >> > >> > library(BiocInstaller) >> > download.packages(c("SomaticSignatures", "gridBase", "NMF", >> > "pcaMethods"), >> > repos=biocinstallRepos(), type="source") >> > >> > This will download all the source package tarballs to your current >> > directory. >> > >> > As Steve and Vince point out, your actual list of packages that >> > you'd >> > need to download would be longer. >> > >> > I think there is another trick to tell you the recursive >> > dependencies >> > of a package, but I don't know if off the top of my head. >> >> Here it is: >> >> library(BiocInstaller) > #oops, you need to do this here: > library(tools) > library(utils) > > Dan > >> pdb <- available.packages(contrib.url(biocinstallRepos())) >> pkgs <- unlist(unname(package_dependencies("SomaticSignatures", >> db=pdb))) >> >> Then use pkgs as the first argument to download.packages() above. >> Dan >> >> >> > >> > Dan >> > >> > >> > > Move them over to your cluster. >> > > >> > > Then install by the command line as you like *into R-3.1-alpha* >> > > >> > > HTH, >> > > -steve >> > > >> > > -- >> > > Steve Lianoglou >> > > Computational Biologist >> > > Genentech >> > > >> > >> > _______________________________________________ >> > 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 >> > > _______________________________________________ > 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 Genentech
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Steve, thanks for the nice summary; much preferable to my dribs and drabs, it's what I should have done. Of course I have more to add (defeating your purpose of summarizing but adding greatly to my sent email count). I'll try to keep it all in this one email. See below: ----- Original Message ----- > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > Sent: Thursday, March 27, 2014 3:10:15 PM > Subject: Re: [BioC] SomaticSignatures > > So, to wrap this all up for the OP. > > To identify the packages needed for installation of > SomaticSignatures, > you will need to be running R-3.1-alpha on an internet connected > machine and enter these commands: > > library(tools) > library(utils) > library(BiocInstaller) > pdb <- available.packages(contrib.url(biocinstallRepos())) > pkgs <- unlist(unname(package_dependencies("SomaticSignatures", > db=pdb))) A very important addition: please add recursive=TRUE to the above line as arguments to package_dependencies, so: pkgs <- unlist(unname(package_dependencies("SomaticSignatures", db=pdb, recursive=TRUE))) This doesn't include SomaticSignatures itself so do this here: pkgs <- c("SomaticSignatures", pkgs) > > Then to download the packages into the *current working directory* > that R is executing in, he would then do: (The OP is a she in this case, I believe) > > download.packages(pkgs, '.', repos=biocinstallRepos(), type="source") > > These copies could then be copied to the cluster and will have to be > installed individually (ensuring that the cluster already has > R-3.1-alpha already installed!). > > The OP will have to be careful to install them in the correct order, > which might require some trial and error, but at least all of the > packages will be available on the filesystem to do so. I *think* you could do this, assuming that all the .tar.gz files are in the current directory: install.packages(dir('.', pattern=".tar.gz$"), repos=NULL, type="source") This will attempt to install ALL the package tarballs in the directory, and will (hopefully) figure out all the dependencies and install things in the right order. One note that I'm not sure has been mentioned: these steps wil install all the R dependencies, but if there are any *system* dependencies, you need to make sure those are installed on your cluster node. I notice that pkgs (above) includes XML and RCurl so this means installing the libxml2 and curl-config libraries. If you are on ubuntu this is done with sudo apt-get install libxml2-dev libcurl-dev Of course this also assumes internet access, and I honestly don't know how to install ubuntu packages offline but I'm sure google can help. > > OP: let us know how that goes. > > On a side note: that's pretty cool! Perhaps parts of this would make > handy utility functions in the BiocInstaller package ... I could > imagine a function to "identify dependent packages" being useful. The main workhorses are already in tools and utils. But I agree this could be useful, not sure BiocInstaller is the right place for it. This issue tends to come up now and then; maybe we need a package that is addressed at the specific case of "offline" installations. Dan > > -steve > > > On Thu, Mar 27, 2014 at 2:01 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > wrote: > > > > > > ----- Original Message ----- > >> From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > >> To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > >> Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, > >> "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> > >> Sent: Thursday, March 27, 2014 1:59:27 PM > >> Subject: Re: [BioC] SomaticSignatures > >> > >> > >> > >> ----- Original Message ----- > >> > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > >> > To: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > >> > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, > >> > "bioconductor at r-project.org > >> > list" <bioconductor at="" r-project.org=""> > >> > Sent: Thursday, March 27, 2014 1:49:13 PM > >> > Subject: Re: [BioC] SomaticSignatures > >> > > >> > > >> > > >> > ----- Original Message ----- > >> > > From: "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> > >> > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > >> > > Cc: "Huma Asif" <humaasif79 at="" yahoo.com="">, > >> > > "bioconductor at r-project.org > >> > > list" <bioconductor at="" r-project.org=""> > >> > > Sent: Thursday, March 27, 2014 1:45:18 PM > >> > > Subject: Re: [BioC] SomaticSignatures > >> > > > >> > > On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum > >> > > <dtenenba at="" fhcrc.org=""> > >> > > wrote: > >> > > [snip] > >> > > >> > >> > > >> Why is installing it via `biocLite('SomaticSignatures')` > >> > > >> out > >> > > >> of > >> > > >> the > >> > > >> question here? You obviously have access to an internet > >> > > >> connection > >> > > >> -- > >> > > >> you are sending email and downloading the dependent > >> > > >> packages > >> > > >> by > >> > > >> hand > >> > > >> -- > >> > > >> so, why don't you just install it that way? > >> > > > > >> > > > I think the machine in question (a cluster?) has no direct > >> > > > access > >> > > > to the internet, so packages > >> > > > must be downloaded to some other machine and then copied > >> > > > there. > >> > > > >> > > I see. > >> > > > >> > > > > >> > > > Though usually we direct people in the opposite direction, > >> > > > this > >> > > > StackOverflow post may help: > >> > > > > >> > > > https://stackoverflow.com/questions/19268515/installing- bioconductor-without-internet/19269962#19269962 > >> > > > > >> > > > If the machine that has internet and the machine that > >> > > > doesn't > >> > > > are > >> > > > similar enough and have the same libraries installed, this > >> > > > could > >> > > > work. You could also create your own internal CRAN and BioC > >> > > > mirrors though this may be overkill, but our mirror page > >> > > > will > >> > > > provide more info: > >> > > > > >> > > > http://www.bioconductor.org/about/mirrors/mirror-how-to/ > >> > > > >> > > An altertnative would be to "cheat" and follow along with what > >> > > Vincent did. > >> > > > >> > > You could start on your own machine w/ a brand new empty > >> > > R-3.1-alpha > >> > > install. > >> > > > >> > > Then do: > >> > > > >> > > R> source('http://bioconductor.org/biocLite.R') > >> > > R> biocLite('SomaticSignatures') > >> > > > >> > > You will then see all of the packages that were downloaded to > >> > > satisfy > >> > > the dependency tree required for the installation (here are > >> > > just > >> > > three > >> > > of them that Vincent required): > >> > > > >> > > """ > >> > > trying URL > >> > > 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' > >> > > Content type 'application/x-gzip' length 153373 bytes (149 Kb) > >> > > opened URL > >> > > ================================================== > >> > > downloaded 149 Kb > >> > > > >> > > trying URL > >> > > 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' > >> > > Content type 'application/x-gzip' length 1763782 bytes (1.7 > >> > > Mb) > >> > > opened URL > >> > > ================================================== > >> > > downloaded 1.7 Mb > >> > > > >> > > trying URL ' > >> > > http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMet hods_1.53.4.tar.gz > >> > > ' > >> > > """ > >> > > > >> > > Now you have the packages required (here he needed gridBase, > >> > > NMF > >> > > and > >> > > pcaMethods) *as well as* the URLs required to download them. > >> > > > >> > > Go back and pull out all of the URLs > >> > > > >> > > Download the packages. > >> > > > >> > > >> > A trick I learned from Martin yesterday may help with this step > >> > (eliminating the need to know URLs): > >> > > >> > library(BiocInstaller) > >> > download.packages(c("SomaticSignatures", "gridBase", "NMF", > >> > "pcaMethods"), > >> > repos=biocinstallRepos(), type="source") > >> > > >> > This will download all the source package tarballs to your > >> > current > >> > directory. > >> > > >> > As Steve and Vince point out, your actual list of packages that > >> > you'd > >> > need to download would be longer. > >> > > >> > I think there is another trick to tell you the recursive > >> > dependencies > >> > of a package, but I don't know if off the top of my head. > >> > >> Here it is: > >> > >> library(BiocInstaller) > > #oops, you need to do this here: > > library(tools) > > library(utils) > > > > Dan > > > >> pdb <- available.packages(contrib.url(biocinstallRepos())) > >> pkgs <- unlist(unname(package_dependencies("SomaticSignatures", > >> db=pdb))) > >> > >> Then use pkgs as the first argument to download.packages() above. > >> Dan > >> > >> > >> > > >> > Dan > >> > > >> > > >> > > Move them over to your cluster. > >> > > > >> > > Then install by the command line as you like *into > >> > > R-3.1-alpha* > >> > > > >> > > HTH, > >> > > -steve > >> > > > >> > > -- > >> > > Steve Lianoglou > >> > > Computational Biologist > >> > > Genentech > >> > > > >> > > >> > _______________________________________________ > >> > 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 > >> > > > > _______________________________________________ > > 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 > Genentech >
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On Thu, Mar 27, 2014 at 3:27 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: [snip] >> Then to download the packages into the *current working directory* >> that R is executing in, he would then do: > > (The OP is a she in this case, I believe) Woops! Sorry, that's why I was originally using OP instead of he/she, but I let that one slip through ... apologies. >> On a side note: that's pretty cool! Perhaps parts of this would make >> handy utility functions in the BiocInstaller package ... I could >> imagine a function to "identify dependent packages" being useful. > > The main workhorses are already in tools and utils. But I agree this could be useful, not sure > BiocInstaller is the right place for it. Hmm ... not sure why we'd want to different installer-helper packages for on and offline functionality, but you folks are the boss(es)! -steve -- Steve Lianoglou Computational Biologist Genentech
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Thank you everyone I will try again and will write back Regards Huma Sent from my iPhone > On 27-Mar-2014, at 8:06 pm, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > > On Thu, Mar 27, 2014 at 3:27 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > [snip] >>> Then to download the packages into the *current working directory* >>> that R is executing in, he would then do: >> >> (The OP is a she in this case, I believe) > > Woops! Sorry, that's why I was originally using OP instead of he/she, > but I let that one slip through ... apologies. > >>> On a side note: that's pretty cool! Perhaps parts of this would make >>> handy utility functions in the BiocInstaller package ... I could >>> imagine a function to "identify dependent packages" being useful. >> >> The main workhorses are already in tools and utils. But I agree this could be useful, not sure >> BiocInstaller is the right place for it. > > Hmm ... not sure why we'd want to different installer-helper packages > for on and offline functionality, but you folks are the boss(es)! > > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech
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Hi every one, here is the new summary of what i did. sorry in advance for if it bothers u much. first R R version 3.1.0 alpha (2014-03-25 r65283) Copyright (C) 2014 The R Foundation for Statistical Computing Platform: i686-pc-linux-gnu (32-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. Then?> source("http://bioconductor.org/biocLite.R") Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : ? 'lib = "/usr/local/lib/R/library"' is not writable Would you like to use a personal library instead? ?(y/n) y Would you like to create a personal library ~/R/i686-pc-linux-gnu-library/3.1 to install packages into? ?(y/n) y trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib /BiocInstaller_1.13.3.tar.gz' Content type 'application/x-gzip' length 14183 bytes (13 Kb) opened URL ================================================== downloaded 13 Kb * installing *source* package ?BiocInstaller? ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help * DONE (BiocInstaller) The downloaded source packages are in ?/tmp/RtmpM1d0B0/downloaded_packages? Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help > library(tools) > library(utils) > library(BiocInstaller) > pdb <- available.packages(contrib.url(biocinstallRepos())) > pkgs <- unlist(unname(package_dependencies("SomaticSignatures",? + db=pdb, recursive=TRUE))) > pkgs <- c("SomaticSignatures", pkgs) > download.packages(pkgs, '.', repos=biocinstallRepos(), type="source") trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Som aticSignatures_0.99.0.tar.gz' Content type 'application/x-gzip' length 1270216 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Gen omicRanges_1.15.41.tar.gz' Content type 'application/x-gzip' length 550470 bytes (537 Kb) opened URL ================================================== downloaded 537 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/IRa nges_1.21.38.tar.gz' Content type 'application/x-gzip' length 679767 bytes (663 Kb) opened URL ================================================== downloaded 663 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Var iantAnnotation_1.9.48.tar.gz' Content type 'application/x-gzip' length 1297449 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Bio strings_2.31.20.tar.gz' Content type 'application/x-gzip' length 1514126 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb trying URL 'http://cran.fhcrc.org/src/contrib/ggplot2_0.9.3.1.tar.gz' Content type 'application/x-gzip' length 2330942 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/ggb io_1.11.15.tar.gz' Content type 'application/x-gzip' length 3151730 bytes (3.0 Mb) opened URL ================================================== downloaded 3.0 Mb trying URL 'http://cran.fhcrc.org/src/contrib/stringr_0.6.2.tar.gz' Content type 'application/x-gzip' length 20636 bytes (20 Kb) opened URL ================================================== downloaded 20 Kb trying URL 'http://cran.fhcrc.org/src/contrib/reshape2_1.2.2.tar.gz' Content type 'application/x-gzip' length 27220 bytes (26 Kb) opened URL ================================================== downloaded 26 Kb trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?methods? at the repositories trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/pca Methods_1.53.4.tar.gz' Content type 'application/x-gzip' length 714560 bytes (697 Kb) opened URL ================================================== downloaded 697 Kb trying URL 'http://cran.fhcrc.org/src/contrib/gtools_3.3.1.tar.gz' Content type 'application/x-gzip' length 54766 bytes (53 Kb) opened URL ================================================== downloaded 53 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Bio cGenerics_0.9.3.tar.gz' Content type 'application/x-gzip' length 32264 bytes (31 Kb) opened URL ================================================== downloaded 31 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/XVe ctor_0.3.7.tar.gz' Content type 'application/x-gzip' length 53528 bytes (52 Kb) opened URL ================================================== downloaded 52 Kb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?graphics? at the repositories Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?stats? at the repositories Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?utils? at the repositories trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/zli bbioc_1.9.0.tar.gz' Content type 'application/x-gzip' length 257656 bytes (251 Kb) opened URL ================================================== downloaded 251 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Gen omeInfoDb_0.99.26.tar.gz' Content type 'application/x-gzip' length 190989 bytes (186 Kb) opened URL ================================================== downloaded 186 Kb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?grid? at the repositories Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?grDevices? at the repositories trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/bio vizBase_1.11.13.tar.gz' Content type 'application/x-gzip' length 1050572 bytes (1.0 Mb) opened URL ================================================== downloaded 1.0 Mb trying URL 'http://cran.fhcrc.org/src/contrib/gtable_0.1.2.tar.gz' Content type 'application/x-gzip' length 19667 bytes (19 Kb) opened URL ================================================== downloaded 19 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Bio base_2.23.6.tar.gz' Content type 'application/x-gzip' length 1865270 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Gen omicFeatures_1.15.13.tar.gz' Content type 'application/x-gzip' length 765992 bytes (748 Kb) opened