ReadAffy Error: new versions causing problems?
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Boel Brynedal ▴ 200
@boel-brynedal-2091
Last seen 7.2 years ago
Dear List, I am a PhD student at Karolinska Institutet in Sweden. I have a problem thats been evolving the last couple of days. The net result is that much of what I do produces error messages. I'll give an example: > raw<-ReadAffy() Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : VECTOR_ELT() can only be applied to a 'list', not a 'char' Is there something wrong with my CEL-files? I exported some of them to another computer with the same version of R and packages, and there it worked fine. When I use the biocLite installing route, the installation of both tkWidgets and tcltk seams to fail: Loading required package: tkWidgets Error: package 'tkWidgets' could not be loaded In addition: Warning message: there is no package called 'tkWidgets' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) Execution halted ERROR: execution of package source for 'marray' failed ** Removing '/usr/local/lib64/R/library/marray' ** Restoring previous '/usr/local/lib64/R/library/marray' Could this be the reason for my problems; that old and new versions of packages are mixed? My sessionInfo(): R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: gcrma matchprobes simpleaffy genefilter survival affy "2.8.1" "1.8.1" "2.8.0" "1.14.1" "2.31" "1.14.0" affyio Biobase "1.4.0" "1.14.0" Or can it be a more general problem? I just installed a new versions of both R and bioconductor packages. I'm not an expert in Linux or R, so I'll appreciate any advice! Thank you, Boel Brynedal --~*~**~***~*~***~**~*~-- Boel Brynedal, MSc, PhD student Karolinska Institutet Department of Clinical neuroscience Karolinska University hospital Huddinge Division of Neurology, R54 141 86 Stockholm SWEDEN Phone: +46 8 585 819 27 Fax: +46 8 585 870 80 E-mail: boel.brynedal at ki.se
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@james-w-macdonald-5106
Last seen 7 days ago
United States
Hi Boel, Boel Brynedal wrote: > Dear List, > > I am a PhD student at Karolinska Institutet in Sweden. I have a problem > thats been evolving the last couple of days. The net result is that much > of what I do produces error messages. I'll give an example: > > >>raw<-ReadAffy() > > Error in read.affybatch(filenames = l$filenames, phenoData = l >$phenoData, : > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > Is there something wrong with my CEL-files? I exported some of them to > another computer with the same version of R and packages, and there it > worked fine. I don't know that there is anything wrong with your celfiles. This error usually means that ReadAffy() is sending something wrong to the C code, most often due to errant passing of arguments as celfile names. However, in your case this not what I would expect. What do you get when you do list.celfiles()? Also, does raw <- ReadAffy(filenames=list.celfiles()) help? Best, Jim > > When I use the biocLite installing route, the installation of both > tkWidgets and tcltk seams to fail: > Loading required package: tkWidgets > Error: package 'tkWidgets' could not be loaded > In addition: Warning message: > there is no package called 'tkWidgets' in: library(pkg, character.only = > TRUE, logical = TRUE, lib.loc = lib.loc) > Execution halted > ERROR: execution of package source for 'marray' failed > ** Removing '/usr/local/lib64/R/library/marray' > ** Restoring previous '/usr/local/lib64/R/library/marray' > > Could this be the reason for my problems; that old and new versions of > packages are mixed? > > My sessionInfo(): > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > gcrma matchprobes simpleaffy genefilter survival affy > "2.8.1" "1.8.1" "2.8.0" "1.14.1" "2.31" "1.14.0" > affyio Biobase > "1.4.0" "1.14.0" > > Or can it be a more general problem? I just installed a new versions of > both R and bioconductor packages. > > I'm not an expert in Linux or R, so I'll appreciate any advice! > Thank you, > > Boel Brynedal > > --~*~**~***~*~***~**~*~-- > Boel Brynedal, MSc, PhD student > Karolinska Institutet > Department of Clinical neuroscience > > Karolinska University hospital Huddinge > Division of Neurology, R54 > 141 86 Stockholm > SWEDEN > Phone: +46 8 585 819 27 > Fax: +46 8 585 870 80 > E-mail: boel.brynedal at ki.se > > _______________________________________________ > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Thank you, this works! On Wed, 2007-05-23 at 11:58 -0400, James W. MacDonald wrote: > Hi Boel, > > Boel Brynedal wrote: > > Dear List, > > > > I am a PhD student at Karolinska Institutet in Sweden. I have a problem > > thats been evolving the last couple of days. The net result is that much > > of what I do produces error messages. I'll give an example: > > > > > >>raw<-ReadAffy() > > > > Error in read.affybatch(filenames = l$filenames, phenoData = l > >$phenoData, : > > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > > > Is there something wrong with my CEL-files? I exported some of them to > > another computer with the same version of R and packages, and there it > > worked fine. > > I don't know that there is anything wrong with your celfiles. This error > usually means that ReadAffy() is sending something wrong to the C code, > most often due to errant passing of