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...lem in the past 3 months on this R installation, whereas some users had success before then. It could be that something on our system changed, but I am not an admin so I wouldn't know where to look. Can anyone help with this problem? ## A LOCAL INSTALLATION OF HAPLO.STATS APPEARS SUCCESSFUL [sinnwell at dnode0 rpack]$ R CMD INSTALL -l /home/sinnwell/rdir/tmplib haplo.stats * Installing *source* package 'haplo.stats' ... ** libs make: `haplo.stats.so' is up to date. ** R ** data ** demo ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages...

...ess how to fix this: System: Solaris 7, Software: R_1.7.1 for unix > R CMD INSTALL -l /Rdir/library haplo.stats_1.1.0.tar.gz -works like a charm-- no syntax errors, etc But problems are when I'm loading the library within R. > library(haplo.stats, lib.loc="/people/biostat3/sinnwell/Rdir/library") > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > "/people/biostat3/sinnwell/Rdir/library/haplo.stats/libs/haplo.stats.so": > ld.so.1: /opt/tools/R/current-version/lib/R/bin/R.bin: fatal: relocation...

I am on Solaris 7, using R_1.7.1 developing packages for both Splus and R. We have a working R-package for haplo.score and now converting to haplo.stats. R CMD INSTALL -l /people/biostat3/sinnwell/Rdir/library haplo.stats_1.1.0.tar.gz works like a charm-- as comparable to our working version of haplo.score. But problems are when I'm loading the library within R. Within my package I have three C files, one of which I believe is causing the dynamic library error below. > library(ha...

...d the data every time the library is loaded. Also considering something like: >if (<check for R using is.R()>) > data(example.data) > <run example> In the example but that would create confusion for users. Thanks for your suggestions. +--------------------------+ |Jason Sinnwell, M.S. | |Mayo Clinic, Rochester |

...ontains a method for analysis of genetic linkage with covariates by regression methods that use identity by descent (IBD) sharing probabilities for relative pairs. The methods account for correlations of IBD statistics for relative pairs within the same pedigree. The reference is: Schaid DJ, Sinnwell JP, Thibodeau SN. Testing Genetic Linkage with Relative Pairs and Covariates by Quasi-Likelihood Score Statistics. Submitted. Cheers, Jason Sinnwell ============================ Mayo Clinic, Rochester Division of Biostatistics ph: 507.284.3270 fax: 507.284.954...

...> </s-topics> using R CMD Sd2Rd would convert to: \name{my.function} \alias{my.function} \name{print.my.function} \alias{print.my.function} which is a syntax error. Rd format would understand it if the third line were not there. (R-exts 2.1.1) +--------------------------+ |Jason P. Sinnwell, M.S. | |Mayo Clinic, Rochester | |Health Sciences Research | |Division of Biostatistics | |Harwick 7-97 | |507.284.3270 | +--------------------------+

...exts 1.1.4: ..'exec/' could contain additional executables the package needs, ... This mechanism is currently used only by very few packages, and still experimental. Any help or referral to the proper documentation would be appreciated. Jason +--------------------------+ |Jason P. Sinnwell, M.S. | |Mayo Clinic, Rochester | |Health Sciences Research | |Division of Biostatistics | |Harwick 7-97 | |507.284.3270 | +--------------------------+

...ontains a method for analysis of genetic linkage with covariates by regression methods that use identity by descent (IBD) sharing probabilities for relative pairs. The methods account for correlations of IBD statistics for relative pairs within the same pedigree. The reference is: Schaid DJ, Sinnwell JP, Thibodeau SN. Testing Genetic Linkage with Relative Pairs and Covariates by Quasi-Likelihood Score Statistics. Submitted. Cheers, Jason Sinnwell ============================ Mayo Clinic, Rochester Division of Biostatistics ph: 507.284.3270 fax: 507.284.954...

