Question: BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
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I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems: The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio. The second is a bit more problematic. I have been able to follow the vignette without too many problems up until Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioconductor.org/packages/devel/data/annotat ion/html/BSgenome.Dmelanogaster.UCSC.dm3.html) and by entering the following code: >source("http://bioconductor.org/biocLite.R") >biocLite("BSgenome.Dmelanogaster.UCSC.dm3") However, when I try to load the library, I get the following: > library(BSgenome.Dmelanogaster.UCSC.dm3) Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before R 3.0.0: please re-install it The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette. Any advice on either of these two issues, but particularly the second, would be greatly appreciated. Sean -- output of sessionInfo(): > sessionInfo() R Under development (unstable) (2013-02-21 r62017) Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biostrings_2.27.11 [2] IntermediateSequenceAnalysis2013_0.1.1 [3] SequenceAnalysisData_0.1.4 [4] edgeR_3.1.4 [5] limma_3.15.14 [6] GenomicFeatures_1.11.11 [7] AnnotationDbi_1.21.10 [8] Biobase_2.19.2 [9] GenomicRanges_1.11.30 [10] IRanges_1.17.35 [11] BiocGenerics_0.5.6 loaded via a namespace (and not attached): [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9 [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 > -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 6.8 years ago by Dan Tenenbaum8.2k • written 6.8 years ago by Guest User12k
Answer: BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
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gravatar for Dan Tenenbaum
6.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi Sean, On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at="" bioconductor.org=""> wrote: > > I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). > > I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems: > > The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio. > > The second is a bit more problematic. I have been able to follow the vignette without too many problems up until > Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioconductor.org/packages/devel/data/annotat ion/html/BSgenome.Dmelanogaster.UCSC.dm3.html) and by entering the following code: > >>source("http://bioconductor.org/biocLite.R") >>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") > > However, when I try to load the library, I get the following: > >> library(BSgenome.Dmelanogaster.UCSC.dm3) > Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before R 3.0.0: please re-install it > > The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette. > > Any advice on either of these two issues, but particularly the second, would be greatly appreciated. > Try this: biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") As for RStudio, I'm not sure, what is your OS and output of sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that the first R in your path is R-devel. Dan > Sean > > -- output of sessionInfo(): > >> sessionInfo() > R Under development (unstable) (2013-02-21 r62017) > Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Biostrings_2.27.11 > [2] IntermediateSequenceAnalysis2013_0.1.1 > [3] SequenceAnalysisData_0.1.4 > [4] edgeR_3.1.4 > [5] limma_3.15.14 > [6] GenomicFeatures_1.11.11 > [7] AnnotationDbi_1.21.10 > [8] Biobase_2.19.2 > [9] GenomicRanges_1.11.30 > [10] IRanges_1.17.35 > [11] BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 > [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9 > [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 >> > > -- > 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
ADD COMMENTlink written 6.8 years ago by Dan Tenenbaum8.2k
Hi Dan, Was the bug you reported regarding recent Rstudio-server and R-devel (3.0) builds resolved? thanks, --t On Thu, Feb 28, 2013 at 1:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Sean, > > > On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest@bioconductor.org> > wrote: > > > > I am trying to get myself more familiar with Bioconductor, so I have > been walking through the vignette of the 2013 Intermediate R/Bioconductor > for Sequence Analysis course offered earlier this month (February 2013). > (Link to course page and vignette: > http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). > > > > I have installed R 3.0 and Bioconductor 2.12 as per the instructions in > the vignette. I now have two problems: > > > > The first seems relatively minor: I cannot seem to get RStudio to open R > 3.0. I simply get a message that says that "The R session had a fatal > error." I can open R using its own GUI, but it would be nice to work within > RStudio. > > > > The second is a bit more problematic. I have been able to follow the > vignette without too many problems up until > > Chapter 5 "Strings and Reads". The exercise has you load the > BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the > package using the provided link to the development version of the > Drosophila genome ( > http://bioconductor.org/packages/devel/data/annotation/html/BSgenome .Dmelanogaster.UCSC.dm3.html) > and by entering the following code: > > > >>source("http://bioconductor.org/biocLite.R") > >>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") > > > > However, when I try to load the library, I get the following: > > > >> library(BSgenome.Dmelanogaster.UCSC.dm3) > > Error: package ‘BSgenome.Dmelanogaster.UCSC.dm3’ was built before R > 3.0.0: please re-install it > > > > The library installs on earlier releases of R, but I cannot convince it > to run on R 3.0 where I can make use of the current vignette. > > > > Any advice on either of these two issues, but particularly the second, > would be greatly appreciated. > > > > Try this: > biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") > > As for RStudio, I'm not sure, what is your OS and output of > sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that > the first R in your path is R-devel. > > Dan > > > > Sean > > > > -- output of sessionInfo(): > > > >> sessionInfo() > > R Under development (unstable) (2013-02-21 r62017) > > Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] Biostrings_2.27.11 > > [2] IntermediateSequenceAnalysis2013_0.1.1 > > [3] SequenceAnalysisData_0.1.4 > > [4] edgeR_3.1.4 > > [5] limma_3.15.14 > > [6] GenomicFeatures_1.11.11 > > [7] AnnotationDbi_1.21.10 > > [8] Biobase_2.19.2 > > [9] GenomicRanges_1.11.30 > > [10] IRanges_1.17.35 > > [11] BiocGenerics_0.5.6 > > > > loaded via a namespace (and not attached): > > [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 > > [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 > rtracklayer_1.19.9 > > [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 > zlibbioc_1.5.0 > >> > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Tim Triche4.2k
On Thu, Feb 28, 2013 at 1:54 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > Hi Dan, > > Was the bug you reported regarding recent Rstudio-server and R-devel (3.0) > builds resolved? > Not yet as far as I know, I hope to see an update here soon: http://support.rstudio.org/help/discussions/problems/4946-rstudio- server-broken-with-recent-r-devel Dan > thanks, > > --t > > > > On Thu, Feb 28, 2013 at 1:45 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> Hi Sean, >> >> >> On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at="" bioconductor.org=""> >> wrote: >> > >> > I am trying to get myself more familiar with Bioconductor, so I have >> > been walking through the vignette of the 2013 Intermediate R/Bioconductor >> > for Sequence Analysis course offered earlier this month (February 2013). >> > (Link to course page and vignette: >> > http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). >> > >> > I have installed R 3.0 and Bioconductor 2.12 as per the instructions in >> > the vignette. I now have two problems: >> > >> > The first seems relatively minor: I cannot seem to get RStudio to open R >> > 3.0. I simply get a message that says that "The R session had a fatal >> > error." I can open R using its own GUI, but it would be nice to work within >> > RStudio. >> > >> > The second is a bit more problematic. I have been able to follow the >> > vignette without too many problems up until >> > Chapter 5 "Strings and Reads". The exercise has you load the >> > BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the >> > package using the provided link to the development version of the Drosophila >> > genome >> > (http://bioconductor.org/packages/devel/data/annotation/html/BSge nome.Dmelanogaster.UCSC.dm3.html) >> > and by entering the following code: >> > >> >>source("http://bioconductor.org/biocLite.R") >> >>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") >> > >> > However, when I try to load the library, I get the following: >> > >> >> library(BSgenome.Dmelanogaster.UCSC.dm3) >> > Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before R >> > 3.0.0: please re-install it >> > >> > The library installs on earlier releases of R, but I cannot convince it >> > to run on R 3.0 where I can make use of the current vignette. >> > >> > Any advice on either of these two issues, but particularly the second, >> > would be greatly appreciated. >> > >> >> Try this: >> biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") >> >> As for RStudio, I'm not sure, what is your OS and output of >> sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that >> the first R in your path is R-devel. >> >> Dan >> >> >> > Sean >> > >> > -- output of sessionInfo(): >> > >> >> sessionInfo() >> > R Under development (unstable) (2013-02-21 r62017) >> > Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods >> > [8] base >> > >> > other attached packages: >> > [1] Biostrings_2.27.11 >> > [2] IntermediateSequenceAnalysis2013_0.1.1 >> > [3] SequenceAnalysisData_0.1.4 >> > [4] edgeR_3.1.4 >> > [5] limma_3.15.14 >> > [6] GenomicFeatures_1.11.11 >> > [7] AnnotationDbi_1.21.10 >> > [8] Biobase_2.19.2 >> > [9] GenomicRanges_1.11.30 >> > [10] IRanges_1.17.35 >> > [11] BiocGenerics_0.5.6 >> > >> > loaded via a namespace (and not attached): >> > [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 >> > [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 >> > rtracklayer_1.19.9 >> > [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 >> > zlibbioc_1.5.0 >> >> >> > >> > -- >> > 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 >> >> _______________________________________________ >> 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 > > > > > -- > A model is a lie that helps you see the truth. > > Howard Skipper
ADD REPLYlink written 6.8 years ago by Dan Tenenbaum8.2k
Yeah I just tried it and no dice. At one point I looked into patching R-devel so that this wouldn't be such an issue but the scope of the extern/extern0 declarations foiled me. Plus Prof Ripley probably would not have accepted the patch anyways, as it's more of an Rstudio issue really thanks! --t On Thu, Feb 28, 2013 at 1:56 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Thu, Feb 28, 2013 at 1:54 PM, Tim Triche, Jr. <tim.triche@gmail.com> > wrote: > > Hi Dan, > > > > Was the bug you reported regarding recent Rstudio-server and R-devel > (3.0) > > builds resolved? > > > > Not yet as far as I know, I hope to see an update here soon: > > > http://support.rstudio.org/help/discussions/problems/4946-rstudio- server-broken-with-recent-r-devel > > Dan > > > > thanks, > > > > --t > > > > > > > > On Thu, Feb 28, 2013 at 1:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > >> > >> Hi Sean, > >> > >> > >> On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest@bioconductor.org> > >> wrote: > >> > > >> > I am trying to get myself more familiar with Bioconductor, so I have > >> > been walking through the vignette of the 2013 Intermediate > R/Bioconductor > >> > for Sequence Analysis course offered earlier this month (February > 2013). > >> > (Link to course page and vignette: > >> > > http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). > >> > > >> > I have installed R 3.0 and Bioconductor 2.12 as per the instructions > in > >> > the vignette. I now have two problems: > >> > > >> > The first seems relatively minor: I cannot seem to get RStudio to > open R > >> > 3.0. I simply get a message that says that "The R session had a fatal > >> > error." I can open R using its own GUI, but it would be nice to work > within > >> > RStudio. > >> > > >> > The second is a bit more problematic. I have been able to follow the > >> > vignette without too many problems up until > >> > Chapter 5 "Strings and Reads". The exercise has you load the > >> > BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download > the > >> > package using the provided link to the development version of the > Drosophila > >> > genome > >> > ( > http://bioconductor.org/packages/devel/data/annotation/html/BSgenome .Dmelanogaster.UCSC.dm3.html > ) > >> > and by entering the following code: > >> > > >> >>source("http://bioconductor.org/biocLite.R") > >> >>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") > >> > > >> > However, when I try to load the library, I get the following: > >> > > >> >> library(BSgenome.Dmelanogaster.UCSC.dm3) > >> > Error: package ‘BSgenome.Dmelanogaster.UCSC.dm3’ was built before > R > >> > 3.0.0: please re-install it > >> > > >> > The library installs on earlier releases of R, but I cannot convince > it > >> > to run on R 3.0 where I can make use of the current vignette. > >> > > >> > Any advice on either of these two issues, but particularly the second, > >> > would be greatly appreciated. > >> > > >> > >> Try this: > >> biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") > >> > >> As for RStudio, I'm not sure, what is your OS and output of > >> sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that > >> the first R in your path is R-devel. > >> > >> Dan > >> > >> > >> > Sean > >> > > >> > -- output of sessionInfo(): > >> > > >> >> sessionInfo() > >> > R Under development (unstable) (2013-02-21 r62017) > >> > Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets > methods > >> > [8] base > >> > > >> > other attached packages: > >> > [1] Biostrings_2.27.11 > >> > [2] IntermediateSequenceAnalysis2013_0.1.1 > >> > [3] SequenceAnalysisData_0.1.4 > >> > [4] edgeR_3.1.4 > >> > [5] limma_3.15.14 > >> > [6] GenomicFeatures_1.11.11 > >> > [7] AnnotationDbi_1.21.10 > >> > [8] Biobase_2.19.2 > >> > [9] GenomicRanges_1.11.30 > >> > [10] IRanges_1.17.35 > >> > [11] BiocGenerics_0.5.6 > >> > > >> > loaded via a namespace (and not attached): > >> > [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 > DBI_0.2-5 > >> > [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 > >> > rtracklayer_1.19.9 > >> > [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 > >> > zlibbioc_1.5.0 > >> >> > >> > > >> > -- > >> > Sent via the guest posting facility at bioconductor.org. > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@r-project.org > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > -- > > A model is a lie that helps you see the truth. > > > > Howard Skipper > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Tim Triche4.2k
Hi Dan, Thanks for the biocLite tip, that seems to have gotten me past that particular hurdle. For the RStudio issue, I am running Windows 7, 64-bit. I will append my sessionInfo() again at the end. I had a previous version of R on this machine, 2.15.1. I tried installing the R-devel in parallel, but when that wasn't working I uninstalled it. Now I just have the R-devel version. To open RStudio, I have tried holding down the Ctrl key while opening. Here I have the option of selecting the 32-bit or the 64-bit version of R-devel. I have tried both with the same result, i.e. fatal error. Is there a way of checking to see if there is still some part of the previous version that is getting in the way? Thanks Sean > sessionInfo() R Under development (unstable) (2013-02-21 r62017) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.19 BSgenome_1.27.1 [3] BiocInstaller_1.9.6 Biostrings_2.27.11 [5] IntermediateSequenceAnalysis2013_0.1.1 SequenceAnalysisData_0.1.4 [7] edgeR_3.1.4 limma_3.15.14 [9] GenomicFeatures_1.11.11 AnnotationDbi_1.21.10 [11] Biobase_2.19.2 GenomicRanges_1.11.30 [13] IRanges_1.17.35 BiocGenerics_0.5.6 loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(c("biomaRt", "bitops", "DBI", "RCurl", "Rsamtools", "RSQLite", : DESCRIPTION file of package 'Rsamtools' is missing or broken > -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Thursday, February 28, 2013 1:46 PM To: Sean [guest] Cc: bioconductor at r-project.org; Taylor, Sean D Subject: Re: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0 Hi Sean, On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at="" bioconductor.org=""> wrote: > > I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). > > I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems: > > The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio. > > The second is a bit more problematic. I have been able to follow the > vignette without too many problems up until Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioco nductor.org/packages/devel/data/annotation/html/BSgenome.Dmelanogaster .UCSC.dm3.html) and by entering the following code: > >>source("http://bioconductor.org/biocLite.R") >>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") > > However, when I try to load the library, I get the following: > >> library(BSgenome.Dmelanogaster.UCSC.dm3) > Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before > R 3.0.0: please re-install it > > The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette. > > Any advice on either of these two issues, but particularly the second, would be greatly appreciated. > Try this: biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") As for RStudio, I'm not sure, what is your OS and output of sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that the first R in your path is R-devel. Dan > Sean > > -- output of sessionInfo(): > >> sessionInfo() > R Under development (unstable) (2013-02-21 r62017) > Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Biostrings_2.27.11 > [2] IntermediateSequenceAnalysis2013_0.1.1 > [3] SequenceAnalysisData_0.1.4 > [4] edgeR_3.1.4 > [5] limma_3.15.14 > [6] GenomicFeatures_1.11.11 > [7] AnnotationDbi_1.21.10 > [8] Biobase_2.19.2 > [9] GenomicRanges_1.11.30 > [10] IRanges_1.17.35 > [11] BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 > [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9 > [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 >> > > -- > 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
