From danae_hazel at yahoo.co.uk Mon Mar 11 14:26:16 2013 From: danae_hazel at yahoo.co.uk (Danae Dodge) Date: Mon, 11 Mar 2013 18:26:16 +0000 (GMT) Subject: [Bio-Linux] Installing Plotrix in R Message-ID: <1363026376.16540.YahooMailClassic@web171703.mail.ir2.yahoo.com> Hello all, I've been trying to install the library Plotrix from R for awhile unsuccessfully. I first updated R (I'm using BioLinux on a USB) to see if Plotrix was included and then I set the R LIB environmental variable so I could do this: source("http://bioconductor.org/biocLite.R") biocLite("pkgname") ? but with replacing it with the web address for Plotrix on the R website to download directly (this being the website that I went to: http://cran.r-project.org/web/packages/plotrix/index.html So my command line is as follows: R CMD INSTALL /http://www.cran.r-project.org/web/packages/plotrix/plotrix_3.4-6.tar.gz But I keep getting a Warning message: invalid package followed by the url and an error telling me no package specified. So now I don't know how to download and install this package into R. Can anyone help? Thanks, Danae Dr Danae Dodge http://independent.academia.edu/DanaeDodge Skype: danaedodge -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmartins at pitt.edu Tue Mar 12 10:38:40 2013 From: jmartins at pitt.edu (Martinson, Jeremy James) Date: Tue, 12 Mar 2013 10:38:40 -0400 Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 Message-ID: <8F8CC874-D347-40E7-8F7E-8BB217724031@pitt.edu> Hi Is there a preferred method for installing the BL7 programs on top of an existing Ubuntu installation? I have a workstation in my lab, and the Bio-Linux install DVD simply will not boot on it, no matter what I try. I can boot it from a standard Ubuntu 12.10 DVD though, and I've installed that instead, so now I'm trying to get BL7 up and running. I'm following the instructions on http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository but I'm running into a few dependency issues. Also, I notice that there are several packages that are present in both the bio-linux and Launchpad repositories (for example, emboss, paml, and qiime) - which one takes precedence? Any pointers would be much appreciated. best regards Jeremy -- Dr. Jeremy Martinson University of Pittsburgh (412) 624-5646 jmartins at pitt.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From A.J.Pemberton at bham.ac.uk Tue Mar 12 11:05:14 2013 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Tue, 12 Mar 2013 15:05:14 +0000 Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 In-Reply-To: <8F8CC874-D347-40E7-8F7E-8BB217724031@pitt.edu> References: <8F8CC874-D347-40E7-8F7E-8BB217724031@pitt.edu> Message-ID: <5FAE4EF51F20774D9C21A133494A3FE0236473251F@LESMBX1.adf.bham.ac.uk> Jeremy, The dependency problems probably arise from the fact that the BL7 programs (the debs) are designed to run on Ubuntu 12.04 - the LTS version. Try installing that version, then follow the instructions. I was able to do this (also with Mint Maya (13)), Regards, Tony P. From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Martinson, Jeremy James Sent: 12 March 2013 14:39 To: Bio Linux NEBC Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 Hi Is there a preferred method for installing the BL7 programs on top of an existing Ubuntu installation? I have a workstation in my lab, and the Bio-Linux install DVD simply will not boot on it, no matter what I try. I can boot it from a standard Ubuntu 12.10 DVD though, and I've installed that instead, so now I'm trying to get BL7 up and running. I'm following the instructions on http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository but I'm running into a few dependency issues. Also, I notice that there are several packages that are present in both the bio-linux and Launchpad repositories (for example, emboss, paml, and qiime) - which one takes precedence? Any pointers would be much appreciated. best regards Jeremy -- Dr. Jeremy Martinson University of Pittsburgh (412) 624-5646 jmartins at pitt.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Mar 12 11:58:55 2013 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Tue, 12 Mar 2013 15:58:55 +0000 Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE0236473251F@LESMBX1.adf.bham.ac.uk> References: <8F8CC874-D347-40E7-8F7E-8BB217724031@pitt.edu>, <5FAE4EF51F20774D9C21A133494A3FE0236473251F@LESMBX1.adf.bham.ac.uk> Message-ID: <1DCCED50D0696A498958BA6B254456E222EE35ED2A@nerckwmb1.ad.nerc.ac.uk> hi, (apologies for lack of caps i'm typing one-handed with my right hand in a plaster cast) I do need to clean up the packages as there are some of the bio-linux-xxx ones that simply don't work in bl7, plus there are a few that will break bl6 that are installed on the dvd but are not yet in the repo. that should happen in the next week or so. but in general if you see both bio-linux-emboss and emboss, say, you should install both as the emboss package is the core package from debian-med and the bio-linux-emboss package