similar to: bioinformatics repository?

Hi all, is there a function (or variable) I can use in a custom init script that identifies the init script name? i.e. I'm porting some init scripts from gentoo, where the $SVCNAME variable identifies the init script name within the script itself... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail:

Hi all, Is there a way to dump the current packages installed on a machine and use it do install/uninstall packages on other machines? I've configured one at install time but to speed up other installations I would like to install default packages and then install/uninstall some starting from my first machine configuration... thanks d PS Oh, I'm going to RTFM too... but I'm

Hi all, I'm migrating from Gentoo to CentOS... I'm experiencing a rather low performance in NFS r/w (as client). NFS server is solaris (which exports zfs volumes via nfs). The very same exports were mounted with the same parameters (auto,nosuid,exec) on gentoo and centos server (bot x86_64)... It happens that centos is 5-10 times slower either in read and write operations... Ok,

Dear R developers, I noticed a bug in the stats4 package, specifically in the confint method applied to ?mle? objects. In particular, when some ?fixed? parameters define the log likelihood, these parameters are stored within the mle object but they are not used by the ?confint" method, which retrieves their value from the global environment (whenever they still exist). Sample code: >

I was modifying a source to add OpenMP capabilities. I knew that gcc supports OpenMP since version 4.2, so I've compiled a recent (4.3.2) gcc and installed in my home directory, this because gcc shipped with CentOS 5.2 is 4.1. I've then noticed that my executable links /usr/lib64/libgomp.so, installed with gcc 4.1 from CentOS rpms... Is CentOS default compiler OpenMP ready? Does

I am planning to use ZFS on my Centos 5.2 systems. The data I am storing is very large text files where each file can range from 10M to 20G. I am very interested on the compression feature of ZFS, and it seems no other native Linux FS supports it. My question are: Is ZFS stable? How does it scale for very large filesytems, ie, 2TB to 9TB? How is the performance of fuse? I plan to use it on my

Is there a way to have an R program send an email? Something like this: address <- 'abc at d.com' text <- 'This is the email body' send.email(address, text) Thanks. FS

Hi everybody, this is a little OT. We are using Lighttpd as a webserver for Rails. Our problem is that when we rotate the logs everyday at the end of the process, lighttpd stops writing the logs. To solve this we have to restart the server manually each time. We use a common Debian, lighttpd-1.4.7, Rails 1.0 and fcgi-2.4.0. I have tracked the lighttpd bugs, and I haven''t found

Hi everyone, I did my homework and read the posting guideline :-) I want to eMail the results of a computing automatically. So I get the results (the parameters of a garch process) and I want to eMail them to another person. How can I do that? Thx ______________________________ Thomas Schwander MVV Energie Konzern-Risikocontrolling Telefon 0621 - 290-3115 Telefax 0621 - 290-3664 E-Mail:

Just a question, should it be possible to run bat files with wine. Basically the application is java, I know the java will run under windows. I also know that java will run under linux natively, but I am curious if this is possible to start under wine. I get wine: can't exec 'blue.bat': invalid exe file.

I'm trying to read some web tables directly into R. These are both genome sequencing projects (eukaryotes and metagenomes) from NCBI and look very similar; however, only the first one works. http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi I added ?dump=selected to the end of the url string to get a tab- delimited file (which is what happens

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Hi, > url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > download.file(url, tempfile()) trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' Error in download.file(url, tempfile()) : cannot open URL

Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following methods give the same results: f <- url("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", open="r") download.file("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", destfile=tempfile())

I am running R 2.0.0 on a SunOs 5.9 machine and using Oracle 8i.1.7.0.0 (enterprise edition) and when I try to load ROracle I receive the following error: "require(ROracle) Loading required package: ROracle Loading required package: DBI Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

Hi, May be you can try this: dat1New<-? dat1[!(duplicated(dat1$gene)|duplicated(dat1$gene,fromLast=TRUE)),] dat2<-dat1[duplicated(dat1$gene)|duplicated(dat1$gene,fromLast=TRUE),] ?lst1<-split(dat2,dat2$gene) dat3<-unsplit(lapply(lst1,function(x) {x1<- sum(apply(x[,6:32],2,function(y) y[1]>=y[2]));x2<- sum(apply(x[,6:32],2, function(y) y[1]<=y[2])); if(x1>x2) x[1,] else

Hi, I am trying to use a CGI service (Pubchem PUG) via RCurl and am running into a problem where the data must be supplied via POST - but I don't know the keyword for the argument. The data to be sent is an XML fragment. I can do this via the command line using curl: I save the XML string to a file called query.xml and then do curl -d @query.xml

Hi everyone, Now I read the posting guidelines again; COMPLETELY! ;-) I use Windows XP Professional, R 2.5.1 and I have Blat to send eMails out of R. Works perfect! Thank you for your help! Now I want to send an SMS out of R! Any idea how it could work? Could I send an eMail to a mobile phone number? Thank you Thomas [[alternative HTML version deleted]]

Hi, I wanted to download a file and did the following: --------------------------------------------------------- > fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > download.file(fileLink,'/geoDat') trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' ftp data connection made,

Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download using download.file("