Hi Ting-Yuan, Thanks a lot for your directions -- I've never had contact with creating packages so far. Creating a proper DESCRIPTION file did help indeed. Rainer Ting-Yuan Liu wrote: > Hi, Rainer, > > On Fri, 25 Nov 2005, Rainer Grohmann wrote: > > >>Hi All! >> >>I'm really new to bioconductor, so may this is a dumb question... >> >>So, I went through the AnnBuilder vignette, added my own data -- no >>problem. As a result, I get a directory with three sub-dirs (data, man, >>R), with some .rda-files in the data directory (the others are empty). >> >>The vignette says, that this is package may be installed as any other >>package. Now this is where my problems start. >> >>If I try to install it, the following happens: >> >>$ R CMD INSTALL -d tmp/R/myPkg >>WARNING: invalid package 'tmp/R/myPkg' >>'Rcmd INSTALL': in startdir= /home/rainer with tmpdir= /tmp/R.INSTALL.IjH8U0 >> lib= '/usr/local/lib/R/site-library', pkgs= '' >>ERROR: no packages specified >> >>I also tried to tar the dir, with the following result: >>$ R CMD INSTALL -d tmp/R/myPkg.tar.gz >>ERROR: cannot extract package from 'tmp/R/myPkg.tar.gz' >> >>Finally, I tried to check the package: >>$ R CMD check tmp/R/myPkg >>* checking for working latex ... OK >>* using log directory '/home/rainer/myPkg.Rcheck' >>* using R version 2.1.1, 2005-06-20 >>* checking for file 'myPkg/DESCRIPTION' ... NO >> >>So what to do? >> > > > Your package is not completed. You still need to provide a file called > "DESCRIPTION" in your package. This is why you got such a error message. > Please refer to the "Writing R Extensions" manual for more information. > > >>By the way, I installed bioconductor just this week using the biocLite.R >>script from the web. However, a very old version of Annbuilder was >>installed, which was in bioconductor 1.6. I upgraded it manually to >>1.8.0. Still, all other packages seem to be bioconductor 1.6 versions. >>Does that cause problems? How to upgrade to 1.7? >> >> > > > Do you notice that you are using R 2.1.1? The latest version of R is > 2.2.0. biocLite will get the suitable version of BioConductor for your > R. BioC 1.6 is for R 2.1.x, and BioC 1.7 is for R 2.2.x. You have to > upgrade your R to version 2.2.0 so that biocLite can install BioC 1.7 for > you. > > >>Thanks a lot in advance, >> >> Rainer >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > > While your package is completed, use "R CMD build" to build the source > package (*.tar.gz) and you can install it by "R CMD INSTALL *.tar.gz". > You can also use "R CMD check *.tar.gz" to see if you have any problem in > your package. > > HTH, > Ting-Yuan >