[AnnBuilder] How to use/load generated annotation packages
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@rainer-grohmann-1516
Last seen 9.6 years ago
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? 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? Thanks a lot in advance, Rainer
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@ting-yuan-liu-fhcrc-1221
Last seen 9.6 years ago
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
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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 >
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