From paumarc at gmail.com Mon Nov 24 08:53:21 2014 From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=) Date: Mon, 24 Nov 2014 14:53:21 +0100 Subject: [Bio-Linux] problem with bioconductor Message-ID: Hy everybody i have aproblem with bioconductor packages. I'm trying to use some databases as hgu95av2.db with it, when I install it, the package org.Hs.eg.db is also required. When I install it R gives an error Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: match.arg(synchronous, c("off", "normal", "full")) error: 'arg' must be NULL or a character vector Error: package ?org.Hs.eg.db? could not be loaded I have been looking at bioconductor site and it seems that the problem comes because i have an old R or sql version, Nevertheless i have the R version that comes with the last biolinux distribution R version 3.1.2 what can I do (it worked before i update biolinux last September) thanks Pau Marc Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From hwh at u.arizona.edu Wed Nov 26 10:15:08 2014 From: hwh at u.arizona.edu (Hans-Werner Herrmann) Date: Wed, 26 Nov 2014 08:15:08 -0700 Subject: [Bio-Linux] BioLinux 8.0 cannot connect to windows file server Message-ID: <5475EE7C.6070704@u.arizona.edu> I am running a server with BioLinux 8.0 and am trying to access our Windows file server through "Connect to server..." every time I enter smb:// I get a message saying "This file server type is not recognized" and the Connect botton is grayed out. Can you help with this? -- Hans-Werner Herrmann, PhD School of Plant Sciences Joint Appointments with School of Natural Resources and the Environment and the Department of Soil, Water and Environmental Science University of Arizona hwh at u.arizona.edu (520)780-1440 From tony.travis at abdn.ac.uk Wed Nov 26 11:17:36 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 26 Nov 2014 16:17:36 +0000 Subject: [Bio-Linux] BioLinux 8.0 cannot connect to windows file server In-Reply-To: <5475EE7C.6070704@u.arizona.edu> References: <5475EE7C.6070704@u.arizona.edu> Message-ID: <5475FD20.1050100@abdn.ac.uk> On 26/11/14 15:15, Hans-Werner Herrmann wrote: > I am running a server with BioLinux 8.0 and am trying to access our > Windows file server through "Connect to server..." every time I enter > smb:// I get a message saying "This file server type is not recognized" > and the Connect botton is grayed out. Can you help with this? Hi, Hans-Werner. I can connect to Windows using Nautilus "connect to server" OK, but the server is NOT in an NT domain. I suspect that your problem is the Windows server you are trying to access is using NT domain security and it won't let you in unless your Bio-Linux machine joins the NT domain. You could, instead, use cifs to connect and this might be a better solution because it means the files are accessible to any program. I put a line like this in /etc/fstab: > //windows-server /share cifs noauto,credentials=filename 0 0 Where: //windows-server is DNS name of your Windows server /share is the name of the Windows share you want to access cifs is the filesystem type noauto means don't automatically mount it when booting Linux credentials is a file containing the Windows login credentials Please note that the credentials file MUST be well protected(!). You can debug the connection using "smbclient" - Try: smbclient -L servername [Just press enter when asked for a password] HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Wed Nov 26 11:20:30 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 26 Nov 2014 16:20:30 +0000 Subject: [Bio-Linux] BioLinux 8.0 cannot connect to windows file server In-Reply-To: <5475EE7C.6070704@u.arizona.edu> References: <5475EE7C.6070704@u.arizona.edu> Message-ID: <1417018830.9614.54.camel@wllt1771.nerc-wallingford.ac.uk> Hi Hans-Werner, Firstly, please ensure the packages gvfs-backends and cifs-utils are both installed on the machine. Secondly, the fact that Bio-Linux 8 is running as a server implies you are connecting in to it remotely, I guess? Via x2go or via "ssh -X", maybe? Depending how you log on, you may not have a valid DBUS session, which is a thing that the "Connect to server" feature needs. In any case, try running this command in a terminal: dbus-launch nautilus & Then use "connect to server" in this window. Does that work? Alternatively if your fileserver isn't going anywhere you can just connect it permanently as a mounted filesystem, using the mount.cifs program in the cifs-utils package. This is the old-school way and avoids DBUS but requires using 'sudo'. I'll not go into the details of that but see the mount.cifs and fstab manpages for guidance. Cheers, TIM On Wed, 2014-11-26 at 15:15 +0000, Hans-Werner Herrmann wrote: > I am running a server with BioLinux 8.0 and am trying to access our > Windows file server through "Connect to server..." every time I enter > smb:// I get a message saying "This file server type is not recognized" > and the Connect botton is grayed out. Can you help with this? > -- 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