Error message with RNAither
2
0
Entering edit mode
@catherine-garry-5054
Last seen 9.6 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]]
• 1.2k views
ADD COMMENT •
0
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.2 years ago
United States
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
ADD COMMENT •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.2 years ago
United States
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 >
ADD COMMENT •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 826 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6