search for: nih

What exactly are the current limitations for using -O4 to create shared libraries with llvm/llvm-gcc-4.2 2.5? I tried a build of xplor-nih at -O4 with llvm-gcc, llvm-g++ and llvm-gfortran. The build fails to link shared libraries with errors such as... Building xplor-nih for platform: Darwin_9_x86 [ -d /Users/howarth/xplor-nih-2.21/bin.Darwin_9_x86/ ] || mkdir /Users/howarth/xplor-nih-2.21/bin.Darwin_9_x86/ touch /Users/howarth/xplo...

...ul: how can I obtain a list C that contains all the members in the list B that are not in list A? This are lists of nanes, not numbers! Thank you Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov

...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 but I have a problem to use URI to retrieve that file, since URI can also contain characters, which should not be there according to http://www.faqs.org/rfcs/rfc2396.html I encountered problems with "[&...

Hi, Round(0.55,1)=0.5 Round(2.55,1)=2.6 Can this be right? Thanks, Ed [[alternative HTML version deleted]]

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 if you click the Save button on either page). > options(internet.info=0) ## this one works > x1<-url("h...

I'm not certain yet which commit in the last couple of days caused this, but the current llvm/dragonegg svn shows a major improvement in the runtime of the xplor-nih testsuite when xplor-nih is built with FSF gcc 4.6.1 and the dragonegg plugin at -O3 -ffast-math -funroll-loops. Previously the xplor-nih testsuite always executed in ~40 sec but now it is coming it at 34.5 sec which is about the same result seen for xplor-nih built with native FSF gcc 4.6.1. It w...

Hi how can I find, in a vector of characters, which is the most frequent one? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov

...ecause functions get called and therefore, the calling sequence matters. It?s just protecting you from yourself, but as someone pointed out, there?s a way to silence such notes. G From: Herv? Pag?s <hpages.on.github at gmail.com> Sent: Tuesday, February 6, 2024 2:40 PM To: Izmirlian, Grant (NIH/NCI) [E] <izmirlig at mail.nih.gov>; Duncan Murdoch <murdoch.duncan at gmail.com>; r-devel at r-project.org Subject: Re: [EXTERNAL] Re: [Rd] NOTE: multiple local function definitions for ?fun? with different formal arguments On 2/6/24 11:19, Izmirlian, Grant (NIH/NCI) [E] wrote: The n...

Is the new EH scheme completely compatible with the existing linker in Xcode 4.1? I am finding that today's changes break the ability to link xplor-nih with dragonegg under FSF gcc 4.6.2... de-g++46 -c thread.cc -O3 -ffast-math -funroll-loops -g -DX_MMAP_FLAGS=0 -DFORTRAN_INIT -fno-common -DDARWIN -D_REENTRANT -DNDEBUG -I/Users/howarth/xplor-nih-2.27/vmd/ -I/Users/howarth/xplor-nih-2.27/arch/Darwin_11_x86_64/include -I/Users/howarth/xplor-nih-...

...l the values below 0 go downwards, and all the positive values go upward. How can I make them all begin from the minimum pointing upwards? Thanks! Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov

...ction(mode) { if (mode == 1) fun <- function(a, b, ...) a*b else fun <- function(u, v, w) (u + v) / w fun } to make sure that toto() returns functions that accept the same minimal number of arguments. /Henrik On Tue, Feb 6, 2024 at 1:15?PM Izmirlian, Grant (NIH/NCI) [E] via R-devel <r-devel at r-project.org> wrote: > > Because functions get called and therefore, the calling sequence matters. It?s just protecting you from yourself, but as someone pointed out, there?s a way to silence such notes. > G > > > From: Herv? Pag?s <hpage...

...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 "http://pubchem.ncbi.nlm.nih.gov/pug/pug.cgi" I get the expected response. More importantly, the verbose option shows: > Accept: */* > Content-Length: 1227 > Content-Type: application/x-www-form-urlencoded However, when I try to do this via RCurl, the data doesn't seem to get sent: q <- "<...

...vector#x# = rnorm(100) x=x+1 } where each vector has, at its hand, instead of #x# a number which goes from 1 to 99. How can I do this? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov

Dear All, I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [....

...alculations", "data matrices", "data tables", and "CRAN", and I didn't find anything useful. Thank you all Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov

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/GDS1...

...ely to be related to Andy's SCEV-unroll-loops changes. --Owen On Sep 6, 2011, at 11:56 AM, Jack Howarth wrote: > I'm not certain yet which commit in the last couple of days caused this, > but the current llvm/dragonegg svn shows a major improvement in the runtime > of the xplor-nih testsuite when xplor-nih is built with FSF gcc 4.6.1 and the > dragonegg plugin at -O3 -ffast-math -funroll-loops. Previously the xplor-nih > testsuite always executed in ~40 sec but now it is coming it at 34.5 sec which > is about the same result seen for xplor-nih built with native FSF...

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 'ftp://ftp.ncbi.nlm.nih...

Has the Levene test of homogeneity of variance been implemented in any library in R? Thanks, Maurice Haynes National Institute of Child Health and Human Development Child and Family Research Section 6705 Rockledge Drive Bethesda, MD 20892 Voice: 301-496-8180 Fax: 301-496-2766 E-Mail: mh192j at nih.gov

...colums do not appear to have the first row as header. How can I do to have all the newly created columns have their first row as a header? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov