biomaRt/RMySQL installation help
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@jane-fridlyand-106
Last seen 7.7 years ago
I am trying to install package biomaRt under windows XP. I fetched appropriate versions oDBI and RMySQL from http://stat.bell-labs.com/RS-DBI/download/ and (successfully: no errors) installed them from local zip files. I then installed biomaRt off Bioconductor (1.6 release). However when I attempt to load the library , it gives me the following error: > library(RMySQL) Loading required package: DBI Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error in library(RMySQL) : .First.lib failed for 'RMySQL' This particular file is present though in the appropriate directory: C:\Program Files\R\rw2011\library\RMySQL\libs . Also R has no troible loading other packages with dll files located in equivalent directories. I am working under R.2.1.0 i.e. latest stable R version. I am encountering the same problem on my desktop and my laptop. Any help would be appreciated. Thank you in advance Jane ********************************************************************** ********** Jane Fridlyand, Assistant Professor Department of Epidemiology and Biostatistics Center for Bioinformatics and Molecular Biostatistics UCSF Comprehensive Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179
Cancer biomaRt Cancer biomaRt • 1.1k views
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Ye, Bin ▴ 150
@ye-bin-1280
Last seen 7.7 years ago
Probably others can give more valuable suggestions. I've work with R 2.1.1, bioconductor 1.6, DBI 0.1-9, RMySQL 0.5-5. Everything is fine. Maybe try install RMySQL 0.5-5? Bin -----Original Message----- From: Jane Fridlyand [mailto:janef@stat.Berkeley.EDU] Sent: Fri 8/12/2005 4:11 PM To: Ye, Bin Subject: RE: [BioC] biomaRt/RMySQL installation help Dear Bin I have done this. Here is my PATH (the last entry is the relevant one): C:\PROGRAM FILES\THINKPAD\UTILITIES;%SystemRoot%\system32;%SystemRoot%;%SystemRoo t%\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\PC-Doctor for Windows\services;C:\Program Files\Common Files\Adaptec Shared\System;C:\Program Files\R\rw1090\bin;C:\Program Files\R\rw2011\library\RMySQL\libs\RMySQL.dll the problem still persists., i don't quite understand what is going on ... > utils:::menuInstallLocal() package 'RMySQL' successfully unpacked and MD5 sums checked updating HTML package descriptions > library(RMySQL) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error in library(RMySQL) : .First.lib failed for 'RMySQL' thank you for your help jane ********************************************************************** ********** Jane Fridlyand, Assistant Professor Department of Epidemiology and Biostatistics Center for Bioinformatics and Molecular Biostatistics UCSF Comprehensive Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 ********************************************************************** ********** On Fri, 12 Aug 2005, Ye, Bin wrote: > Did you include the 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll' into the PATH? > Copy the above path and paste it into > Start-> Settings-> Control Panel-> System-> Advanced-> Environment variables-> System variables ->Path > > Hope this help! > > Bin > > > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Jane Fridlyand > Sent: Fri 8/12/2005 1:11 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] biomaRt/RMySQL installation help > > > I am trying to install package biomaRt under windows XP. I fetched appropriate versions oDBI and RMySQL from > http://stat.bell-labs.com/RS-DBI/download/ and (successfully: no > errors) installed them from local zip files. I then installed biomaRt off > Bioconductor (1.6 release). However when I attempt to load the library > , it gives me the following error: > > > library(RMySQL) > Loading required package: DBI > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll': > LoadLibrary failure: The specified module could not be found. > Error in library(RMySQL) : .First.lib failed for 'RMySQL' > > This particular file is present though in the appropriate directory: > C:\Program Files\R\rw2011\library\RMySQL\libs . Also R has no troible > loading other packages with dll files located in equivalent directories. > > I am working under R.2.1.0 i.e. latest stable R version. I am > encountering the same problem on my desktop and my laptop. Any help would be > appreciated. > > Thank you in advance > > Jane > > > > ******************************************************************** ************ > Jane Fridlyand, Assistant Professor > Department of Epidemiology and Biostatistics > Center for Bioinformatics and Molecular Biostatistics > UCSF Comprehensive Cancer Center, > Box 0128 San Francisco, CA 94143-0128 > Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
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Ye, Bin ▴ 150
@ye-bin-1280
Last seen 7.7 years ago
Find some notes about exactly the same problem. http://www.phaget4.org/R/R_notes.html Hope it will work! Bin -----Original Message----- From: Jane Fridlyand [mailto:janef@stat.Berkeley.EDU] Sent: Fri 8/12/2005 4:11 PM To: Ye, Bin Subject: RE: [BioC] biomaRt/RMySQL installation help Dear Bin I have done this. Here is my PATH (the last entry is the relevant one): C:\PROGRAM FILES\THINKPAD\UTILITIES;%SystemRoot%\system32;%SystemRoot%;%SystemRoo t%\System32\Wbem;C:\Program Files\ATI Technologies\ATI Control Panel;C:\Program Files\PC-Doctor for Windows\services;C:\Program Files\Common Files\Adaptec Shared\System;C:\Program Files\R\rw1090\bin;C:\Program Files\R\rw2011\library\RMySQL\libs\RMySQL.dll the problem still persists., i don't quite understand what is going on ... > utils:::menuInstallLocal() package 'RMySQL' successfully unpacked and MD5 sums checked updating HTML package descriptions > library(RMySQL) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error in library(RMySQL) : .First.lib failed for 'RMySQL' thank you for your help jane ********************************************************************** ********** Jane Fridlyand, Assistant Professor Department of Epidemiology and Biostatistics Center for Bioinformatics and Molecular Biostatistics UCSF Comprehensive Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 ********************************************************************** ********** On Fri, 12 Aug 2005, Ye, Bin wrote: > Did you include the 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll' into the PATH? > Copy the above path and paste it into > Start-> Settings-> Control Panel-> System-> Advanced-> Environment variables-> System variables ->Path > > Hope this help! > > Bin > > > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Jane Fridlyand > Sent: Fri 8/12/2005 1:11 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] biomaRt/RMySQL installation help > > > I am trying to install package biomaRt under windows XP. I fetched appropriate versions oDBI and RMySQL from > http://stat.bell-labs.com/RS-DBI/download/ and (successfully: no > errors) installed them from local zip files. I then installed biomaRt off > Bioconductor (1.6 release). However when I attempt to load the library > , it gives me the following error: > > > library(RMySQL) > Loading required package: DBI > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > 'C:/PROGRA~1/R/rw2011/library/RMySQL/libs/RMySQL.dll': > LoadLibrary failure: The specified module could not be found. > Error in library(RMySQL) : .First.lib failed for 'RMySQL' > > This particular file is present though in the appropriate directory: > C:\Program Files\R\rw2011\library\RMySQL\libs . Also R has no troible > loading other packages with dll files located in equivalent directories. > > I am working under R.2.1.0 i.e. latest stable R version. I am > encountering the same problem on my desktop and my laptop. Any help would be > appreciated. > > Thank you in advance > > Jane > > > > ******************************************************************** ************ > Jane Fridlyand, Assistant Professor > Department of Epidemiology and Biostatistics > Center for Bioinformatics and Molecular Biostatistics > UCSF Comprehensive Cancer Center, > Box 0128 San Francisco, CA 94143-0128 > Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
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@narendra-kaushik-1390
Last seen 7.7 years ago
I am trying to install package biomaRt under windows XP under R.2.1.0. I have copied libmySQL.dll from library\RMySQL to the bin directory under R as is suggested in http://www.phaget4.org/R/R_notes.html. I am getting following message: library(biomaRt) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: RMySQL Loading required package: DBI Warning message: DLL attempted to change FPU control word from 8001f to 9001f > mart <- martConnect() - Connected to: ensembl_mart_32 - - Connected to: vega_mart_32 - - Connected to: snp_mart_32 - - Connected to: sequence_mart_32 - > gene <- getGene (id = "1939_at", array = "hg_u95av2", mart = mart) > seq <- getSequence(martTable = gene, mart = mart) Error in if (end[i] - start[i] > 1e+05) { : missing value where TRUE/FALSE needed Any suggestions? Narendra Narendra Kaushik School of Biosciences, University of Cardiff, Cardiff CF10 3US UK kaushiknk at cardiff@cardiff.ac.uk
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
On 12 Aug 2005, kaushiknk at cardiff.ac.uk wrote: > I am trying to install package biomaRt under windows XP under > R.2.1.0. I have copied libmySQL.dll from library\RMySQL to the bin > directory under R as is suggested in > http://www.phaget4.org/R/R_notes.html. > > I am getting following message: > > library(biomaRt) > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: RMySQL > Loading required package: DBI > Warning message: > DLL attempted to change FPU control word from 8001f to 9001f > >> mart <- martConnect() > - Connected to: ensembl_mart_32 - > - Connected to: vega_mart_32 - > - Connected to: snp_mart_32 - > - Connected to: sequence_mart_32 - >> gene <- getGene (id = "1939_at", array = "hg_u95av2", mart = mart) >> seq <- getSequence(martTable = gene, mart = mart) > Error in if (end[i] - start[i] > 1e+05) { : > missing value where TRUE/FALSE needed > > Any suggestions? What version of biomaRt are you using?
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