...now handled with setupGeno o Add test suite with .R and .Rout.save files o Major update to user manual in doc/ o Suggest Harrell's rms package instead of Design for haplo.score with ordinal traits o Add NAMESPACE and NEWS files Cheers, -Jason Jason Sinnwell, MS | Division of Biomedical Statistics and Informatics | 507.284.3270 | sinnwell at mayo.edu Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | www.mayoclinic.org

...now handled with setupGeno o Add test suite with .R and .Rout.save files o Major update to user manual in doc/ o Suggest Harrell's rms package instead of Design for haplo.score with ordinal traits o Add NAMESPACE and NEWS files Cheers, -Jason Jason Sinnwell, MS | Division of Biomedical Statistics and Informatics | 507.284.3270 | sinnwell at mayo.edu Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | www.mayoclinic.org

...manual available as a vignette: http://cran.r-project.org/web/packages/pedgene/index.html The pedgene package performs gene-level kernel and burden association tests with disease status and continuous response for pedigree data, as described in our recent paper: Schaid, D. J., McDonnell, S. K., Sinnwell, J. P. and Thibodeau, S. N. (2013), Multiple Genetic Variant Association Testing by Collapsing and Kernel Methods With Pedigree or Population Structured Data. Genet. Epidemiol., 37: 409-418. doi: 10.1002/gepi.21727 LINK: http://onlinelibrary.wiley.com/doi/10.1002/gepi.21727/abstract We hav...

...manual available as a vignette: http://cran.r-project.org/web/packages/pedgene/index.html The pedgene package performs gene-level kernel and burden association tests with disease status and continuous response for pedigree data, as described in our recent paper: Schaid, D. J., McDonnell, S. K., Sinnwell, J. P. and Thibodeau, S. N. (2013), Multiple Genetic Variant Association Testing by Collapsing and Kernel Methods With Pedigree or Population Structured Data. Genet. Epidemiol., 37: 409-418. doi: 10.1002/gepi.21727 LINK: http://onlinelibrary.wiley.com/doi/10.1002/gepi.21727/abstract We hav...

..., now more robust * kinship matrices now implemented with Matrix package classes * utilities to trim the pedigree object with various criteria A vignette is available with vignette("pedigree") For details and updates, see: https://r-forge.r-project.org/projects/kinship2/ Best, Jason Sinnwell _______________________________________________ R-packages mailing list R-packages at r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages

..., now more robust * kinship matrices now implemented with Matrix package classes * utilities to trim the pedigree object with various criteria A vignette is available with vignette("pedigree") For details and updates, see: https://r-forge.r-project.org/projects/kinship2/ Best, Jason Sinnwell _______________________________________________ R-packages mailing list R-packages at r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages

...\name{} tag is written once (given the value of the first <s-topic>) and an \alias tag is written for each <s-topic> tag. Having multiple \name{} tags caused R CMD check to holler the following: * checking Rd files ... WARNING Rd files with duplicate 'name': /people/biostat3/sinnwell/Rdir/Make/haplo.stats/man/haplo.score.Rd These entries must be unique in an Rd file. I believe that the developers of Sd2Rd attempted to prevent this from happening. They use a variable named nalias (used as a Boolean and initialized to 0). If nalias is equal to 0 then the \name{} tag is written...

...tion. The method estimates the maximum likelihood interval sizes, and the speciation and extinction rates in each interval. Note that the method takes into account the whole phylogeny, in particular it accounts for the &quot;pull of the present&quot; effect. * trex (0.1) Jason P. Sinnwell http://crantastic.org/packages/trex The first stage is screening to detect rare variants in only cases. If the number of case-carriers of any rare variants exceeds a user-specified threshold, then additional cases and controls are genotyped for the detected variants and carrier status of...

First of all, this is my first post so please go easy if I'm a little off-topic. Just let me know nicely off-list. Thanks! As Mike already knows, I am currently trying to develop a plug-in for playing Shorten files over Audion on the Macintosh platform. When I proposed this to him to get some information on contacting the right people, he mentioned you guys and I need a little info.