Error message with RNAither
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@catherine-garry-5054
Last seen 10.2 years ago
Hi, I keep getting an error message when i try to generate the dataset file in RNAither. This is the error i keep getting. > generateDatasetFile("DGS", "DGScreen in cells", + NA_character_, "RNAither_output_Rep1.txt", plateLayout1, plateLayout2, + 8, 12, 1, emptyWells, poorWells, controlCoordsOutput, backgroundValOutput, cellnumOutput) Error: could not find function "generateDatasetFile" Can anyone help explain why this is happening? At the beginning, as usual, i add in: library("RNAither"). but i also get an error here: Loading required package: robustbase Error: package ‘robustbase’ could not be loaded In addition: Warning messages: 1: package ‘AnnotationDbi’ was built under R version 2.14.1 2: package ‘SparseM’ was built under R version 2.14.1 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called ‘robustbase’ I also used: source("http://www.bioconductor.org/biocLite.R") biocLite("RNAither") , to install all the files etc. Can anyone help me rectify whatever is happening? Thank you. [[alternative HTML version deleted]]
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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On Wed, Feb 8, 2012 at 10:58 AM, Catherine Garry <cagarry at="" tcd.ie=""> wrote: > Hi, > > I keep getting an error message when i try to generate the dataset file in > RNAither. This is the error i keep getting. > >> generateDatasetFile("DGS", "DGScreen in cells", > + NA_character_, "RNAither_output_Rep1.txt", plateLayout1, plateLayout2, > + 8, 12, 1, emptyWells, poorWells, controlCoordsOutput, > backgroundValOutput, cellnumOutput) > > Error: could not find function "generateDatasetFile" > Can anyone help explain why this is happening? > At the beginning, as usual, i add in: > > library("RNAither"). but i also get an error here: > > Loading required package: robustbase > Error: package ?robustbase? could not be loaded > In addition: Warning messages: > 1: package ?AnnotationDbi? was built under R version 2.14.1 > 2: package ?SparseM? was built under R version 2.14.1 > 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = > lib.loc) : > ?there is no package called ?robustbase? > > I also used: > > source("http://www.bioconductor.org/biocLite.R") > biocLite("RNAither") > > , to install all the files etc. > > Can anyone help me rectify whatever is happening? It would be helpful to see the output of sessionInfo() so we can see exactly what packages you have, and a little bit about your system configuration. Without seeing it, I can guess that you have some out of date packages, and you can fix this as follows: biocLite(character(), ask=FALSE) That will update ALL Bioconductor and CRAN packages on your system which are outdated. It would also be good to see the complete output of biocLite("RNAither"). Thanks, Dan > > Thank you. > > ? ? ? ?[[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
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Hi Dan, When i tried all of this, this is what i got: > source("http://www.bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("RNAither") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'RNAither' Installing package(s) into ‘C:/Users/Catherine/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 /RNAither_2.2.0.zip ' Content type 'application/zip' length 1414362 bytes (1.3 Mb) opened URL downloaded 1.3 Mb package ‘RNAither’ successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\Catherine\AppData\Local\Temp\RtmpETRn43\downloaded_packages Warning message: 'boot' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'foreign' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'KernSmooth' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'Matrix' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'mgcv' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'nlme' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'rpart' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'survival' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable > biocLite(character(), ask=FALSE) BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Warning message: 'boot' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'foreign' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'KernSmooth' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'Matrix' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'mgcv' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'nlme' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'rpart' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable 'survival' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable > Any ideas on how to recify this? On 8 February 2012 19:13, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Wed, Feb 8, 2012 at 10:58 AM, Catherine Garry <cagarry@tcd.ie> wrote: > > Hi, > > > > I keep getting an error message when i try to generate the dataset file > in > > RNAither. This is the error i keep getting. > > > >> generateDatasetFile("DGS", "DGScreen in cells", > > + NA_character_, "RNAither_output_Rep1.txt", plateLayout1, plateLayout2, > > + 8, 12, 1, emptyWells, poorWells, controlCoordsOutput, > > backgroundValOutput, cellnumOutput) > > > > Error: could not find function "generateDatasetFile" > > Can anyone help explain why this is happening? > > At the beginning, as usual, i add in: > > > > library("RNAither"). but i also get an error here: > > > > Loading required package: robustbase > > Error: package ‘robustbase’ could not be loaded > > In addition: Warning messages: > > 1: package ‘AnnotationDbi’ was built under R version 2.14.1 > > 2: package ‘SparseM’ was built under R version 2.14.1 > > 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc > = > > lib.loc) : > > there is no package called ‘robustbase’ > > > > I also used: > > > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("RNAither") > > > > , to install all the files etc. > > > > Can anyone help me rectify whatever is happening? > > It would be helpful to see the output of sessionInfo() so we can see > exactly what packages you have, and a little bit about your system > configuration. > > Without seeing it, I can guess that you have some out of date > packages, and you can fix this as follows: > > biocLite(character(), ask=FALSE) > That will update ALL Bioconductor and CRAN packages on your system > which are outdated. > > It would also be good to see the complete output of > biocLite("RNAither"). > > Thanks, > Dan > > > > > > Thank you. > > > > [[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 > > -- *Catherine Garry *PhD Research Student *Rm. 0.36/ Lab 1.16 Department of Clinical Medicine Institute of Molecular Medicine Trinity Centre for Health Sciences Trinity College Dublin St James's Hospital Dublin 8 Republic of Ireland * Tel: +353 1 896 3350 Mob: +353 87 911 4936 [[alternative HTML version deleted]]
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On 02/09/2012 02:54 AM, Catherine Garry wrote: > Hi Dan, > > When i tried all of this, this is what i got: > >> source("http://www.bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >> biocLite("RNAither") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'RNAither' > Installing package(s) into ?C:/Users/Catherine/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/RNAither_2.2.0.zip > ' > Content type 'application/zip' length 1414362 bytes (1.3 Mb) > opened URL > downloaded 1.3 Mb > package ?RNAither? successfully unpacked and MD5 sums checked > The downloaded packages are in > C:\Users\Catherine\AppData\Local\Temp\RtmpETRn43\downloaded_packages > Warning message: > 'boot' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'foreign' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'KernSmooth' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'Matrix' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'mgcv' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'nlme' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'rpart' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'survival' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable >> biocLite(character(), ask=FALSE) > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Warning message: > 'boot' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'foreign' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'KernSmooth' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'Matrix' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'mgcv' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'nlme' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'rpart' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'survival' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable >> > Any ideas on how to recify this? These are warnings, and can be ignored; you could update your R installation to R-2.14.1 but that is not strictly necessary. The good news is > package ?RNAither? successfully unpacked and MD5 sums checked do you still have the problems >>> library("RNAither"). but i also get an error here: >>> >>> Loading required package: robustbase >>> Error: package ?robustbase? could not be loaded >>> In addition: Warning messages: >>> 1: package ?AnnotationDbi? was built under R version 2.14.1 >>> 2: package ?SparseM? was built under R version 2.14.1 >>> 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc ? Martin > > On 8 February 2012 19:13, Dan Tenenbaum<dtenenba at="" fhcrc.org=""> wrote: > >> On Wed, Feb 8, 2012 at 10:58 AM, Catherine Garry<cagarry at="" tcd.ie=""> wrote: >>> Hi, >>> >>> I keep getting an error message when i try to generate the dataset file >> in >>> RNAither. This is the error i keep getting. >>> >>>> generateDatasetFile("DGS", "DGScreen in cells", >>> + NA_character_, "RNAither_output_Rep1.txt", plateLayout1, plateLayout2, >>> + 8, 12, 1, emptyWells, poorWells, controlCoordsOutput, >>> backgroundValOutput, cellnumOutput) >>> >>> Error: could not find function "generateDatasetFile" >>> Can anyone help explain why this is happening? >>> At the beginning, as usual, i add in: >>> >>> library("RNAither"). but i also get an error here: >>> >>> Loading required package: robustbase >>> Error: package ?robustbase? could not be loaded >>> In addition: Warning messages: >>> 1: package ?AnnotationDbi? was built under R version 2.14.1 >>> 2: package ?SparseM? was built under R version 2.14.1 >>> 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc >> = >>> lib.loc) : >>> there is no package called ?robustbase? >>> >>> I also used: >>> >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("RNAither") >>> >>> , to install all the files etc. >>> >>> Can anyone help me rectify whatever is happening? >> >> It would be helpful to see the output of sessionInfo() so we can see >> exactly what packages you have, and a little bit about your system >> configuration. >> >> Without seeing it, I can guess that you have some out of date >> packages, and you can fix this as follows: >> >> biocLite(character(), ask=FALSE) >> That will update ALL Bioconductor and CRAN packages on your system >> which are outdated. >> >> It would also be good to see the complete output of >> biocLite("RNAither"). >> >> Thanks, >> Dan >> >> >>> >>> Thank you. >>> >>> [[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 >> >> > > > > > _______________________________________________ > 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
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Dan Tenenbaum ★ 8.2k
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On Wed, Feb 8, 2012 at 11:44 AM, Catherine Garry <cagarry at="" tcd.ie=""> wrote: > This is the output from sessionInfo() > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=English_Ireland.1252? LC_CTYPE=English_Ireland.1252 > [3] LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C > [5] LC_TIME=English_Ireland.1252 > attached base packages: > [1] grid????? stats???? graphics? grDevices utils???? datasets? methods > [8] base > other attached packages: > ?[1] RColorBrewer_1.0-5??? RankProd_2.26.0?????? topGO_2.6.0 > ?[4] SparseM_0.91????????? GO.db_2.6.1?????????? RSQLite_0.11.1 > ?[7] DBI_0.2-5???????????? AnnotationDbi_1.16.11 Biobase_2.14.0 > [10] graph_1.32.0 > loaded via a namespace (and not attached): > [1] IRanges_1.12.6 lattice_0.20-0 tools_2.14.0 > Thanks. > When i put in biocLite("RNAither"), i am also getting the error message > (Error: could not find function "biocLite") Do this first: source("http://bioconductor.org/biocLite.R") Also please CC the list because others may also be able to help. Thanks, Dan > > On 8 February 2012 19:13, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Wed, Feb 8, 2012 at 10:58 AM, Catherine Garry <cagarry at="" tcd.ie=""> wrote: >> > Hi, >> > >> > I keep getting an error message when i try to generate the dataset file >> > in >> > RNAither. This is the error i keep getting. >> > >> >> generateDatasetFile("DGS", "DGScreen in cells", >> > + NA_character_, "RNAither_output_Rep1.txt", plateLayout1, plateLayout2, >> > + 8, 12, 1, emptyWells, poorWells, controlCoordsOutput, >> > backgroundValOutput, cellnumOutput) >> > >> > Error: could not find function "generateDatasetFile" >> > Can anyone help explain why this is happening? >> > At the beginning, as usual, i add in: >> > >> > library("RNAither"). but i also get an error here: >> > >> > Loading required package: robustbase >> > Error: package ?robustbase? could not be loaded >> > In addition: Warning messages: >> > 1: package ?AnnotationDbi? was built under R version 2.14.1 >> > 2: package ?SparseM? was built under R version 2.14.1 >> > 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc >> > = >> > lib.loc) : >> > ?there is no package called ?robustbase? >> > >> > I also used: >> > >> > source("http://www.bioconductor.org/biocLite.R") >> > biocLite("RNAither") >> > >> > , to install all the files etc. >> > >> > Can anyone help me rectify whatever is happening? >> >> It would be helpful to see the output of sessionInfo() so we can see >> exactly what packages you have, and a little bit about your system >> configuration. >> >> Without seeing it, I can guess that you have some out of date >> packages, and you can fix this as follows: >> >> biocLite(character(), ask=FALSE) >> That will update ALL Bioconductor and CRAN packages on your system >> which are outdated. >> >> It would also be good to see the complete output of >> biocLite("RNAither"). >> >> Thanks, >> Dan >> >> >> > >> > Thank you. >> > >> > ? ? ? ?[[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 >> > > > > -- > Catherine Garry > PhD Research Student > > Rm. 0.36/ Lab 1.16 > Department of Clinical Medicine > Institute of Molecular Medicine > Trinity Centre for Health Sciences > Trinity College Dublin > St James's Hospital > Dublin 8 > Republic of Ireland > > Tel: +353 1 896 3350 > Mob: +353 87 911 4936 >
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