biomaRt doesn't load RCurl automatically
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Hi list, This only happened after I switched to R-2.8.0 and the latest biomaRt and RCurl. I was using R-2.7.0 before and everything worked fine. Currently, manually loading RCurl after loading biomaRt solves the problem. Please see the R outputs below. Many thanks! ##============================================================== R version 2.8.0 (2008-10-20) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(biomaRt) > ?getSNP > mart <- useMart("snp",dataset="hsapiens_snp") Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) : could not find function "findHTTPHeaderEncoding" > > snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) Error in martCheck(mart, "snp") : object "mart" not found In addition: Warning message: The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data > show(snp) Error: object "snp" not found Error in show(snp) : error in evaluating the argument 'object' in selecting a method for function 'show' > ?findHTTPHeaderEncoding No documentation for 'findHTTPHeaderEncoding' in specified packages and libraries: you could try '??findHTTPHeaderEncoding' > library(RCurl) > mart <- useMart("snp",dataset="hsapiens_snp") Checking attributes and filters ... ok > snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) Warning message: The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data > snp refsnp_id allele chrom_start chrom_strand 1 rs13291 C/T 148462 1 2 rs1134186 T/C 148569 1 3 rs1134187 G/A 148539 -1 4 rs1134189 G/A 148535 -1 5 rs1134190 C/T 148533 -1 6 rs1134191 C/T 148499 -1 7 rs1134192 G/A 148462 -1 8 rs1134195 G/T 148394 -1 9 rs3965587 C/T 148535 1 10 rs4046274 C/A 148394 1 11 rs4046275 A/G 148411 1 12 rs4046276 C/T 148462 1 13 rs4046277 G/A 148499 1 14 rs4046278 G/A 148533 1 15 rs4378731 G/A 148601 1 16 rs11136408 G/A 148525 1 17 rs12019378 T/G 148471 1 > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RCurl_0.9-4 biomaRt_1.16.0 loaded via a namespace (and not attached): [1] XML_1.96-0 >
SNP biomaRt SNP biomaRt • 1000 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Tao, Works for me: > library(biomaRt) > mart <- useMart("snp", "hsapiens_snp") Checking attributes and filters ... ok > snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) Warning message: The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_1.16.0 loaded via a namespace (and not attached): [1] RCurl_0.91-0 XML_1.98-1 Although it looks like you have a really old version of RCurl. Best, Jim Shi, Tao wrote: > Hi list, > > This only happened after I switched to R-2.8.0 and the latest biomaRt and RCurl. I was using R-2.7.0 before and everything worked fine. Currently, manually loading RCurl after loading biomaRt solves the problem. Please see the R outputs below. Many thanks! > > ##============================================================== > R version 2.8.0 (2008-10-20) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(biomaRt) >> ?getSNP >> mart <- useMart("snp",dataset="hsapiens_snp") > Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) : > could not find function "findHTTPHeaderEncoding" >> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) > Error in martCheck(mart, "snp") : object "mart" not found > In addition: Warning message: > The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data >> show(snp) > Error: object "snp" not found > Error in show(snp) : > error in evaluating the argument 'object' in selecting a method for function 'show' >> ?findHTTPHeaderEncoding > No documentation for 'findHTTPHeaderEncoding' in specified packages and libraries: > you could try '??findHTTPHeaderEncoding' >> library(RCurl) >> mart <- useMart("snp",dataset="hsapiens_snp") > Checking attributes and filters ... ok >> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) > Warning message: > The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data >> snp > refsnp_id allele chrom_start chrom_strand > 1 rs13291 C/T 148462 1 > 2 rs1134186 T/C 148569 1 > 3 rs1134187 G/A 148539 -1 > 4 rs1134189 G/A 148535 -1 > 5 rs1134190 C/T 148533 -1 > 6 rs1134191 C/T 148499 -1 > 7 rs1134192 G/A 148462 -1 > 8 rs1134195 G/T 148394 -1 > 9 rs3965587 C/T 148535 1 > 10 rs4046274 C/A 148394 1 > 11 rs4046275 A/G 148411 1 > 12 rs4046276 C/T 148462 1 > 13 rs4046277 G/A 148499 1 > 14 rs4046278 G/A 148533 1 > 15 rs4378731 G/A 148601 1 > 16 rs11136408 G/A 148525 1 > 17 rs12019378 T/G 148471 1 >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RCurl_0.9-4 biomaRt_1.16.0 > > loaded via a namespace (and not attached): > [1] XML_1.96-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Hi Jim, Thanks. After updating my RCurl package, everything works fine now. ...Tao ============================================================ Hi Tao, Works for me: > library(biomaRt) > mart <- useMart("snp", "hsapiens_snp") Checking attributes and filters ... ok > snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) Warning message: The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_1.16.0 loaded via a namespace (and not attached): [1] RCurl_0.91-0 XML_1.98-1 Although it looks like you have a really old version of RCurl. Best, Jim Shi, Tao wrote: > Hi list, > [[elided Yahoo spam]] > > ##============================================================== > R version 2.8.0 (2008-10-20) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(biomaRt) >> ?getSNP >> mart <- useMart("snp",dataset="hsapiens_snp") > Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) : > could not find function "findHTTPHeaderEncoding" >> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) > Error in martCheck(mart, "snp") : object "mart" not found > In addition: Warning message: > The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data >> show(snp) > Error: object "snp" not found > Error in show(snp) : > error in evaluating the argument 'object' in selecting a method for function 'show' >> ?findHTTPHeaderEncoding > No documentation for 'findHTTPHeaderEncoding' in specified packages and libraries: > you could try '??findHTTPHeaderEncoding' >> library(RCurl) >> mart <- useMart("snp",dataset="hsapiens_snp") > Checking attributes and filters ... ok >> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart) > Warning message: > The getSNP function will be removed in the next release of biomaRt. Use the getBM function instead. The biomaRt vignette contains examples of retrieving SNP data >> snp > refsnp_id allele chrom_start chrom_strand > 1 rs13291 C/T 148462 1 > 2 rs1134186 T/C 148569 1 > 3 rs1134187 G/A 148539 -1 > 4 rs1134189 G/A 148535 -1 > 5 rs1134190 C/T 148533 -1 > 6 rs1134191 C/T 148499 -1 > 7 rs1134192 G/A 148462 -1 > 8 rs1134195 G/T 148394 -1 > 9 rs3965587 C/T 148535 1 > 10 rs4046274 C/A 148394 1 > 11 rs4046275 A/G 148411 1 > 12 rs4046276 C/T 148462 1 > 13 rs4046277 G/A 148499 1 > 14 rs4046278 G/A 148533 1 > 15 rs4378731 G/A 148601 1 > 16 rs11136408 G/A 148525 1 > 17 rs12019378 T/G 148471 1 >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RCurl_0.9-4 biomaRt_1.16.0 > > loaded via a namespace (and not attached): > [1] XML_1.96-0 > > _______________________________________________ > Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662
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