Question: AnnotationDbi package only available for R 2.6.0 or higher version?
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gravatar for lidaof
12.3 years ago by
lidaof450
United States
lidaof450 wrote:
hi list, i want to make an annotation package for Medicago. i searched the mailing list and found AnnBuilder maybe help me solve this i found in the ABPrimer.pdf from bioconductor.org mentions AnnotationDbi as a attached package.i am wondering AnnotationDbi will as a requriement for AnnBuilder. so i use biocLite to install AnnBuilder,RSQLite,DBI,AnnotationDbi one by one the first 3 without problem but AnnotationDbi failed this is the wrong message and sessioninfo: > biocLite("AnnotationDbi") Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. Warning message: package 'AnnotationDbi' is not available in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > sessionInfo() R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: AnnBuilder annotate XML Biobase "1.14.0" "1.14.1" "1.9-0" "1.14.0" > library(RSQLite) Loading required package: DBI > sessionInfo() R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: RSQLite DBI AnnBuilder annotate XML Biobase "0.5-4" "0.2-3" "1.14.0" "1.14.1" "1.9-0" "1.14.0" Thanks for any response! Best! -- Daofeng Li,PhD Candidate China Agricultural University
ADD COMMENTlink modified 12.3 years ago by Sean Davis21k • written 12.3 years ago by lidaof450
Answer: AnnotationDbi package only available for R 2.6.0 or higher version?
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gravatar for Sean Davis
12.3 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
Daofeng Li wrote: > hi list, > > i want to make an annotation package for Medicago. > i searched the mailing list and found AnnBuilder maybe help me solve this > i found in the ABPrimer.pdf from bioconductor.org mentions > AnnotationDbi as a attached package.i am wondering AnnotationDbi will > as a requriement for AnnBuilder. > so i use biocLite to install AnnBuilder,RSQLite,DBI,AnnotationDbi one by one > the first 3 without problem > but AnnotationDbi failed AnnotationDbi is in development and is not needed for AnnBuilder 1.14.0, which is the version that is to be used for R-2.5.0. All one needs to do to install a particular package for bioconductor is to use biocLite('packagename'). In this case, biocLite('AnnBuilder') would have been all that was needed. As for ABPrimer.pdf, make sure that you are using the correct version of that document. In particular, you need that document to match the AnnBuilder version that you are using. The correct version for AnnBuilder 1.14.0 does not mention AnnotationDbi. Hope that helps. Sean
ADD COMMENTlink written 12.3 years ago by Sean Davis21k
Hi Sean, Thank you for reply! That helps! Best Li On 6/15/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > Daofeng Li wrote: > > hi list, > > > > i want to make an annotation package for Medicago. > > i searched the mailing list and found AnnBuilder maybe help me solve this > > i found in the ABPrimer.pdf from bioconductor.org mentions > > AnnotationDbi as a attached package.i am wondering AnnotationDbi will > > as a requriement for AnnBuilder. > > so i use biocLite to install AnnBuilder,RSQLite,DBI,AnnotationDbi one by one > > the first 3 without problem > > but AnnotationDbi failed > > AnnotationDbi is in development and is not needed for AnnBuilder 1.14.0, > which is the version that is to be used for R-2.5.0. > > All one needs to do to install a particular package for bioconductor is > to use biocLite('packagename'). In this case, biocLite('AnnBuilder') > would have been all that was needed. As for ABPrimer.pdf, make sure > that you are using the correct version of that document. In particular, > you need that document to match the AnnBuilder version that you are > using. The correct version for AnnBuilder 1.14.0 does not mention > AnnotationDbi. > > Hope that helps. > > Sean > -- Daofeng Li,PhD Candidate China Agricultural University
ADD REPLYlink written 12.3 years ago by lidaof450
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