URL ================================================== downloaded 748 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Rsa mtools_1.15.37.tar.gz' Content type 'application/x-gzip' length 2935389 bytes (2.8 Mb) opened URL ================================================== downloaded 2.8 Mb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Gen omicAlignments_0.99.32.tar.gz' Content type 'application/x-gzip' length 1936773 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BSg enome_1.31.12.tar.gz' Content type 'application/x-gzip' length 540283 bytes (527 Kb) opened URL ================================================== downloaded 527 Kb trying URL 'http://cran.fhcrc.org/src/contrib/gridExtra_0.9.1.tar.gz' Content type 'application/x-gzip' length 29183 bytes (28 Kb) opened URL ================================================== downloaded 28 Kb trying URL 'http://cran.fhcrc.org/src/contrib/scales_0.2.3.tar.gz' Content type 'application/x-gzip' length 39429 bytes (38 Kb) opened URL ================================================== downloaded 38 Kb trying URL 'http://cran.fhcrc.org/src/contrib/Hmisc_3.14-3.tar.gz' Content type 'application/x-gzip' length 603295 bytes (589 Kb) opened URL ================================================== downloaded 589 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtr acklayer_1.23.20.tar.gz' Content type 'application/x-gzip' length 1337394 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb trying URL 'http://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz' Content type 'application/x-gzip' length 393233 bytes (384 Kb) opened URL ================================================== downloaded 384 Kb trying URL 'http://cran.fhcrc.org/src/contrib/digest_0.6.4.tar.gz' Content type 'application/x-gzip' length 79309 bytes (77 Kb) opened URL ================================================== downloaded 77 Kb trying URL 'http://cran.fhcrc.org/src/contrib/proto_0.3-10.tar.gz' Content type 'application/x-gzip' length 530758 bytes (518 Kb) opened URL ================================================== downloaded 518 Kb trying URL 'http://cran.fhcrc.org/src/contrib/MASS_7.3-31.tar.gz' Content type 'application/x-gzip' length 486427 bytes (475 Kb) opened URL ================================================== downloaded 475 Kb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?stats4? at the repositories trying URL 'http://cran.fhcrc.org/src/contrib/pkgmaker_0.20.tar.gz' Content type 'application/x-gzip' length 351323 bytes (343 Kb) opened URL ================================================== downloaded 343 Kb trying URL 'http://cran.fhcrc.org/src/contrib/registry_0.2.tar.gz' Content type 'application/x-gzip' length 196136 bytes (191 Kb) opened URL ================================================== downloaded 191 Kb trying URL 'http://cran.fhcrc.org/src/contrib/rngtools_1.2.4.tar.gz' Content type 'application/x-gzip' length 120986 bytes (118 Kb) opened URL ================================================== downloaded 118 Kb trying URL 'http://cran.fhcrc.org/src/contrib/cluster_1.15.2.tar.gz' Content type 'application/x-gzip' length 271734 bytes (265 Kb) opened URL ================================================== downloaded 265 Kb trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' Content type 'application/x-gzip' length 153373 bytes (149 Kb) opened URL ================================================== downloaded 149 Kb trying URL 'http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz' Content type 'application/x-gzip' length 242791 bytes (237 Kb) opened URL ================================================== downloaded 237 Kb trying URL 'http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz' Content type 'application/x-gzip' length 10656 bytes (10 Kb) opened URL ================================================== downloaded 10 Kb trying URL 'http://cran.fhcrc.org/src/contrib/foreach_1.4.1.tar.gz' Content type 'application/x-gzip' length 359347 bytes (350 Kb) opened URL ================================================== downloaded 350 Kb trying URL 'http://cran.fhcrc.org/src/contrib/doParallel_1.0.8.tar.gz' Content type 'application/x-gzip' length 172665 bytes (168 Kb) opened URL ================================================== downloaded 168 Kb trying URL 'http://cran.fhcrc.org/src/contrib/Rcpp_0.11.1.tar.gz' Content type 'application/x-gzip' length 2003515 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL 'http://cran.fhcrc.org/src/contrib/lattice_0.20-27.tar.gz' Content type 'application/x-gzip' length 346525 bytes (338 Kb) opened URL ================================================== downloaded 338 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Ann otationDbi_1.25.17.tar.gz' Content type 'application/x-gzip' length 4253121 bytes (4.1 Mb) opened URL ================================================== downloaded 4.1 Mb trying URL 'http://cran.fhcrc.org/src/contrib/DBI_0.2-7.tar.gz' Content type 'application/x-gzip' length 194699 bytes (190 Kb) opened URL ================================================== downloaded 190 Kb trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.11.4.tar.gz' Content type 'application/x-gzip' length 1599919 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?parallel? at the repositories trying URL 'http://cran.fhcrc.org/src/contrib/dichromat_2.0-0.tar.gz' Content type 'application/x-gzip' length 84320 bytes (82 Kb) opened URL ================================================== downloaded 82 Kb trying URL 'http://cran.fhcrc.org/src/contrib/iterators_1.0.6.tar.gz' Content type 'application/x-gzip' length 287154 bytes (280 Kb) opened URL ================================================== downloaded 280 Kb trying URL 'http://cran.fhcrc.org/src/contrib/codetools_0.2-8.tar.gz' Content type 'application/x-gzip' length 12392 bytes (12 Kb) opened URL ================================================== downloaded 12 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Bio cParallel_0.5.18.tar.gz' Content type 'application/x-gzip' length 296586 bytes (289 Kb) opened URL ================================================== downloaded 289 Kb trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/bio maRt_2.19.3.tar.gz' Content type 'application/x-gzip' length 276803 bytes (270 Kb) opened URL ================================================== downloaded 270 Kb trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz' Content type 'application/x-gzip' length 870915 bytes (850 Kb) opened URL ================================================== downloaded 850 Kb trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.37-7.tar.gz' Content type 'application/x-gzip' length 4132583 bytes (3.9 Mb) opened URL ================================================== downloaded 3.9 Mb trying URL 'http://cran.fhcrc.org/src/contrib/Formula_1.1-1.tar.gz' Content type 'application/x-gzip' length 148430 bytes (144 Kb) opened URL ================================================== downloaded 144 Kb trying URL 'http://cran.fhcrc.org/src/contrib/latticeExtra_0.6-26.tar.gz' Content type 'application/x-gzip' length 1295154 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?tools? at the repositories trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.7-3.tar.gz' Content type 'application/x-gzip' length 357303 bytes (348 Kb) opened URL ================================================== downloaded 348 Kb trying URL 'http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz' Content type 'application/x-gzip' length 8734 bytes opened URL ================================================== downloaded 8734 bytes trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz' Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL 'http://cran.fhcrc.org/src/contrib/munsell_0.4.2.tar.gz' Content type 'application/x-gzip' length 91026 bytes (88 Kb) opened URL ================================================== downloaded 88 Kb trying URL 'http://cran.fhcrc.org/src/contrib/labeling_0.2.tar.gz' Content type 'application/x-gzip' length 9998 bytes opened URL ================================================== downloaded 9998 bytes trying URL 'http://cran.fhcrc.org/src/contrib/BatchJobs_1.2.tar.gz' Content type 'application/x-gzip' length 98568 bytes (96 Kb) opened URL ================================================== downloaded 96 Kb trying URL 'http://cran.fhcrc.org/src/contrib/BBmisc_1.5.tar.gz' Content type 'application/x-gzip' length 54602 bytes (53 Kb) opened URL ================================================== downloaded 53 Kb Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") : ? no package ?splines? at the repositories trying URL 'http://cran.fhcrc.org/src/contrib/sendmailR_1.1-2.tar.gz' Content type 'application/x-gzip' length 7071 bytes opened URL ================================================== downloaded 7071 bytes trying URL 'http://cran.fhcrc.org/src/contrib/brew_1.0-6.tar.gz' Content type 'application/x-gzip' length 83315 bytes (81 Kb) opened URL ================================================== downloaded 81 Kb trying URL 'http://cran.fhcrc.org/src/contrib/fail_1.2.tar.gz' Content type 'application/x-gzip' length 10599 bytes (10 Kb) opened URL ================================================== downloaded 10 Kb trying URL 'http://cran.fhcrc.org/src/contrib/base64enc_0.1-1.tar.gz' Content type 'application/x-gzip' length 6296 bytes opened URL ================================================== downloaded 6296 bytes ? ? ? [,1] ? ? ? ? ? ? ? ?[,2] ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?[1,] "SomaticSignatures" "./SomaticSignatures_0.99.0.tar.gz"? ?[2,] "GenomicRanges" ? ? "./GenomicRanges_1.15.41.tar.gz" ? ? ?[3,] "IRanges" ? ? ? ? ? "./IRanges_1.21.38.tar.gz" ? ? ? ? ? ?[4,] "VariantAnnotation" "./VariantAnnotation_1.9.48.tar.gz"? ?[5,] "Biostrings" ? ? ? ?"./Biostrings_2.31.20.tar.gz" ? ? ?? ?[6,] "ggplot2" ? ? ? ? ? "./ggplot2_0.9.3.1.tar.gz" ? ? ? ? ? ?[7,] "ggbio" ? ? ? ? ? ? "./ggbio_1.11.15.tar.gz" ? ? ? ? ? ? ?[8,] "stringr" ? ? ? ? ? "./stringr_0.6.2.tar.gz" ? ? ? ? ? ? ?[9,] "reshape2" ? ? ? ? ?"./reshape2_1.2.2.tar.gz" ? ? ? ? ?? [10,] "NMF" ? ? ? ? ? ? ? "./NMF_0.20.5.tar.gz" ? ? ? ? ? ? ?? [11,] "pcaMethods" ? ? ? ?"./pcaMethods_1.53.4.tar.gz" ? ? ? ? [12,] "gtools" ? ? ? ? ? ?"./gtools_3.3.1.tar.gz" ? ? ? ? ? ?? [13,] "BiocGenerics" ? ? ?"./BiocGenerics_0.9.3.tar.gz" ? ? ?? [14,] "XVector" ? ? ? ? ? "./XVector_0.3.7.tar.gz" ? ? ? ? ? ? [15,] "zlibbioc" ? ? ? ? ?"./zlibbioc_1.9.0.tar.gz" ? ? ? ? ?? [16,] "GenomeInfoDb" ? ? ?"./GenomeInfoDb_0.99.26.tar.gz" ? ?? [17,] "biovizBase" ? ? ? ?"./biovizBase_1.11.13.tar.gz" ? ? ?? [18,] "gtable" ? ? ? ? ? ?"./gtable_0.1.2.tar.gz" ? ? ? ? ? ?? [19,] "Biobase" ? ? ? ? ? "./Biobase_2.23.6.tar.gz" ? ? ? ? ?? [20,] "GenomicFeatures" ? "./GenomicFeatures_1.15.13.tar.gz" ? [21,] "Rsamtools" ? ? ? ? "./Rsamtools_1.15.37.tar.gz" ? ? ? ? [22,] "GenomicAlignments" "./GenomicAlignments_0.99.32.tar.gz" [23,] "BSgenome" ? ? ? ? ?"./BSgenome_1.31.12.tar.gz" ? ? ? ?? [24,] "gridExtra" ? ? ? ? "./gridExtra_0.9.1.tar.gz" ? ? ? ? ? [25,] "scales" ? ? ? ? ? ?"./scales_0.2.3.tar.gz" ? ? ? ? ? ?? [26,] "Hmisc" ? ? ? ? ? ? "./Hmisc_3.14-3.tar.gz" ? ? ? ? ? ?? [27,] "rtracklayer" ? ? ? "./rtracklayer_1.23.20.tar.gz" ? ? ? [28,] "plyr" ? ? ? ? ? ? ?"./plyr_1.8.1.tar.gz" ? ? ? ? ? ? ?? [29,] "digest" ? ? ? ? ? ?"./digest_0.6.4.tar.gz" ? ? ? ? ? ?? [30,] "proto" ? ? ? ? ? ? "./proto_0.3-10.tar.gz" ? ? ? ? ? ?? [31,] "MASS" ? ? ? ? ? ? ?"./MASS_7.3-31.tar.gz" ? ? ? ? ? ? ? [32,] "pkgmaker" ? ? ? ? ?"./pkgmaker_0.20.tar.gz" ? ? ? ? ? ? [33,] "registry" ? ? ? ? ?"./registry_0.2.tar.gz" ? ? ? ? ? ?? [34,] "rngtools" ? ? ? ? ?"./rngtools_1.2.4.tar.gz" ? ? ? ? ?? [35,] "cluster" ? ? ? ? ? "./cluster_1.15.2.tar.gz" ? ? ? ? ?? [36,] "gridBase" ? ? ? ? ?"./gridBase_0.4-7.tar.gz" ? ? ? ? ?? [37,] "colorspace" ? ? ? ?"./colorspace_1.2-4.tar.gz" ? ? ? ?? [38,] "RColorBrewer" ? ? ?"./RColorBrewer_1.0-5.tar.gz" ? ? ?? [39,] "foreach" ? ? ? ? ? "./foreach_1.4.1.tar.gz" ? ? ? ? ? ? [40,] "doParallel" ? ? ? ?"./doParallel_1.0.8.tar.gz" ? ? ? ?? [41,] "Rcpp" ? ? ? ? ? ? ?"