one problem about IRanges Package
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cao zongfu ▴ 50
@cao-zongfu-4344
Last seen 7.1 years ago
Dear Prof. , Hi I am a R user from National Engineering Research Center for Beijing Biochip Technology of China. Recently, I used simpleaffy package to perform quality control of Affymetrix expression profile chip. I met one problem: I found that simpleaffy can not work under R2.11.1-X64 on my computer. As we known, IRanges was used in the simpleaffy package. I used R2.11.1-X64 under 64-bit Windows XP. I found that IRanges 1.8.2 can not work.When I used library(IRanges) command, the error said: package "Iranges" is not install for the 'arch=x64'. But I have install the IRanges into the R in deed. I want to know whether the simpleaffy can only work under the R32. If I hope to used the R64 in order to increasing the efficiency, Would you please help me how to deal with?Thank you in advance. R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=Chinese_People's Republic of China.936 LC_CTYPE=Chinese_People's Republic of China.936 [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C [5] LC_TIME=Chinese_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] genefilter_1.30.0 affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.28.0 AnnotationDbi_1.12.0 DBI_0.2-5 preprocessCore_1.10.0 [6] RSQLite_0.9-2 splines_2.11.1 survival_2.35-8 tools_2.11.1 xtable_1.5-6 > library(IRanges) error: Package "Iranges" is not install for the 'arch=x64'. Zongfu Cao National Engineering Research Center for Beijing Biochip Technology of China
simpleaffy IRanges simpleaffy IRanges • 985 views
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@vincent-j-carey-jr-4
Last seen 4 days ago
United States
Dr Zongfu: It will be easier to help you if you will use updated resources. Please install R 2.12, the current version, and then use biocLite() to install the packages you need. After this if you find an error, please send all details to the list. I personally maintain a 64 bit windows 7 (not XP) machine so may not be able to reproduce your situation well. It would be advisable to use windows 7 if available. On Mon, Nov 8, 2010 at 11:56 PM, cao zongfu <caozongfu at="" gmail.com=""> wrote: > Dear Prof. , Hi > > ? ? ? I am a R user from National Engineering Research Center for > Beijing Biochip Technology ?of China. Recently, I used simpleaffy > package to perform quality control of Affymetrix expression profile > chip. I met one problem: > > ? ? ? I found that simpleaffy can not work under R2.11.1-X64 on my > computer. As we known, IRanges was used in the simpleaffy package. I > used R2.11.1-X64 under 64-bit Windows XP. I found that IRanges 1.8.2 > can not work.When I used library(IRanges) command, the error said: > package "Iranges" is not install for the 'arch=x64'. But I have > install the IRanges into the R in deed. I want to know ?whether the > simpleaffy can only work under the R32. If I hope to used the R64 in > order to increasing the efficiency, Would you please help me how to > deal with?Thank you in advance. > > > R version 2.11.1 (2010-05-31) > x86_64-pc-mingw32 > > locale: > [1] LC_COLLATE=Chinese_People's Republic of China.936 > LC_CTYPE=Chinese_People's Republic of China.936 > [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C > [5] LC_TIME=Chinese_People's Republic of China.936 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] genefilter_1.30.0 affy_1.26.1 ? ? ? Biobase_2.8.0 > > loaded via a namespace (and not attached): > ?[1] affyio_1.16.0 ? ? ? ? annotate_1.28.0 ? ? ? AnnotationDbi_1.12.0 > DBI_0.2-5 ? ? ? ? ? ? preprocessCore_1.10.0 > ?[6] RSQLite_0.9-2 ? ? ? ? splines_2.11.1 ? ? ? ?survival_2.35-8 > tools_2.11.1 ? ? ? ? ?xtable_1.5-6 >> ? ? ? ?library(IRanges) > error: Package "Iranges" is not install for the 'arch=x64'. > > > > > > > > Zongfu Cao > > National Engineering Research Center for Beijing Biochip Technology ?of China > > _______________________________________________ > 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 >
