Hi, My server is running Debian and the most stable version of R for Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0" to install a backport version of R but that command just upgraded it to R 3.1.1. I don't know why it installed 3.1.1 instead of 3.1.0? I have 2 software that I would like to run on my server: ChAMP and MeDIPS. It seems that ChAMP will not run on R 2.1.5 but is fine with R 3.1.1. The reverse is true for MeDIPS. I was told by someone that a compromise is to install R 3.1.0. I have tried to force Synaptic Package Manager to install R 3.1.0 by following the instructions on this webpage: askubuntu.com/questions/292314/how-to-downgrade-packages-on-ubuntu but no matter which mirror I use, I am told by Synaptic Package Manager that it cannot install R3.1.0 because of broken packages. I have tried to use Synaptic Package Manager to fix the packages but it doesn't work. So my question is: 1) Can anyone suggest a way to downgrade to a working R 3.1.0? Maybe through a command line instruction or 2) Is there a way to get MeDIPS to work with R3.1.1 Thanks in advance for any help. Allen

----- Original Message ----- > From: "Chong Kim San Allen" <patcksa at="" nus.edu.sg=""> > To: bioconductor at r-project.org > Sent: Tuesday, August 12, 2014 10:43:16 PM > Subject: [BioC] Downgrading R to an older version > > Hi, > My server is running Debian and the most stable version of R for > Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0" > to install a backport version of R but that command just upgraded it > to R 3.1.1. I don't know why it installed 3.1.1 instead of 3.1.0? > > I have 2 software that I would like to run on my server: ChAMP and > MeDIPS. It seems that ChAMP will not run on R 2.1.5 but is fine with > R 3.1.1. The reverse is true for MeDIPS. I was told by someone that > a compromise is to install R 3.1.0. MeDIPS will run fine on R-3.1.1. If it's not working for you, please send the error message you are getting (and the line that causes it) and the output of the sessionInfo() command. > > I have tried to force Synaptic Package Manager to install R 3.1.0 by > following the instructions on this webpage: > > askubuntu.com/questions/292314/how-to-downgrade-packages-on-ubuntu > > but no matter which mirror I use, I am told by Synaptic Package > Manager that it cannot install R3.1.0 because of broken packages. I > have tried to use Synaptic Package Manager to fix the packages but > it doesn't work. > > So my question is: > > 1) Can anyone suggest a way to downgrade to a working R 3.1.0? Maybe > through a command line instruction > or > 2) Is there a way to get MeDIPS to work with R3.1.1 Again, let us know what problems you're having with MeDIPS on R-3.1.1. Dan > > Thanks in advance for any help. > > Allen > _______________________________________________ > 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 >

Hi, On Tue, Aug 12, 2014 at 10:43 PM, Chong Kim San Allen <patcksa at="" nus.edu.sg=""> wrote: > Hi, > My server is running Debian and the most stable version of R for Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0" to install a backport version of R but that command just upgraded it to R 3.1.1. I don't know why it installed 3.1.1 instead of 3.1.0? > > I have 2 software that I would like to run on my server: ChAMP and MeDIPS. It seems that ChAMP will not run on R 2.1.5 but is fine with R 3.1.1. The reverse is true for MeDIPS. I was told by someone that a compromise is to install R 3.1.0. There really shouldn't be any difference between 3.1.1 and 3.1.0 -- which is to say that you should prefer to use the former. The bioconductor folks provide daily build reports for the package in the "release" and "devel" branch. "release" should be run using R 3.1.x (3.1.1), and their build system uses 3.1.1 to build these. Their reports suggest that everything is feng shui, so perhaps there's likely something not quite right with your server. Here are the build reports I'm talking about: http://bioconductor.org/checkResults/2.14/bioc-LATEST/ and you'll see that MeDIPS is being built fine. So, we'd need some more info from you to help sort you out. The error messages you get when you try to install MeDIPS via biocLite on your server would be a good place to start. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech

----- Original Message ----- > From: "Chong Kim San Allen" <patcksa at="" nus.edu.sg=""> > To: "Steve Lianoglou" <lianoglou.steve at="" gene.com="">, dtenenba at fhcrc.org > Cc: bioconductor at r-project.org > Sent: Wednesday, August 13, 2014 10:21:03 AM > Subject: RE: [BioC] Downgrading R to an older version > > Dear Dan, Steve, > Thanks for replying so quickly. > > Initially, I was getting an error message that MeDIPS needs an older > version of R. However, I decided to re-installed R 3.1.1 and then > tried installing MeDIPS again and it seems to have installed well > and is now running. > > I don't know what happened but I am just glad it is now working. > Probably you had somehow installed a version of MeDIPS that was meant for an earlier version of R/Bioconductor. Dan > Once again, thank you. > > Best. > Allen > > > ________________________________________ > From: mailinglist.honeypot at gmail.com [mailinglist.honeypot at gmail.com] > On Behalf Of Steve Lianoglou [lianoglou.steve at gene.com] > Sent: Wednesday, August 13, 2014 11:05 PM > To: Chong Kim San Allen > Cc: bioconductor at r-project.org > Subject: Re: [BioC] Downgrading R to an older version > > Hi, > > On Tue, Aug 12, 2014 at 10:43 PM, Chong Kim San Allen > <patcksa at="" nus.edu.sg=""> wrote: > > Hi, > > My server is running Debian and the most stable version of R for > > Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0" > > to install a backport version of R but that command just upgraded > > it to R 3.1.1. I don't know why it installed 3.1.1 instead of > > 3.1.0? > > > > I have 2 software that I would like to run on my server: ChAMP and > > MeDIPS. It seems that ChAMP will not run on R 2.1.5 but is fine > > with R 3.1.1. The reverse is true for MeDIPS. I was told by > > someone that a compromise is to install R 3.1.0. > > There really shouldn't be any difference between 3.1.1 and 3.1.0 -- > which is to say that you should prefer to use the former. > > The bioconductor folks provide daily build reports for the package in > the "release" and "devel" branch. > > "release" should be run using R 3.1.x (3.1.1), and their build system > uses 3.1.1 to build these. Their reports suggest that everything is > feng shui, so perhaps there's likely something not quite right with > your server. > > Here are the build reports I'm talking about: > > http://bioconductor.org/checkResults/2.14/bioc-LATEST/ > > and you'll see that MeDIPS is being built fine. > > So, we'd need some more info from you to help sort you out. The error > messages you get when you try to install MeDIPS via biocLite on your > server would be a good place to start. > > HTH, > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech >