similar to: DESeq package install error

Dear list, How can I detect a package is installed or not? If not, then install it. For example, in a script, I want to check the package DESeq is installed or not. If not, then I will using this script to install it. source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq") The pseudo script would be like this: try: library("DESeq") catch:

Hello, I have RNAseq data, which I am trying to analyze with DESeq. My file (tab delimited .txt) appears to be correct: >head(myfile) VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a ENSG00000253101 0 0 0 0 0 0 ENSG00000223972 0 0 0 0 0 0... However, when I try to analyze the data with >cds <-

To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by > (.packages(all.available=TRUE)) if installed in the R library. Thanks Hermann

Hi, I am new to bioconductor, trying to install KEGGSOAP package, but got warnings() when installing and error message when trying to load the package, can anyone suggest what went wrong? many thanks John > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("KEGGSOAP") BioC_mirror:

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Hi, I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the relevant lines: sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

Hi All, I posted this on the bioconductor list and didn't get a response there, so I'm hoping someone here can help. I don't know a heck of a lot about R, so I apologize if this seems like a trivial issue. This error comes up when trying to install the bioconductor globaltest package. Any clues? Thanks! Rusty -----Original Message----- From: bioconductor-bounces at r-project.org

Hi all, i'm just starting out with LLVM (although i've been observing its evolution since that first release some years ago :) I would like to develop a backend for a generic assembly-like language, called NAC (N-Address Code). More info on NAC can be found here: http://www.nkavvadias.com/hercules/nac-refman.html (HTML) http://www.nkavvadias.com/hercules/nac-refman.pdf (PDF) You

Hi, I am trying to set up a SAMBA PDC using LDAP for authentication. I am using this document as a guide: http://download.gna.org/smbldap-tools/docs/samba-ldap-howto/ SAMBA and openldap are running on the same machine for R&D purposes and I am using the following software: OpenSuSE 10.3 samba-3.0.26a-3 openldap2-2.3.37-6 smbldap-tools-0.9.2 I have configured slapd.conf:

On Thu, Jan 24, 2013 at 12:46 PM, <nkavv at physics.auth.gr> wrote: > Hi all, > > i'm just starting out with LLVM (although i've been observing its evolution > since that first release some years ago :) > > I would like to develop a backend for a generic assembly-like language, > called NAC (N-Address Code). More info on NAC can be found here: >

Hello, I'm trying to install KEGGSOAP with bioconductor but i'm facing this problem: /> biocLite("KEGGSOAP") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'KEGGSOAP' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/KEGGSOAP_1.30.0.tar.gz' Content type

Hello R experts: I need a developer version of a Bioconductor library. > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 When I try to useDevel it fails. I've removed packages and again loaded but I get the same error message. remove.packages("BiocInstaller")

Hello, I am trying to install SJava but I haven't been able to complete it successfully. I have tried to install it from bioconductor using the followin code and got the following output: > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("SJava") Using R version 2.12.2, biocinstall

Hello, I have the fellowing problem and I am thankful for any advice! Regards, Samuel ################################################################ >   source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). >     biocLite("SSPA") Using R version 2.11.0, biocinstall version 2.6.7. Installing

I've asked a question in the BioConductor list about package management. My solution depends on your answer to the following question. Are installed R packages "relocatable"? I mean relocatable in the same sense that files in a RedHat RPM file might be "relocatable" after compiling (http://www.rpm.org/max-rpm/ch-rpm-reloc.html). This allows one to build a package as the

I currently set the Bioconductor repository in my .Rprofile using this code (which needs editing for every version number change of Bioconductor): # Choose repositories repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", CRANextra="http://www.stats.ox.ac.uk/pub/RWin",

Hi I am trying to install a package (bioconductor) but every time I try to install it I get this message: source("http://bioconductor.org/biocLite.R") Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 'lib = "C:/Program Files/R/R-3.0.0/library"' is not writable Error in

On Thu, Jan 24, 2013 at 7:20 AM, Ahmed Bougacha <ahmed.bougacha at gmail.com>wrote: > On Thu, Jan 24, 2013 at 12:46 PM, <nkavv at physics.auth.gr> wrote: > > Hi all, > > > > i'm just starting out with LLVM (although i've been observing its > evolution > > since that first release some years ago :) > > > > I would like to develop a

Hello, Sorry if this question has been posted before but could't find out exactly an answer to the question.... I'm doing bioinformatics and doing small RNA sequencing that make use of packages such as DESeq and EDGE. For those familiar with this data you will notice that you end up having large matrices with millions of entries. So i guess many people might be facing the same problem

centos.mirror.nac.net is out of sync (at least for updates) http://centos.mirror.nac.net/5.3/updates/x86_64/RPMS/ vs http://ftp.osuosl.org/pub/centos/5.3/updates/x86_64/RPMS/ this is what is causing the nss/nss-devel error when doing a yum update Transaction Check Error: package nss-3.12.2.0-4.el5.centos (which is newer than nss-3.12.2.0-2.el5.centos) is already installed Kingsly --