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@vincent-j-carey-jr-4
Last seen 4 days ago
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You are welcome. In future please carbon the main list so that the knowledge of the solution may be shared. On Wed, Nov 10, 2010 at 10:51 PM, cao zongfu <caozongfu at="" gmail.com=""> wrote: > Thank you for your help.There is no more any errro. I have suceeded. > > 2010/11/10, Vincent Carey <stvjc at="" channing.harvard.edu="">: >> you need to restart R. ?try that and do library(gcrma) and tell me if >> you still see an error >> >> On Wed, Nov 10, 2010 at 2:13 AM, cao zongfu <caozongfu at="" gmail.com=""> wrote: >>> Dear Prof., >>> ? ? I am sorry to troble you again. I have checked the IRanges path, >>> I found that it ?maybe because the file 'IRanges.dll' missing, which >>> should be in the path of '.\Program >>> Files\R\R-2.12.0\library\IRanges\libs\x64', not in the path of >>> '.\Program Files\R\R-2.12.0\library\IRanges\libs\i386'. Would you >>> please send me the file? I'd like to try again. I think if I get the >>> file, I will be suceed. >>> ? ? Thank you again. >>> >>> Cao Zongfu >>> >>> >>> >>> >>> >>> >>> >>> 2010/11/10, cao zongfu <caozongfu at="" gmail.com="">: >>>> Dear Prof., >>>> ? ? ? I have installed R2.12.0 on personal computer, and use >>>> biocLite() toinstall the packages simpleaffy,but I failed again. >>>> ?IRanges? is not available yet.Some details are as follows >>>> >>>> >>>>> source("http://bioconductor.org/biocLite.R") >>>> BioC_mirror = http://www.bioconductor.org >>>> Change using chooseBioCmirror(). >>>>> biocLite("simpleaffy") >>>> Using R version 2.12.0, biocinstall version 2.7.4. >>>> Installing Bioconductor version 2.7 packages: >>>> [1] "simpleaffy" >>>> Please wait... >>>> >>>> Warning: dependency ?IRanges? is not available >>>> also installing the dependencies ?DBI?, ?RSQLite?, ?xtable?, ?affyio?, >>>> ?preprocessCore?, ?AnnotationDbi?, ?annotate?, ?Biostrings?, ?affy?, >>>> ?genefilter?, ?Biobase?, ?gcrma? >>>> >>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/DBI_0.2-5.zip' >>>> Content type 'application/zip' length 386424 bytes (377 Kb) >>>> opened URL >>>> downloaded 377 Kb >>>> >>>> trying URL >>>> 'http://cran.fhcrc.org/bin/windows/contrib/2.12/RSQLite_0.9-3.zip' >>>> Content type 'application/zip' length 978646 bytes (955 Kb) >>>> opened URL >>>> downloaded 955 Kb >>>> >>>> trying URL >>>> 'http://cran.fhcrc.org/bin/windows/contrib/2.12/xtable_1.5-6.zip' >>>> Content type 'application/zip' length 178958 bytes (174 Kb) >>>> opened URL >>>> downloaded 174 Kb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/affyio_1.18.0.zip' >>>> Content type 'application/zip' length 152256 bytes (148 Kb) >>>> opened URL >>>> downloaded 148 Kb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/preprocessCore_1.12.0.zip' >>>> Content type 'application/zip' length 180568 bytes (176 Kb) >>>> opened URL >>>> downloaded 176 Kb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/AnnotationDbi_1.12.0.zip' >>>> Content type 'application/zip' length 5267008 bytes (5.0 Mb) >>>> opened URL >>>> downloaded 5.0 Mb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/annotate_1.28.0.zip' >>>> Content type 'application/zip' length 2210479 bytes (2.1 Mb) >>>> opened URL >>>> downloaded 2.1 Mb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/Biostrings_2.18.0.zip' >>>> Content type 'application/zip' length 2360722 bytes (2.3 Mb) >>>> opened URL >>>> downloaded 2.3 Mb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/affy_1.28.0.zip' >>>> Content type 'application/zip' length 2067173 bytes (2.0 Mb) >>>> opened URL >>>> downloaded 2.0 Mb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/genefilter_1.32.0.zip' >>>> Content type 'application/zip' length 965461 bytes (942 Kb) >>>> opened URL >>>> downloaded 942 Kb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/Biobase_2.10.0.zip' >>>> Content type 'application/zip' length 2594549 bytes (2.5 Mb) >>>> opened URL >>>> downloaded 2.5 Mb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/gcrma_2.22.0.zip' >>>> Content type 'application/zip' length 236187 bytes (230 Kb) >>>> opened URL >>>> downloaded 230 Kb >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/simpleaffy_2.26.0.zip' >>>> Content type 'application/zip' length 804264 bytes (785 Kb) >>>> opened URL >>>> downloaded 785 Kb >>>> >>>> package 'DBI' successfully unpacked and MD5 sums checked >>>> package 'RSQLite' successfully unpacked and MD5 sums checked >>>> package 'xtable' successfully unpacked and MD5 sums checked >>>> package 'affyio' successfully unpacked and MD5 sums checked >>>> package 'preprocessCore' successfully unpacked and MD5 sums checked >>>> package 'AnnotationDbi' successfully unpacked and MD5 sums checked >>>> package 'annotate' successfully unpacked and MD5 sums checked >>>> package 'Biostrings' successfully unpacked and MD5 sums checked >>>> package 'affy' successfully unpacked and MD5 sums checked >>>> package 'genefilter' successfully unpacked and MD5 sums checked >>>> package 'Biobase' successfully unpacked and MD5 sums checked >>>> package 'gcrma' successfully unpacked and MD5 sums checked >>>> package 'simpleaffy' successfully unpacked and MD5 sums checked >>>> >>>> The downloaded packages are in >>>> ? ? ? ? C:\Documents and Settings\Administrator\Local >>>> Settings\Temp\Rtmp1Ycqzb\downloaded_packages >>>>> library(simpleaffy) >>>> Loading required package: affy >>>> Loading required package: Biobase >>>> >>>> Welcome to Bioconductor >>>> >>>> ? Vignettes contain introductory material. To view, type >>>> ? 'openVignette()'. To cite Bioconductor, see >>>> ? 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>> Loading required package: genefilter >>>> Loading required package: gcrma >>>> Error in loadNamespace(i, c(lib.loc, .libPaths())) : >>>> ? there is no package called 'IRanges' >>>> Error: package 'gcrma' could not be loaded >>>>> biocLite("gcrma") >>>> Using R version 2.12.0, biocinstall version 2.7.4. >>>> Installing Bioconductor version 2.7 packages: >>>> [1] "gcrma" >>>> Please wait... >>>> >>>> trying URL >>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contri b/2.12/gcrma_2.22.0.zip' >>>> Content type 'application/zip' length 236187 bytes (230 Kb) >>>> opened URL >>>> downloaded 230 Kb >>>> >>>> package 'gcrma' successfully unpacked and MD5 sums checked >>>> >>>> The downloaded packages are in >>>> ? ? ? ? C:\Documents and Settings\Administrator\Local >>>> Settings\Temp\Rtmp1Ycqzb\downloaded_packages >>>>> library(gcrma) >>>> Error in loadNamespace(i, c(lib.loc, .libPaths())) : >>>> ? there is no package called 'IRanges' >>>> Error: package/namespace load failed for 'gcrma' >>>>> biocLite("IRanges") >>>> Using R version 2.12.0, biocinstall version 2.7.4. >>>> Installing