adds some extra bits. you can find a full package manifest here, as well as the script to update from bl6 to bl7: http://nebc.nerc.ac.uk/downloads/bl7_only/ running the bl_do_update_to7.sh script on a vanilla ubuntu 12.04 has been tested and should turn the ubuntu installation into bl7 for you. i'm not sure how well it will work on a 12.10 release and i suspect a few packages will just refuse to install but i guess it wouldn't hurt to try if you are really keen to use 12.10. cheers, tim ________________________________________ From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Anthony Pemberton [A.J.Pemberton at bham.ac.uk] Sent: 12 March 2013 15:05 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 Jeremy, The dependency problems probably arise from the fact that the BL7 programs (the debs) are designed to run on Ubuntu 12.04 ? the LTS version. Try installing that version, then follow the instructions. I was able to do this (also with Mint Maya (13)), Regards, Tony P. From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Martinson, Jeremy James Sent: 12 March 2013 14:39 To: Bio Linux NEBC Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 Hi Is there a preferred method for installing the BL7 programs on top of an existing Ubuntu installation? I have a workstation in my lab, and the Bio-Linux install DVD simply will not boot on it, no matter what I try. I can boot it from a standard Ubuntu 12.10 DVD though, and I've installed that instead, so now I'm trying to get BL7 up and running. I'm following the instructions on http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository but I'm running into a few dependency issues. Also, I notice that there are several packages that are present in both the bio-linux and Launchpad repositories (for example, emboss, paml, and qiime) - which one takes precedence? Any pointers would be much appreciated. best regards Jeremy -- Dr. Jeremy Martinson University of Pittsburgh (412) 624-5646 jmartins at pitt.edu This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tbooth at ceh.ac.uk Wed Mar 13 05:59:27 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 13 Mar 2013 09:59:27 +0000 Subject: [Bio-Linux] Installing Plotrix in R In-Reply-To: <1363026376.16540.YahooMailClassic@web171703.mail.ir2.yahoo.com> References: <1363026376.16540.YahooMailClassic@web171703.mail.ir2.yahoo.com> Message-ID: <1363168767.3208.83.camel@balisaur> Hi Danae, On my machine, if I run "sudo R" and then: source("http://bioconductor.org/biocLite.R") biocLite("plotrix") It installs fine. There is no need to give the full URL to the tar.gz as biocLite knows how to find it. If this fails, could you please post the errors you see when running this command? Cheers, TIM On Mon, 2013-03-11 at 18:26 +0000, Danae Dodge wrote: > Hello all, > I've been trying to install the library Plotrix from R for awhile > unsuccessfully. I first updated R (I'm using BioLinux on a USB) to see > if Plotrix was included and then I set the R LIB environmental > variable so I could do this: > source("http://bioconductor.org/biocLite.R") > biocLite("pkgname") > > but with replacing it with the web address for Plotrix on the R > website to download directly > (this being the website that I went to: > http://cran.r-project.org/web/packages/plotrix/index.html > So my command line is as follows: > R CMD > INSTALL /http://www.cran.r-project.org/web/packages/plotrix/plotrix_3.4-6.tar.gz > > But I keep getting a Warning message: invalid package followed by the > url and an error telling me no package specified. > So now I don't know how to download and install this package into R. > Can anyone help? > > Thanks, > Danae > > > > > > Dr Danae Dodge > http://independent.academia.edu/DanaeDodge > Skype: danaedodge -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From gawbul at gmail.com Wed Mar 13 08:05:49 2013 From: gawbul at gmail.com (Steve Moss) Date: Wed, 13 Mar 2013 12:05:49 +0000 Subject: [Bio-Linux] Installing Plotrix in R (Danae Dodge) Message-ID: Dear Danae, The following worked for me from within an R session: install.packages("plotrix", dependencies=T) > If you need to do it from the command line, perhaps try download the package first? wget -c > http://star-www.st-andrews.ac.uk/cran/bin/macosx/leopard/contrib/2.15/plotrix_3.4-6.tgz > R CMD INSTALL plotrix_3.4-6.tgz > Kindest regards, Steve Moss http://about.me/gawbul On 12 March 2013 12:00, wrote: > Send Bio-Linux mailing list submissions to > bio-linux at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > or, via email, send a message with subject or body 'help' to > bio-linux-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-owner at nebclists.nerc.ac.uk > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-Linux digest..." > > > Today's Topics: > > 1. Installing Plotrix in R (Danae Dodge) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 11 Mar 2013 18:26:16 +0000 (GMT) > From: Danae Dodge > Subject: [Bio-Linux] Installing Plotrix in R > To: Bio Linux NEBC > Message-ID: > <1363026376.16540.YahooMailClassic at web171703.mail.ir2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > I've been trying to install the library Plotrix from R for awhile > unsuccessfully. I first updated R (I'm using BioLinux on a USB) to see if > Plotrix was included and then I set the R LIB environmental variable so I > could do this: > source("http://bioconductor.org/biocLite.R") > > biocLite("pkgname") > > ? > but with replacing it with the web address for Plotrix on the R website to > download directly > (this being the website that I went to: > http://cran.r-project.org/web/packages/plotrix/index.html > So my command line is as follows: > R CMD INSTALL / > http://www.cran.r-project.org/web/packages/plotrix/plotrix_3.4-6.tar.gz > > But I keep getting a Warning message: invalid package followed by the url > and an error telling me no package specified. > So now I don't know how to download and install this package into R. > Can anyone help? > > Thanks, > Danae > > > > > > Dr Danae Dodge > > http://independent.academia.edu/DanaeDodge > > Skype: danaedodge > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20130311/43ab98bf/attachment.html > > > > ------------------------------ > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > End of Bio-Linux Digest, Vol 55, Issue 1 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From P.L.M.Lee at swansea.ac.uk Wed Mar 13 08:18:44 2013 From: P.L.M.Lee at swansea.ac.uk (Lee P.L.M.) Date: Wed, 13 Mar 2013 12:18:44 -0000 Subject: [Bio-Linux] unsubscribe Message-ID: <7B320B507C445840BD72C998A0B871DB12AD4FC5@CCS-EXCHANGE1.brynmill.swan.ac.uk> Please unsubscribe me from biolinux mailist Thank you pat -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmartins at pitt.edu Wed Mar 13 16:12:00 2013 From: jmartins at pitt.edu (Martinson, Jeremy James) Date: Wed, 13 Mar 2013 16:12:00 -0400 Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 In-Reply-To: <1DCCED50D0696A498958BA6B254456E222EE35ED2A@nerckwmb1.ad.nerc.ac.uk> References: <8F8CC874-D347-40E7-8F7E-8BB217724031@pitt.edu> <5FAE4EF51F20774D9C21A133494A3FE0236473251F@LESMBX1.adf.bham.ac.uk> <1DCCED50D0696A498958BA6B254456E222EE35ED2A@nerckwmb1.ad.nerc.ac.uk> Message-ID: Thanks for your suggestions. I should have worked out that there would be some dependency differences between 12.04 and 12.10. In the end, I was able to get my BL7 DVD to boot properly using the NOMODESET switch in the installer, so I now have the official version up and running. cheers Jeremy On Mar 12, 2013, at 11:58 AM, "Booth, Timothy G." wrote: > hi, > > (apologies for lack of caps i'm typing one-handed with my right hand in a plaster cast) > > I do need to clean up the packages as there are some of the bio-linux-xxx ones that simply don't work in bl7, plus there are a few that will break bl6 that are installed on the dvd but are not yet in the repo. that should happen in the next week or so. but in general if you see both bio-linux-emboss and emboss, say, you should install both as the emboss package is the core package from debian-med and the bio-linux-emboss package adds some extra bits. > > you can find a full package manifest here, as well as the script to update from bl6 to bl7: > > http://nebc.nerc.ac.uk/downloads/bl7_only/ > > running the bl_do_update_to7.sh script on a vanilla ubuntu 12.04 has been tested and should turn the ubuntu installation into bl7 for you. i'm not sure how well it will work on a 12.10 release and i suspect a few packages will just refuse to install but i guess it wouldn't hurt to try if you are really keen to use 12.10. > > cheers, > > tim > > ________________________________________ > From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Anthony Pemberton [A.J.Pemberton at bham.ac.uk] > Sent: 12 March 2013 15:05 > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 > > Jeremy, > > The dependency problems probably arise from the fact that the BL7 programs (the debs) are designed to run on Ubuntu 12.04 ? the LTS version. Try installing that version, then follow the instructions. I was able to do this (also with Mint Maya (13)), > > Regards, > > Tony P. > > > From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Martinson, Jeremy James > Sent: 12 March 2013 14:39 > To: Bio Linux NEBC > Subject: [Bio-Linux] Installing Bio-Linux 7 over Ubuntu 12.10 > > Hi > > Is there a preferred method for installing the BL7 programs on top of an existing Ubuntu installation? I have a workstation in my lab, and the Bio-Linux install DVD simply will not boot on it, no matter what I try. I can boot it from a standard Ubuntu 12.10 DVD though, and I've installed that instead, so now I'm trying to get BL7 up and running. I'm following the instructions on http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository but I'm running into a few dependency issues. Also, I notice that there are several packages that are present in both the bio-linux and Launchpad repositories (for example, emboss, paml, and qiime) - which