Cannot find the package created by pdInfoBuilder package

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Hello, I??? m a bioinformatician at UT Austin and I???m trying to do time series analysis of an arabidopsis tiling array. I used the makePdInfoPackage function to create a pdinfpackage using my bpmap files. It worked successfully and I can see a directory called pd.at35b.mr.v04: ls pd.at35b.mr.v04/ data DESCRIPTION inst man NAMESPACE R For further analysis, I need to provide the name of the "package containing the array probe and annotation information, as produces by the pdInfoBuilder-package". Just providing the name of this directory does not seem to work (no such package error). Do I need to do some installation or additional step after creating this package, to use it? I???m having difficulty finding this from the documentation and any help would be really appreciated. thanks for any help dhivya arasappan Bioinformatician UT Austin -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] pdInfoBuilder_1.22.0 affxparser_1.30.2 [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1 [5] GenomicRanges_1.10.7 pd.atdschip.tiling_0.0.4 [7] RSQLite_0.11.4 DBI_0.2-7 [9] waveTilingData_0.99.1 waveTiling_1.0.0 [11] GenomeGraphs_1.18.0 biomaRt_2.14.0 [13] Biostrings_2.26.3 IRanges_1.16.6 [15] oligo_1.22.0 Biobase_2.18.0 [17] oligoClasses_1.20.0 BiocGenerics_0.4.0 [19] R.utils_1.29.8 R.oo_1.18.0 [21] R.methodsS3_1.6.1 loaded via a namespace (and not attached): [1] affy_1.36.1 affyio_1.26.0 BiocInstaller_1.8.3 [4] bit_1.1-11 codetools_0.2-8 ff_2.2-12 [7] foreach_1.4.1 iterators_1.0.6 parallel_2.15.3 [10] preprocessCore_1.20.0 RCurl_1.95-4.1 splines_2.15.3 [13] stats4_2.15.3 waveslim_1.7.3 XML_3.98-1.1 [16] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Annotation BSgenome probe BSgenome Annotation BSgenome probe BSgenome • 1.0k views

ADD COMMENT • link updated 10.1 years ago by Dan Tenenbaum ★ 8.2k • written 10.1 years ago by Guest User ★ 13k

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Dan Tenenbaum ★ 8.2k

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----- Original Message ----- > From: "dhivya [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, darasappan at gmail.com > Sent: Friday, March 28, 2014 12:45:22 PM > Subject: [BioC] Cannot find the package created by pdInfoBuilder package > > > Hello, > > I??? m a bioinformatician at UT Austin and I???m trying to do time > series analysis of an arabidopsis tiling array. I used the > makePdInfoPackage function to create a pdinfpackage using my bpmap > files. It worked successfully and I can see a directory called > pd.at35b.mr.v04: > > ls pd.at35b.mr.v04/ > data DESCRIPTION inst man NAMESPACE R > > For further analysis, I need to provide the name of the "package > containing the array probe and annotation information, as produces > by the pdInfoBuilder-package". Just providing the name of this > directory does not seem to work (no such package error). Do I need > to do some installation or additional step after creating this > package, to use it? I???m having difficulty finding this from the > documentation and any help would be really appreciated. > I think you just need to do this from the command line: R CMD INSTALL pd.at35b.mr.v04 Dan > thanks for any help > dhivya arasappan > Bioinformatician > UT Austin > > -- output of sessionInfo(): > > R version 2.15.3 (2013-03-01) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] pdInfoBuilder_1.22.0 affxparser_1.30.2 > [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1 > [5] GenomicRanges_1.10.7 pd.atdschip.tiling_0.0.4 > [7] RSQLite_0.11.4 DBI_0.2-7 > [9] waveTilingData_0.99.1 waveTiling_1.0.0 > [11] GenomeGraphs_1.18.0 biomaRt_2.14.0 > [13] Biostrings_2.26.3 IRanges_1.16.6 > [15] oligo_1.22.0 Biobase_2.18.0 > [17] oligoClasses_1.20.0 BiocGenerics_0.4.0 > [19] R.utils_1.29.8 R.oo_1.18.0 > [21] R.methodsS3_1.6.1 > > loaded via a namespace (and not attached): > [1] affy_1.36.1 affyio_1.26.0 BiocInstaller_1.8.3 > [4] bit_1.1-11 codetools_0.2-8 ff_2.2-12 > [7] foreach_1.4.1 iterators_1.0.6 parallel_2.15.3 > [10] preprocessCore_1.20.0 RCurl_1.95-4.1 splines_2.15.3 > [13] stats4_2.15.3 waveslim_1.7.3 XML_3.98-1.1 > [16] zlibbioc_1.4.0 > > > -- > 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 COMMENT • link 10.1 years ago Dan Tenenbaum ★ 8.2k

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Thanks. Im seeing the following error when I try that. Do I need to install an sql R module? R CMD INSTALL pd.at35b.mr.v04 * installing to library /home1/01184/daras/R/x86_64-unknown-linux- gnu-library/2.15 * installing *source* package pd.at35b.mr.v04 ... ** R ** data ** inst ** preparing package for lazy loading Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: database disk image is malformed) Error : unable to load R code in package pd.at35b.mr.v04 ERROR: lazy loading failed for package pd.at35b.mr.v04 * removing /home1/01184/daras/R/x86_64-unknown-linux-gnu- library/2.15/pd.at35b.mr.v04 Thanks dhivya On Mar 28, 2014, at 2:48 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- >> From: "dhivya [guest]" <guest@bioconductor.org> >> To: bioconductor@r-project.org, darasappan@gmail.com >> Sent: Friday, March 28, 2014 12:45:22 PM >> Subject: [BioC] Cannot find the package created by pdInfoBuilder package >> >> >> Hello, >> >> Iâ m a bioinformatician at UT Austin and Iâm trying to do time >> series analysis of an arabidopsis tiling array. I used the >> makePdInfoPackage function to create a pdinfpackage using my bpmap >> files. It worked successfully and I can see a directory called >> pd.at35b.mr.v04: >> >> ls pd.at35b.mr.v04/ >> data DESCRIPTION inst man NAMESPACE R >> >> For further analysis, I need to provide the name of the "package >> containing the array probe and annotation information, as produces >> by the pdInfoBuilder-package". Just providing the name of this >> directory does not seem to work (no such package error). Do I need >> to do some installation or additional step after creating this >> package, to use it? Iâm having difficulty finding this from the >> documentation and any help would be really appreciated. >> > > I think you just need to do this from the command line: > > R CMD INSTALL pd.at35b.mr.v04 > > Dan > > >> thanks for any help >> dhivya arasappan >> Bioinformatician >> UT Austin >> >> -- output of sessionInfo(): >> >> R version 2.15.3 (2013-03-01) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets >> methods >> [8] base >> >> other attached packages: >> [1] pdInfoBuilder_1.22.0 affxparser_1.30.2 >> [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1 >> [5] GenomicRanges_1.10.7 pd.atdschip.tiling_0.0.4 >> [7] RSQLite_0.11.4 DBI_0.2-7 >> [9] waveTilingData_0.99.1 waveTiling_1.0.0 >> [11] GenomeGraphs_1.18.0 biomaRt_2.14.0 >> [13] Biostrings_2.26.3 IRanges_1.16.6 >> [15] oligo_1.22.0 Biobase_2.18.0 >> [17] oligoClasses_1.20.0 BiocGenerics_0.4.0 >> [19] R.utils_1.29.8 R.oo_1.18.0 >> [21] R.methodsS3_1.6.1 >> >> loaded via a namespace (and not attached): >> [1] affy_1.36.1 affyio_1.26.0 BiocInstaller_1.8.3 >> [4] bit_1.1-11 codetools_0.2-8 ff_2.2-12 >> [7] foreach_1.4.1 iterators_1.0.6 parallel_2.15.3 >> [10] preprocessCore_1.20.0 RCurl_1.95-4.1 splines_2.15.3 >> [13] stats4_2.15.3 waveslim_1.7.3 XML_3.98-1.1 >> [16] zlibbioc_1.4.0 >> >> >> -- >> 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 [[alternative HTML version deleted]]

ADD REPLY • link 10.1 years ago dhivya arasappan ▴ 10

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Create the package using a local disk. I've seen this issue raising when one creates the package on, for example, a slow NFS share. 2014-03-28 18:13 GMT-03:00 dhivya arasappan <darasappan@gmail.com>: > Thanks. Im seeing the following error when I try that. Do I need to > install an sql R module? > R CMD INSTALL pd.at35b.mr.v04 > * installing to library > '/home1/01184/daras/R/x86_64-unknown-linux-gnu-library/2.15' > * installing *source* package 'pd.at35b.mr.v04' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: database disk image is malformed) > Error : unable to load R code in package 'pd.at35b.mr.v04' > ERROR: lazy loading failed for package 'pd.at35b.mr.v04' > * removing > '/home1/01184/daras/R/x86_64-unknown-linux-gnu- library/2.15/pd.at35b.mr.v04' > > Thanks > dhivya > > > On Mar 28, 2014, at 2:48 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > > > > > ----- Original Message ----- > >> From: "dhivya [guest]" <guest@bioconductor.org> > >> To: bioconductor@r-project.org, darasappan@gmail.com > >> Sent: Friday, March 28, 2014 12:45:22 PM > >> Subject: [BioC] Cannot find the package created by pdInfoBuilder package > >> > >> > >> Hello, > >> > >> Iâ EURO (tm) m a bioinformatician at UT Austin and Iâ EURO (tm)m trying to do time > >> series analysis of an arabidopsis tiling array. I used the > >> makePdInfoPackage function to create a pdinfpackage using my bpmap > >> files. It worked successfully and I can see a directory called > >> pd.at35b.mr.v04: > >> > >> ls pd.at35b.mr.v04/ > >> data DESCRIPTION inst man NAMESPACE R > >> > >> For further analysis, I need to provide the name of the "package > >> containing the array probe and annotation information, as produces > >> by the pdInfoBuilder-package". Just providing the name of this > >> directory does not seem to work (no such package error). Do I need > >> to do some installation or additional step after creating this > >> package, to use it? Iâ EURO (tm)m having difficulty finding this from the > >> documentation and any help would be really appreciated. > >> > > > > I think you just need to do this from the command line: > > > > R CMD INSTALL pd.at35b.mr.v04 > > > > Dan > > > > > >> thanks for any help > >> dhivya arasappan > >> Bioinformatician > >> UT Austin > >> > >> -- output of sessionInfo(): > >> > >> R version 2.15.3 (2013-03-01) > >> Platform: x86_64-unknown-linux-gnu (64-bit) > >> > >> locale: > >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > >> [7] LC_PAPER=C LC_NAME=C > >> [9] LC_ADDRESS=C LC_TELEPHONE=C > >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >> > >> attached base packages: > >> [1] grid stats graphics grDevices utils datasets > >> methods > >> [8] base > >> > >> other attached packages: > >> [1] pdInfoBuilder_1.22.0 affxparser_1.30.2 > >> [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1 > >> [5] GenomicRanges_1.10.7 pd.atdschip.tiling_0.0.4 > >> [7] RSQLite_0.11.4 DBI_0.2-7 > >> [9] waveTilingData_0.99.1 waveTiling_1.0.0 > >> [11] GenomeGraphs_1.18.0 biomaRt_2.14.0 > >> [13] Biostrings_2.26.3 IRanges_1.16.6 > >> [15] oligo_1.22.0 Biobase_2.18.0 > >> [17] oligoClasses_1.20.0 BiocGenerics_0.4.0 > >> [19] R.utils_1.29.8 R.oo_1.18.0 > >> [21] R.methodsS3_1.6.1 > >> > >> loaded via a namespace (and not attached): > >> [1] affy_1.36.1 affyio_1.26.0 BiocInstaller_1.8.3 > >> [4] bit_1.1-11 codetools_0.2-8 ff_2.2-12 > >> [7] foreach_1.4.1 iterators_1.0.6 parallel_2.15.3 > >> [10] preprocessCore_1.20.0 RCurl_1.95-4.1 splines_2.15.3 > >> [13] stats4_2.15.3 waveslim_1.7.3 XML_3.98-1.1 > >> [16] zlibbioc_1.4.0 > >> > >> > >> -- > >> 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 > > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 > [[alternative HTML version deleted]]

ADD REPLY • link 10.1 years ago Benilton Carvalho ★ 4.3k

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