Bioconductor version 2.7 packages: >>>> [1] "IRanges" >>>> Please wait... >>>> >>>> Warning message: >>>> In getDependencies(pkgs, dependencies, available, lib) : >>>> ? package ?IRanges? is not available >>>>> sessionInfo() >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-pc-mingw32/x64 (64-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United >>>> States.1252 ? ?LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United >>>> States.1252 >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] genefilter_1.32.0 affy_1.28.0 ? ? ? Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> ?[1] affyio_1.18.0 ? ? ? ? annotate_1.28.0 ? ? ? AnnotationDbi_1.12.0 >>>> DBI_0.2-5 ? ? ? ? ? ? preprocessCore_1.12.0 >>>> ?[6] RSQLite_0.9-3 ? ? ? ? splines_2.12.0 ? ? ? ?survival_2.35-8 >>>> tools_2.12.0 ? ? ? ? ?xtable_1.5-6 >>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 2010/11/9, Vincent Carey <stvjc at="" channing.harvard.edu="">: >>>>> Dr Zongfu: >>>>> >>>>> It will be easier to help you if you will use updated resources. >>>>> Please install R 2.12, the current version, and then use biocLite() to >>>>> install the packages you need. ?After this if you find an error, >>>>> please send all details to the list. ?I personally maintain a 64 bit >>>>> windows 7 (not XP) machine so may not be able to reproduce your >>>>> situation well. ?It would be advisable to use windows 7 if available. >>>>> >>>>> On Mon, Nov 8, 2010 at 11:56 PM, cao zongfu <caozongfu at="" gmail.com=""> wrote: >>>>>> Dear Prof. , Hi >>>>>> >>>>>> ? ? ? I am a R user from National Engineering Research Center for >>>>>> Beijing Biochip Technology ?of China. Recently, I used simpleaffy >>>>>> package to perform quality control of Affymetrix expression profile >>>>>> chip. I met one problem: >>>>>> >>>>>> ? ? ? I found that simpleaffy can not work under R2.11.1-X64 on my >>>>>> computer. As we known, IRanges was used in the simpleaffy package. I >>>>>> used R2.11.1-X64 under 64-bit Windows XP. I found that IRanges 1.8.2 >>>>>> can not work.When I used library(IRanges) command, the error said: >>>>>> package "Iranges" is not install for the 'arch=x64'. But I have >>>>>> install the IRanges into the R in deed. I want to know ?whether the >>>>>> simpleaffy can only work under the R32. If I hope to used the R64 in >>>>>> order to increasing the efficiency, Would you please help me how to >>>>>> deal with?Thank you in advance. >>>>>> >>>>>> >>>>>> R version 2.11.1 (2010-05-31) >>>>>> x86_64-pc-mingw32 >>>>>> >>>>>> locale: >>>>>> [1] LC_COLLATE=Chinese_People's Republic of China.936 >>>>>> LC_CTYPE=Chinese_People's Republic of China.936 >>>>>> [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C >>>>>> [5] LC_TIME=Chinese_People's Republic of China.936 >>>>>> >>>>>> attached base packages: >>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>>> >>>>>> other attached packages: >>>>>> [1] genefilter_1.30.0 affy_1.26.1 ? ? ? Biobase_2.8.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> ?[1] affyio_1.16.0 ? ? ? ? annotate_1.28.0 ? ? ? AnnotationDbi_1.12.0 >>>>>> DBI_0.2-5 ? ? ? ? ? ? preprocessCore_1.10.0 >>>>>> ?[6] RSQLite_0.9-2 ? ? ? ? splines_2.11.1 ? ? ? ?survival_2.35-8 >>>>>> tools_2.11.1 ? ? ? ? ?xtable_1.5-6 >>>>>>> ? ? ? ?library(IRanges) >>>>>> error: Package "Iranges" is not install for the 'arch=x64'. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Zongfu Cao >>>>>> >>>>>> National Engineering Research Center for Beijing Biochip Technology ?of >>>>>> China >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>> >>>> >>> >> >
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