Question: DEXSeq availability
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8.0 years ago by
Guest User12k
Guest User12k wrote:
I'm trying to install DEXSeq using the code that I have copied from many places: source("http://bioconductor.org/biocLite.R") biocLite("DEXSeq") The message I always receive following the second command is: Using R version 2.13.0, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "DEXSeq" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???DEXSeq??? is not available (for R version 2.13.0) I have also tried installing it using a zip file and get the following: Error: package 'Biobase' required by 'DEXSeq' could not be found In addition: Warning message: package 'DEXSeq' was built under R version 2.15.0 -- output of sessionInfo(): > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DEGseq_1.6.2 samr_2.0 matrixStats_0.2.2 [4] R.methodsS3_1.2.1 impute_1.26.0 ShortRead_1.10.4 [7] Rsamtools_1.4.2 lattice_0.19-23 Biostrings_2.20.1 [10] GenomicRanges_1.4.6 IRanges_1.10.4 gplots_2.8.0 [13] caTools_1.12 bitops_1.0-4.1 gdata_2.8.2 [16] gtools_2.6.2 qvalue_1.26.0 -- Sent via the guest posting facility at bioconductor.org.
dexseq • 773 views
ADD COMMENTlink modified 8.0 years ago by Dan Tenenbaum8.2k • written 8.0 years ago by Guest User12k
Answer: DEXSeq availability
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gravatar for Dan Tenenbaum
8.0 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi Wyatt, On Mon, Dec 5, 2011 at 12:58 PM, Wyatt McMahon [guest] <guest at="" bioconductor.org=""> wrote: > > I'm trying to install DEXSeq using the code that I have copied from many places: > source("http://bioconductor.org/biocLite.R") > biocLite("DEXSeq") > > The message I always receive following the second command is: > Using R version 2.13.0, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "DEXSeq" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ???DEXSeq??? is not available (for R version 2.13.0) > > I have also tried installing it using a zip file and get the following: > Error: package 'Biobase' required by 'DEXSeq' could not be found > In addition: Warning message: > package 'DEXSeq' was built under R version 2.15.0 > > ?-- output of sessionInfo(): > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > ?[1] DEGseq_1.6.2 ? ? ? ?samr_2.0 ? ? ? ? ? ?matrixStats_0.2.2 > ?[4] R.methodsS3_1.2.1 ? impute_1.26.0 ? ? ? ShortRead_1.10.4 > ?[7] Rsamtools_1.4.2 ? ? lattice_0.19-23 ? ? Biostrings_2.20.1 > [10] GenomicRanges_1.4.6 IRanges_1.10.4 ? ? ?gplots_2.8.0 > [13] caTools_1.12 ? ? ? ?bitops_1.0-4.1 ? ? ?gdata_2.8.2 > [16] gtools_2.6.2 ? ? ? ?qvalue_1.26.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The package DEXSeq did not exist in R 2.13. If you want to use it, you need to upgrade to R 2.14. Then the commands you tried above will work. Dan
ADD COMMENTlink written 8.0 years ago by Dan Tenenbaum8.2k
Thanks so much, Dan! I did that and now it works! -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Monday, December 05, 2011 4:02 PM To: Wyatt McMahon [guest] Cc: bioconductor at r-project.org; wmcmahon at vbi.vt.edu Subject: Re: [BioC] DEXSeq availability Hi Wyatt, On Mon, Dec 5, 2011 at 12:58 PM, Wyatt McMahon [guest] <guest at="" bioconductor.org=""> wrote: > > I'm trying to install DEXSeq using the code that I have copied from many > places: > source("http://bioconductor.org/biocLite.R") > biocLite("DEXSeq") > > The message I always receive following the second command is: > Using R version 2.13.0, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "DEXSeq" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ???DEXSeq??? is not available (for R version 2.13.0) > > I have also tried installing it using a zip file and get the following: > Error: package 'Biobase' required by 'DEXSeq' could not be found In > addition: Warning message: > package 'DEXSeq' was built under R version 2.15.0 > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United > States.1252 [3] LC_MONETARY=English_United States.1252 [4] > LC_NUMERIC=C [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods [8] base > > other attached packages: > [1] DEGseq_1.6.2 samr_2.0 matrixStats_0.2.2 > [4] R.methodsS3_1.2.1 impute_1.26.0 ShortRead_1.10.4 > [7] Rsamtools_1.4.2 lattice_0.19-23 Biostrings_2.20.1 [10] > GenomicRanges_1.4.6 IRanges_1.10.4 gplots_2.8.0 [13] caTools_1.12 > bitops_1.0-4.1 gdata_2.8.2 [16] gtools_2.6.2 qvalue_1.26.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor The package DEXSeq did not exist in R 2.13. If you want to use it, you need to upgrade to R 2.14. Then the commands you tried above will work. Dan
ADD REPLYlink written 8.0 years ago by Wyatt McMahon20
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