ADD REPLYlink written 6.8 years ago by Taylor, Sean D250
On Thu, Feb 28, 2013 at 2:33 PM, Taylor, Sean D <sdtaylor at="" fhcrc.org=""> wrote: > Hi Dan, > > Thanks for the biocLite tip, that seems to have gotten me past that particular hurdle. > > For the RStudio issue, I am running Windows 7, 64-bit. I will append my sessionInfo() again at the end. I had a previous version of R on this machine, 2.15.1. I tried installing the R-devel in parallel, but when that wasn't working I uninstalled it. Now I just have the R-devel version. To open RStudio, I have tried holding down the Ctrl key while opening. Here I have the option of selecting the 32-bit or the 64-bit version of R-devel. I have tried both with the same result, i.e. fatal error. Is there a way of checking to see if there is still some part of the previous version that is getting in the way? > At this point I think your best bet is to report the issue on RStudio's forums: http://support.rstudio.org/ > Thanks > Sean > >> sessionInfo() > R Under development (unstable) (2013-02-21 r62017) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.19 BSgenome_1.27.1 > [3] BiocInstaller_1.9.6 Biostrings_2.27.11 > [5] IntermediateSequenceAnalysis2013_0.1.1 SequenceAnalysisData_0.1.4 > [7] edgeR_3.1.4 limma_3.15.14 > [9] GenomicFeatures_1.11.11 AnnotationDbi_1.21.10 > [11] Biobase_2.19.2 GenomicRanges_1.11.30 > [13] IRanges_1.17.35 BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > Error in x[["Version"]] : subscript out of bounds > In addition: Warning message: > In FUN(c("biomaRt", "bitops", "DBI", "RCurl", "Rsamtools", "RSQLite", : > DESCRIPTION file of package 'Rsamtools' is missing or broken >> This is rather strange, though....this should not be happening. I might suggest completely removing your R installation and starting again from scratch, if that is practical. Dan > > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: Thursday, February 28, 2013 1:46 PM > To: Sean [guest] > Cc: bioconductor at r-project.org; Taylor, Sean D > Subject: Re: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0 > > Hi Sean, > > > On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at="" bioconductor.org=""> wrote: >> >> I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). >> >> I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems: >> >> The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio. >> >> The second is a bit more problematic. I have been able to follow the >> vignette without too many problems up until Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioco nductor.org/packages/devel/data/annotation/html/BSgenome.Dmelanogaster .UCSC.dm3.html) and by entering the following code: >> >>>source("http://bioconductor.org/biocLite.R") >>>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") >> >> However, when I try to load the library, I get the following: >> >>> library(BSgenome.Dmelanogaster.UCSC.dm3) >> Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before >> R 3.0.0: please re-install it >> >> The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette. >> >> Any advice on either of these two issues, but particularly the second, would be greatly appreciated. >> > > Try this: > biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") > > As for RStudio, I'm not sure, what is your OS and output of sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that the first R in your path is R-devel. > > Dan > > >> Sean >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R Under development (unstable) (2013-02-21 r62017) >> Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biostrings_2.27.11 >> [2] IntermediateSequenceAnalysis2013_0.1.1 >> [3] SequenceAnalysisData_0.1.4 >> [4] edgeR_3.1.4 >> [5] limma_3.15.14 >> [6] GenomicFeatures_1.11.11 >> [7] AnnotationDbi_1.21.10 >> [8] Biobase_2.19.2 >> [9] GenomicRanges_1.11.30 >> [10] IRanges_1.17.35 >> [11] BiocGenerics_0.5.6 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 >> [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9 >> [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 >>> >> >> -- >> 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
ADD REPLYlink written 6.8 years ago by Dan Tenenbaum8.2k
