Hi everyone, I am new to R and I had a question in regards to the impute library. This library is no longer supported by CRAN, so I am posting this question to the Bioconductor users. My question is whether I had installed this library correctly. Two observations: 1. When I installed the impute library, there were a list of warnings. I followed the instructions from here - http://www.bioconductor.org/packages/release/bioc/html/impute.html . I also tried to change the permission for the folder manually, but the old permission reverted back to the original status. 2. When I call the impute.knn() function, the error message is "Error: could not find function "impute.knn"" Thank you in advance, Wendy Yim M.S. Candidate at Johns Hopkins University. _____________________________________________________ > source("http://www.bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("impute") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'impute' Installing package(s) into ‘C:/Users/W/Documents/R/win-library/2.14’ (as ‘lib’ is unspecified) trying URL ' http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14 /impute_1.28.0.zip ' Content type 'application/zip' length 1216377 bytes (1.2 Mb) opened URL downloaded 1.2 Mb package ‘impute’ successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\W\AppData\Local\Temp\RtmpKMcIoN\downloaded_packages Warning message: 'boot' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'cluster' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'foreign' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'MASS' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'Matrix' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'mgcv' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'nlme' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'rpart' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable 'survival' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.1/library' not writeable > impute.knn(data=cdc28,k=6) Error: could not find function "impute.knn" > impute.knn Error: object 'impute.knn' not found > knn Error: object 'knn' not found > imputeknn Error: object 'imputeknn' not found [[alternative HTML version deleted]]

for starters, you might want to call library(impute) before attempting to use functions in the package. Since it will bite you momentarily, here's another thing to know about impute: imputed <- impute.knn(not.yet.imputed)$data Use ?impute.knn for more information. It is a very handy package On Sun, Feb 12, 2012 at 5:01 PM, Wendy Yim <wensauyim@gmail.com> wrote: > Hi everyone, > > I am new to R and I had a question in regards to the impute library. This > library is no longer supported by CRAN, so I am posting this question to > the Bioconductor users. > > My question is whether I had installed this library correctly. > > Two observations: > > 1. When I installed the impute library, there were a list of warnings. I > followed the instructions from here - > http://www.bioconductor.org/packages/release/bioc/html/impute.html . I > also tried to change the permission for the folder manually, but the old > permission reverted back to the original status. > 2. When I call the impute.knn() function, the error message is "Error: > could not find function "impute.knn"" > > > Thank you in advance, > > Wendy Yim > M.S. Candidate at Johns Hopkins University. > > > _____________________________________________________ > > > source("http://www.bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help > > > biocLite("impute") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'impute' > Installing package(s) into ‘C:/Users/W/Documents/R/win-library/2.14’ > (as ‘lib’ is unspecified) > trying URL ' > > http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2. 14/impute_1.28.0.zip > ' > Content type 'application/zip' length 1216377 bytes (1.2 Mb) > opened URL > downloaded 1.2 Mb > > package ‘impute’ successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Users\W\AppData\Local\Temp\RtmpKMcIoN\downloaded_packages > Warning message: > 'boot' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'cluster' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'foreign' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'MASS' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'Matrix' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'mgcv' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'nlme' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'rpart' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'survival' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > > > impute.knn(data=cdc28,k=6) > Error: could not find function "impute.knn" > > impute.knn > Error: object 'impute.knn' not found > > knn > Error: object 'knn' not found > > imputeknn > Error: object 'imputeknn' not found > > [[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 > > -- *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]]

On 02/12/2012 05:01 PM, Wendy Yim wrote: > Hi everyone, > > I am new to R and I had a question in regards to the impute library. This > library is no longer supported by CRAN, so I am posting this question to > the Bioconductor users. > > My question is whether I had installed this library correctly. > > Two observations: > > 1. When I installed the impute library, there were a list of warnings. I > followed the instructions from here - > http://www.bioconductor.org/packages/release/bioc/html/impute.html . I > also tried to change the permission for the folder manually, but the old > permission reverted back to the original status. The warning messages likely result because your R was installed with an 'administrator' account, but is being run as a 'user' who doesn't have permission to update the full installation. The warnings are saying that newer versions of the listed packages are available, but cannot be installed, so that you are using slightly out-of-date pacakgs; likely the warnings can be ignored. Martin > 2. When I call the impute.knn() function, the error message is "Error: > could not find function "impute.knn"" > > > Thank you in advance, > > Wendy Yim > M.S. Candidate at Johns Hopkins University. > > > _____________________________________________________ > >> source("http://www.bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help > >> biocLite("impute") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'impute' > Installing package(s) into ?C:/Users/W/Documents/R/win-library/2.14? > (as ?lib? is unspecified) > trying URL ' > http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2. 14/impute_1.28.0.zip > ' > Content type 'application/zip' length 1216377 bytes (1.2 Mb) > opened URL > downloaded 1.2 Mb > > package ?impute? successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Users\W\AppData\Local\Temp\RtmpKMcIoN\downloaded_packages > Warning message: > 'boot' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'cluster' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'foreign' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'MASS' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'Matrix' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'mgcv' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'nlme' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'rpart' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > 'survival' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.1/library' not writeable > >> impute.knn(data=cdc28,k=6) > Error: could not find function "impute.knn" >> impute.knn > Error: object 'impute.knn' not found >> knn > Error: object 'knn' not found >> imputeknn > Error: object 'imputeknn' not found > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793