one takes precedence? Any pointers would be much appreciated. > > best regards > > Jeremy > > -- > Dr. Jeremy Martinson > University of Pittsburgh > (412) 624-5646 > jmartins at pitt.edu > > > This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Thu Mar 28 05:42:26 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 28 Mar 2013 09:42:26 +0000 Subject: [Bio-Linux] [Fwd: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu] Message-ID: <1364463746.3208.538.camel@balisaur> Dear Bio-Linux Users, The message below is relevant to anyone who uses R. The basic gist is that you have until 1st May to decide if you want to upgrade to the latest R 3.0.0 or stay with R 2.15 on your system for now. You will have to take some action either way. I'll prepare some specific instructions for Bio-Linux users when Michael releases more info but you should start to think about this now. This page lists the changes in version 3.0.0: http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html If you do not use R, or if you only use R as part of a larger package like Galaxy, this change will hopefully not trouble you. I will do some testing here to ensure there are no unexpected knock-on effects from the upgrade for non R users. Cheers, TIM -------- Forwarded Message -------- From: Michael Rutter Reply-to: "mar36 at psu.edu" To: r-sig-debian at r-project.org Subject: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu Date: Wed, 27 Mar 2013 20:08:16 +0000 This is a post I just added to my Ubuntu R Blog (http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/2013/03/moving-to-r-300-on-ubuntu.html). As you may (or may not) be aware of, R 3.0.0 is [scheduled to be released](http://www.r-project.org/) on April 3rd. Since this is a major release and there may be some growing pains (but I hope not) in the move 3.0.0, here is some information about how I will handle R 3.0.0 on CRAN and my PPAs for Ubuntu. **All packages must be rebuilt for R 3.0.0** Any installed packages you are currently using will have to be rebuilt using R 3.0.0. This could lead to some issues, especially is you are using the Ubuntu binaries on CRAN or my PPA. I will try to minimize these issues. **CRAN and RRutter PPA are now frozen to R 2.15.3 (with one exception)** Since many users would probably be alarmed to have production machines upgrade to R 3.0.0 without testing to see if any thing breaks, the packages on [CRAN](http://cran.us.r-project.org/bin/linux/ubuntu/) and the [RRutter PPA](https://launchpad.net/~marutter/+archive/rrutter) will not be updated anymore. This means R is frozen with version 2.15.3 and the packages available will not be updated on CRAN or the RRutter PPA for now. At some point, likely around May 1st, I will move CRAN and the RRutter PPA to version 3.0.0. This should give users plenty of time to remove those repositories from apt so the upgrades do not occur. I will warn everyone when I am about to do this. The one exception to this rule will be the forth coming Ubuntu 13.04 (Raring Ringtail). When I add this release to CRAN and the PPA, I will be using R 3.0.0 and packages built against 3.0.0. **R 3.0.0 and recommended packages will be available on RDev PPA** If you do want to upgrade R to 3.0.0, you can use my [RDdev PPA](https://launchpad.net/~marutter/+archive/rdev). This will have the latest version of R and the recommended packages built against it. Instructions on how to install the PPA are available at the [RDdev PPA](https://launchpad.net/~marutter/+archive/rdev) webpage. As of right now, only 12.10 (quantal) builds are available, but others will be added when bugs are worked out. Please, do not have the RDev PPA and (CRAN or RRutter PPA) enabled at the same time, as that could cause issues. **What about c2d4u?** Excellent question. **Stopping support for Hardy and Oneiric** Both Hardy (8.04) and Oneiric (11.10) are ending support in April 2013. Therefore, I will not be updating any version of R for these releases. I, for one, am happy to finally be able to rid myself of the albatross (or should I say heron) that is Hardy. I will not delete these files for a while, but there will be no further updates. Support for Lucid (10.04) will continue until April 2015 or until something becomes very broken. **Are you sure you don't have anything to say about c2d4u?** [c2d4u](https://launchpad.net/~marutter/+archive/c2d4u) is an ambitious project that houses over 1000 packages for R as Ubuntu binaries that can be installed via apt or synaptic. You should really check it out. It has great packages like RCpp and ggplot2, among others. My first priority will be is to build all the packages for Ubuntu 13.04 (Raring Ringtail) using R 3.0.0. After that is complete, I will start rebuilding the packages for 12.04 (Precise), the latest LTS, against 3.0.0. If I still have any patience left, I will convert the 12.10 (Quantal) packages over. If you have any questions, please email me. Michael -- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705