Yes, strange indeed. I just tried uninstalling everything I could think of and reinstalling R 3.0 and RStudio from the RStudio 0.97.318 installer. Still no luck. I will take your other suggestion and post to the RStudio forums. Thanks, Sean -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Thursday, February 28, 2013 2:41 PM To: Taylor, Sean D Cc: Sean [guest]; bioconductor at r-project.org Subject: Re: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0 On Thu, Feb 28, 2013 at 2:33 PM, Taylor, Sean D <sdtaylor at="" fhcrc.org=""> wrote: > Hi Dan, > > Thanks for the biocLite tip, that seems to have gotten me past that particular hurdle. > > For the RStudio issue, I am running Windows 7, 64-bit. I will append my sessionInfo() again at the end. I had a previous version of R on this machine, 2.15.1. I tried installing the R-devel in parallel, but when that wasn't working I uninstalled it. Now I just have the R-devel version. To open RStudio, I have tried holding down the Ctrl key while opening. Here I have the option of selecting the 32-bit or the 64-bit version of R-devel. I have tried both with the same result, i.e. fatal error. Is there a way of checking to see if there is still some part of the previous version that is getting in the way? > At this point I think your best bet is to report the issue on RStudio's forums: http://support.rstudio.org/ > Thanks > Sean > >> sessionInfo() > R Under development (unstable) (2013-02-21 r62017) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.19 BSgenome_1.27.1 > [3] BiocInstaller_1.9.6 Biostrings_2.27.11 > [5] IntermediateSequenceAnalysis2013_0.1.1 SequenceAnalysisData_0.1.4 > [7] edgeR_3.1.4 limma_3.15.14 > [9] GenomicFeatures_1.11.11 AnnotationDbi_1.21.10 > [11] Biobase_2.19.2 GenomicRanges_1.11.30 > [13] IRanges_1.17.35 BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > Error in x[["Version"]] : subscript out of bounds In addition: Warning > message: > In FUN(c("biomaRt", "bitops", "DBI", "RCurl", "Rsamtools", "RSQLite", : > DESCRIPTION file of package 'Rsamtools' is missing or broken >> This is rather strange, though....this should not be happening. I might suggest completely removing your R installation and starting again from scratch, if that is practical. Dan > > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: Thursday, February 28, 2013 1:46 PM > To: Sean [guest] > Cc: bioconductor at r-project.org; Taylor, Sean D > Subject: Re: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0 > > Hi Sean, > > > On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at="" bioconductor.org=""> wrote: >> >> I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). >> >> I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems: >> >> The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio. >> >> The second is a bit more problematic. I have been able to follow the >> vignette without too many problems up until Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioco nductor.org/packages/devel/data/annotation/html/BSgenome.Dmelanogaster .UCSC.dm3.html) and by entering the following code: >> >>>source("http://bioconductor.org/biocLite.R") >>>biocLite("BSgenome.Dmelanogaster.UCSC.dm3") >> >> However, when I try to load the library, I get the following: >> >>> library(BSgenome.Dmelanogaster.UCSC.dm3) >> Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before >> R 3.0.0: please re-install it >> >> The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette. >> >> Any advice on either of these two issues, but particularly the second, would be greatly appreciated. >> > > Try this: > biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source") > > As for RStudio, I'm not sure, what is your OS and output of sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that the first R in your path is R-devel. > > Dan > > >> Sean >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R Under development (unstable) (2013-02-21 r62017) >> Platform: x86_64-w64-mingw32/x64 (64-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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biostrings_2.27.11 >> [2] IntermediateSequenceAnalysis2013_0.1.1 >> [3] SequenceAnalysisData_0.1.4 >> [4] edgeR_3.1.4 >> [5] limma_3.15.14 >> [6] GenomicFeatures_1.11.11 >> [7] AnnotationDbi_1.21.10 >> [8] Biobase_2.19.2 >> [9] GenomicRanges_1.11.30 >> [10] IRanges_1.17.35 >> [11] BiocGenerics_0.5.6 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5 >> [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9 >> [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 >>> >> >> -- >> 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
ADD REPLYlink written 6.8 years ago by Taylor, Sean D250
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