./Rcpp_0.11.1.tar.gz" ? ? ? ? ? ? ? [42,] "lattice" ? ? ? ? ? "./lattice_0.20-27.tar.gz" ? ? ? ? ? [43,] "AnnotationDbi" ? ? "./AnnotationDbi_1.25.17.tar.gz" ? ? [44,] "DBI" ? ? ? ? ? ? ? "./DBI_0.2-7.tar.gz" ? ? ? ? ? ? ? ? [45,] "RSQLite" ? ? ? ? ? "./RSQLite_0.11.4.tar.gz" ? ? ? ? ?? [46,] "dichromat" ? ? ? ? "./dichromat_2.0-0.tar.gz" ? ? ? ? ? [47,] "iterators" ? ? ? ? "./iterators_1.0.6.tar.gz" ? ? ? ? ? [48,] "codetools" ? ? ? ? "./codetools_0.2-8.tar.gz" ? ? ? ? ? [49,] "BiocParallel" ? ? ?"./BiocParallel_0.5.18.tar.gz" ? ? ? [50,] "biomaRt" ? ? ? ? ? "./biomaRt_2.19.3.tar.gz" ? ? ? ? ?? [51,] "RCurl" ? ? ? ? ? ? "./RCurl_1.95-4.1.tar.gz" ? ? ? ? ?? [52,] "survival" ? ? ? ? ?"./survival_2.37-7.tar.gz" ? ? ? ? ? [53,] "Formula" ? ? ? ? ? "./Formula_1.1-1.tar.gz" ? ? ? ? ? ? [54,] "latticeExtra" ? ? ?"./latticeExtra_0.6-26.tar.gz" ? ? ? [55,] "xtable" ? ? ? ? ? ?"./xtable_1.7-3.tar.gz" ? ? ? ? ? ?? [56,] "bitops" ? ? ? ? ? ?"./bitops_1.0-6.tar.gz" ? ? ? ? ? ?? [57,] "XML" ? ? ? ? ? ? ? "./XML_3.98-1.1.tar.gz" ? ? ? ? ? ?? [58,] "munsell" ? ? ? ? ? "./munsell_0.4.2.tar.gz" ? ? ? ? ? ? [59,] "labeling" ? ? ? ? ?"./labeling_0.2.tar.gz" ? ? ? ? ? ?? [60,] "BatchJobs" ? ? ? ? "./BatchJobs_1.2.tar.gz" ? ? ? ? ? ? [61,] "BBmisc" ? ? ? ? ? ?"./BBmisc_1.5.tar.gz" ? ? ? ? ? ? ?? [62,] "sendmailR" ? ? ? ? "./sendmailR_1.1-2.tar.gz" ? ? ? ? ? [63,] "brew" ? ? ? ? ? ? ?"./brew_1.0-6.tar.gz" ? ? ? ? ? ? ?? [64,] "fail" ? ? ? ? ? ? ?"./fail_1.2.tar.gz" ? ? ? ? ? ? ? ?? [65,] "base64enc" ? ? ? ? "./base64enc_0.1-1.tar.gz"? install.packages(dir('.', pattern=".tar.gz$"), repos=NULL, type="source") ?? now the summary of warning after this command ?i attached please see Regards Huma -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: errors after install.packages.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140331="" fe5be561="" attachment.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: warnings summary.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140331="" fe5be561="" attachment-0001.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: path where all packages are.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140331="" fe5be561="" attachment-0002.txt="">
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On 03/31/2014 12:16 PM, Huma Asif wrote: > Hi every one, > here is the new summary of what i did. sorry in advance for if it bothers u much. > first > R > R version 3.1.0 alpha (2014-03-25 r65283) > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: i686-pc-linux-gnu (32-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. > Then > source("http://bioconductor.org/biocLite.R") > Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : > 'lib = "/usr/local/lib/R/library"' is not writable > Would you like to use a personal library instead? (y/n) y > Would you like to create a personal library > ~/R/i686-pc-linux-gnu-library/3.1 > to install packages into? (y/n) y > trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contr ib/BiocInstaller_1.13.3.tar.gz' > Content type 'application/x-gzip' length 14183 bytes (13 Kb) > opened URL > ================================================== > downloaded 13 Kb > > * installing *source* package ?BiocInstaller? ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help > * DONE (BiocInstaller) > > The downloaded source packages are in > ?/tmp/RtmpM1d0B0/downloaded_packages? > Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help >> library(tools) >> library(utils) >> library(BiocInstaller) At this point, to install SomaticSignatures with internet access, you just want to biocLite("SomaticSignatures") If that accomplishes what you want, then stop reading. If this is what you want to do, but there is an error, then please copy and paste the commands you used and the error that occurred. If you want to install SomaticSignatures from your own repository, then continue to read below >> pdb <- available.packages(contrib.url(biocinstallRepos())) >> pkgs <- unlist(unname(package_dependencies("SomaticSignatures", > + db=pdb, recursive=TRUE))) >> pkgs <- c("SomaticSignatures", pkgs) >> download.packages(pkgs, '.', repos=biocinstallRepos(), type="source") > trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/S omaticSignatures_0.99.0.tar.gz' > Content type 'application/x-gzip' length 1270216 bytes (1.2 Mb) > opened URL SNIP! This info WAS useful in the original email > ================================================== > downloaded 10 Kb > > trying URL 'http://cran.fhcrc.org/src/contrib/base64enc_0.1-1.tar.gz' > Content type 'application/x-gzip' length 6296 bytes > opened URL > ================================================== > downloaded 6296 bytes > > [,1] [,2] > [1,] "SomaticSignatures" "./SomaticSignatures_0.99.0.tar.gz" > [2,] "GenomicRanges" "./GenomicRanges_1.15.41.tar.gz" SNIP > [64,] "fail" "./fail_1.2.tar.gz" > [65,] "base64enc" "./base64enc_0.1-1.tar.gz" > > > install.packages(dir('.', pattern=".tar.gz$"), > repos=NULL, type="source") Your command says to install the packages as given, with no information about relation between packages. It fails on the first one (AnnotationDbi) because it has not yet installed dependencies. If you want a one-time, off-line installation, then 1. create a directory, e.g., /tmp/R3.1_Bioc2.14/src/contrib/ 2. download files into that directory 3. create a PACKAGES file to index the repository 4. install packages from your repository Here's what I did, entirely in R: ## 1. create repository repos <- "file:///tmp/R3.1_Bioc2.14" dest <- "/tmp/R3.1_Bioc2.14/src/contrib/" dir.create(dest, recursive=TRUE) ## 2. populate with relevant packages pdb <- available.packages(contrib.url(biocinstallRepos())) deps <- tools::package_dependencies("SomaticSignatures", db=pdb, recursive=TRUE) pkgs <- c("SomaticSignatures", deps$SomaticSignatures) download.packages(pkgs, dest, repos=biocinstallRepos(), type="source") ## 3. create a PACKAGES file tools::write_PACKAGES(dest) ## 4. install from repository install.packages("SomaticSignatures", repos=repos) However, it will usually be better to maintain a proper mirror of the Bioconductor repository, as outlined at http://bioconductor.org/about/mirrors/mirror-how-to/ For instance, to mirror the software only portion of the Bioconductor devel branch /tmp$ mkdir -p 2.14/bioc/src/contrib /tmp$ rsync -zrtlv --delete master.bioconductor.org::2.14/bioc/src/contrib /tmp/2.14/bioc/src/ Likely you would also mirror CRAN http://cran.r-project.org/mirror- howto.html following a similar scenario. You'd update these repositories regularly using the rsync linux command (which just downloads the changes, not the entire repository), and would install packages from them using install.packages("SomaticSignatures", repos="file:///tmp/2.14/bioc") Perhaps you would make your repositories available via a local http server. There are instructions in the 'R-admin' document http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a -package-repository > > now the summary of warning after this command i attached please see > Regards > Huma > > > > _______________________________________________ > 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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Provided you have installed R-devel and the necessary infrastructure as noted by Martin, and properly installed the appropriate biocLite utility with source("http://www.bioconductor.org/biocLite.R") you should proceed with biocLite, which will resolve all dependencies. I suspect you are trying to install the package that you downloaded as source, manually, using R CMD INSTALL. biocLite is provided to resolve the dependencies. [Note, in the transcript below, only a few packages are added to the request because I have already installed a number of the dependencies for other purposes.] > biocLite("SomaticSignatures") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.13.3), R version 3.1.0. Installing package(s) 'SomaticSignatures' also installing the dependencies 'gridBase', 'NMF', 'pcaMethods' trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz' Content type 'application/x-gzip' length 153373 bytes (149 Kb) opened URL ================================================== downloaded 149 Kb trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz' Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb trying URL ' http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1.53 .4.tar.gz ' Content type 'application/x-gzip' length 714560 bytes (697 Kb) opened URL ================================================== On Thu, Mar 27, 2014 at 4:01 PM, Huma Asif <humaasif79@yahoo.com> wrote: > Hi > Though i installed variant annotation and R vesion as suggested. every > package seems dependent on other like somatic > signature....mutationcontext..... variantannotation......GRanges....h5vc > package. > It seems impossible > I need to know is there any other package that can help in signatures > extraction from vcf files with out being dependent on R. > Regards > > > > >________________________________ > > From: Martin Morgan <mtmorgan@fhcrc.org> > >To: Huma Asif <humaasif79@yahoo.com>; Steve Lianoglou < > lianoglou.steve@gene.com> > >Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> > >Sent: Tuesday, March 25, 2014 5:24 PM > >Subject: Re: [BioC] SomaticSignatures > > > > > >On 03/25/2014 01:08 PM, Huma Asif wrote: > >> Hi, > >> i am using Ubuntu 12.04 on VM wareplayer > >> XXXXXXXXXXXXXXXXXXXXXXXXXXX > >> yes i downloaded source package > >> XXXXXXXXXXXXXXXXXXXXXX > >> > >> i have installed some of the packages that are required for > Somaticsignature > >> however i need help with these error during variantannotation > installation > >> > >> source("http://bioconductor.org/biocLite.R") > >> > biocLite() > >> Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies > >> 'BiocGenerics', 'DBI', 'RSQLite' > >> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > >> ERRORS during varriant annotation > >> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > >> ........................................................ > >> ERROR: configuration failed for package 'XML' > >> removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/XML' > >> > >> > >> Cannot find curl-config > >> ERROR: configuration failed for package 'RCurl' > >> * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/RCurl' > >> > >> ERROR: dependencies 'XML', 'RCurl' are not available for package > 'biomaRt' > >> * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/biomaRt' > > > >These are missing system (instead of R) dependencies; you'll need (be > sure to > >get the 'dev' versions) > > > > sudo apt-get install libxml2-dev > > sudo apt-get install libcurl4-openssl-dev > > > >> > >> samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory > > > >This is surprising, suggesting that you have a very minimal system. > You'll need > > > > sudo apt-get install zlib1g-dev > > > >I am not sure of the precise library versions. > > > >Martin > > > >> compilation terminated. > >> make: *** [R_init_Rsamtools.o] Error 1 > >> ERROR: compilation failed for package 'Rsamtools' > >> * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/Rsamtools' > >> > >> ERROR: dependencies 'XML', 'RCurl', 'Rsamtools' are not available for > package > >> 'rtracklayer' > >> * removing '/home/asif/R/i686-pc-linux-gnu- library/3.0/rtracklayer' > >> ERROR: dependencies 'rtracklayer', 'biomaRt', 'RCurl' are not available > for > >> package 'GenomicFeatures' > >> * removing '/home/asif/R/i686-pc-linux-gnu- library/3.0/GenomicFeatures' > >> ERROR: dependencies 'Rsamtools', 'GenomicFeatures', 'rtracklayer' are > not > >> available for package > >> > >> 'VariantAnnotation' > >> * removing > '/home/asif/R/i686-pc-linux-gnu-library/3.0/VariantAnnotation' > >> > >> > >> Warning messages: > >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'XML' had non-zero exit status > >> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'RCurl' had non-zero exit status > >> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'biomaRt' had non-zero exit status > >> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'Rsamtools' had non-zero exit status > >> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'rtracklayer' had non-zero exit status > >> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'GenomicFeatures' had non-zero exit status > >> 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > >> installation of package 'VariantAnnotation' had non-zero exit status > >> > >> > >> i am planning to install R-3.1.0 alpha and removing the current R > version > >> please give me the link for this R version > >> > >> > >> Do you think the packages installed will work with R-3.1.0 alpha > >> confused > >> > >> > >> > >> > >> > >> > >> > >> > >> Regards > >> Huma > >> > >> > ------------------------------------------------------------------- ------------- > >> *From:* Martin Morgan <mtmorgan@fhcrc.org> > >> *To:* Steve Lianoglou <lianoglou.steve@gene.com>; Huma Asif > >> <humaasif79@yahoo.com> > >> *Cc:* "bioconductor@r-project.org list" <bioconductor@r-project.org> > > >> *Sent:* Monday, March 24, 2014 4:44 PM > >> *Subject:* Re: [BioC] SomaticSignatures > >> > >> On 03/24/2014 12:12 PM, Steve Lianoglou wrote: > >> > If you insist on installing this package into your current > working > >> version of R > >> > (after you installed the dependent packages), you may be able to > do so if it > >> > doesn't depend on functionality coming in bioc2.14 that's not in > bioc2.13 > >> -- I > >> > have no idea of knowing the answer to that. > >> > >> Do not try to install a 'devel' version into your current R version. > >> > >> > >> > > >> > If I were you, I'd install a working version of R-devel and all > of the > >> packages > >> > from bioc2.14 -- which will happen automatically when you use > biocLite. > >> > >> > > >> > >> Not R-devel, but R-3.1.0 alpha, followed by the installation > instructions on > >> the > >> SomaticSignatures developer landing page. Do not attempt anything > more > >> elaborate. > >> > >> Martin > >> > >> -- > >> 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 > > > >> > >> > >> > > > > > >-- > >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]] > > > _______________________________________________ > 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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You'll have to administer R and ubuntu properly to make progress. You can have a look at http://ubuntuforums.org/showthread.php?t=1876552 for some relevant pointers on curl and you can follow that with further searches/installs of relevant infrastructure. On Tue, Mar 25, 2014 at 4:08 PM, Huma Asif <humaasif79@yahoo.com> wrote: > Hi, > i am using Ubuntu 12.04 on VM wareplayer > XXXXXXXXXXXXXXXXXXXXXXXXXXX > yes i downloaded source package > XXXXXXXXXXXXXXXXXXXXXX > > i have installed some of the packages that are required for > Somaticsignature however i need help with these error during > variantannotation installation > > > source("http://bioconductor.org/biocLite.R") > > biocLite() > > Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies > 'BiocGenerics', 'DBI', 'RSQLite' > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > ERRORS during varriant annotation > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > ........................................................ > ERROR: configuration failed for package 'XML' > removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/XML' > > > Cannot find curl-config > ERROR: configuration failed for package 'RCurl' > * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/RCurl' > > ERROR: dependencies 'XML', 'RCurl' are not available for package 'biomaRt' > * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/biomaRt' > > samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory > compilation terminated. > make: *** [R_init_Rsamtools.o] Error 1 > ERROR: compilation failed for package 'Rsamtools' > * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/Rsamtools' > > ERROR: dependencies 'XML', 'RCurl', 'Rsamtools' are not available for > package 'rtracklayer' > * removing '/home/asif/R/i686-pc-linux-gnu-library/3.0/rtracklayer' > ERROR: dependencies 'rtracklayer', 'biomaRt', 'RCurl' are not available > for package 'GenomicFeatures' > * removing '/home/asif/R/i686-pc-linux-gnu- library/3.0/GenomicFeatures' > ERROR: dependencies 'Rsamtools', 'GenomicFeatures', 'rtracklayer' are not > available for package > > 'VariantAnnotation' > * removing '/home/asif/R/i686-pc-linux-gnu- library/3.0/VariantAnnotation' > > > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'XML' had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'RCurl' had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'biomaRt' had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'Rsamtools' had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'rtracklayer' had non-zero exit status > 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'GenomicFeatures' had non-zero exit status > 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'VariantAnnotation' had non-zero exit status > > > i am planning to install R-3.1.0 alpha and removing the current R version > please give me the link for this R version > > > Do you think the packages installed will work with R-3.1.0 alpha > confused > > > > > > > > > Regards > Huma > > > >________________________________ > > From: Martin Morgan <mtmorgan@fhcrc.org> > >To: Steve Lianoglou <lianoglou.steve@gene.com>; Huma Asif < > humaasif79@yahoo.com> > >Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> > >Sent: Monday, March 24, 2014 4:44 PM > >Subject: Re: [BioC] SomaticSignatures > > > > > >On 03/24/2014 12:12 PM, Steve Lianoglou wrote: > >> If you insist on installing this package into your current working > version of R > >> (after you installed the dependent packages), you may be able to do so > if it > >> doesn't depend on functionality coming in bioc2.14 that's not in > bioc2.13 -- I > >> have no idea of knowing the answer to that. > > > >Do not try to install a 'devel' version into your current R version. > > > > > >> > >> If I were you, I'd install a working version of R-devel and all of the > packages > >> from bioc2.14 -- which will happen automatically when you use biocLite. > >> > > > >Not R-devel, but R-3.1.0 alpha, followed by the installation instructions > on the > >SomaticSignatures developer landing page. Do not attempt anything more > elaborate. > > > >Martin > > > >-- > >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]] > > > _______________________________________________ > 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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