arguments as celfile names. However, > in your case this not what I would expect. > > What do you get when you do > > list.celfiles()? > > Also, does > > raw <- ReadAffy(filenames=list.celfiles()) > > help? > > Best, > > Jim > > > > > When I use the biocLite installing route, the installation of both > > tkWidgets and tcltk seams to fail: > > Loading required package: tkWidgets > > Error: package 'tkWidgets' could not be loaded > > In addition: Warning message: > > there is no package called 'tkWidgets' in: library(pkg, character.only = > > TRUE, logical = TRUE, lib.loc = lib.loc) > > Execution halted > > ERROR: execution of package source for 'marray' failed > > ** Removing '/usr/local/lib64/R/library/marray' > > ** Restoring previous '/usr/local/lib64/R/library/marray' > > > > Could this be the reason for my problems; that old and new versions of > > packages are mixed? > > > > My sessionInfo(): > > R version 2.5.0 (2007-04-23) > > x86_64-unknown-linux-gnu > > > > attached base packages: > > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > > [7] "datasets" "methods" "base" > > > > other attached packages: > > gcrma matchprobes simpleaffy genefilter survival affy > > "2.8.1" "1.8.1" "2.8.0" "1.14.1" "2.31" "1.14.0" > > affyio Biobase > > "1.4.0" "1.14.0" > > > > Or can it be a more general problem? I just installed a new versions of > > both R and bioconductor packages. > > > > I'm not an expert in Linux or R, so I'll appreciate any advice! > > Thank you, > > > > Boel Brynedal > > > > --~*~**~***~*~***~**~*~-- > > Boel Brynedal, MSc, PhD student > > Karolinska Institutet > > Department of Clinical neuroscience > > > > Karolinska University hospital Huddinge > > Division of Neurology, R54 > > 141 86 Stockholm > > SWEDEN > > Phone: +46 8 585 819 27 > > Fax: +46 8 585 870 80 > > E-mail: boel.brynedal at ki.se > > > > _______________________________________________ > > 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 > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@julien-gagneur-2179
Last seen 7.2 years ago
James W. MacDonald <jmacdon at="" ...=""> writes: > Hi Boel, > > Boel Brynedal wrote: > > Dear List, > > > >>raw<-ReadAffy() > > > > Error in read.affybatch(filenames = l$filenames, phenoData = l > >$phenoData, : > > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > [...] > > Also, does > > raw <- ReadAffy(filenames=list.celfiles()) > > help? Dear List, I have a problem similar to the one raised by Boel but for which list.celfiles() would not help. This is what I get under R version 2.5.0 (2007-04-23), x86_64-redhat- linux-gnu affy 1.14.0: > a = ReadAffy(filenames="tmp.CEL.gz", celfile.path="data/celfiles", verbose=TRUE, compress=TRUE) 1 reading data/celfiles/tmp.CEL.gz ...instantiating an AffyBatch (intensity a 6553600x1 matrix)...done. Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : VECTOR_ELT() can only be applied to a 'list', not a 'char' The problem seems to be environment related, everything goes fine under windows, using R version 2.5.0 (2007-04-23) i386-pc-mingw32, affy 1.14.0. It may be due to a change in the code of read.affybatch. If I use the read.affybatch function of affy 1.12.0, the linux problem does not occur any more. If this helps, I noticed that in the .Call("read_abatch", ...) 'filenames' used to be a list of vectors and is now only a vector. Thanks for your help, Julien.
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These errors are typically caused by a mismatch between your version of affy and your version of affyio. Given that you note that it works fine using affy 1.12.0, this likely means you are uing an older affyio (not the one from the current BioC 2.0 release) Ben On Mon, 2007-05-28 at 16:43 +0000, Julien Gagneur wrote: > James W. MacDonald <jmacdon at="" ...=""> writes: > > > Hi Boel, > > > > Boel Brynedal wrote: > > > Dear List, > > > > > >>raw<-ReadAffy() > > > > > > Error in read.affybatch(filenames = l$filenames, phenoData = l > > >$phenoData, : > > > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > > > [...] > > > > Also, does > > > > raw <- ReadAffy(filenames=list.celfiles()) > > > > help? > > > Dear List, > > I have a problem similar to the one raised by Boel but for which list.celfiles() > would not help. > > This is what I get under R version 2.5.0 (2007-04-23), x86_64 -redhat-linux-gnu > affy 1.14.0: > > > a = ReadAffy(filenames="tmp.CEL.gz", celfile.path="data/celfiles", > verbose=TRUE, compress=TRUE) > 1 reading data/celfiles/tmp.CEL.gz ...instantiating an AffyBatch > (intensity a 6553600x1 matrix)...done. > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > > > The problem seems to be environment related, everything goes fine under windows, > using R version 2.5.0 (2007-04-23) i386-pc-mingw32, affy 1.14.0. > > > It may be due to a change in the code of read.affybatch. If I use the > read.affybatch function of affy 1.12.0, the linux problem does not occur any > more. If this helps, I noticed that in the .Call("read_abatch", ...) 'filenames' > used to be a list of vectors and is now only a vector. > > Thanks for your help, > > Julien. > > _______________________________________________ > 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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@julien-gagneur-2179
Last seen 7.2 years ago
Ben Bolstad <bmb at="" ...=""> writes: > > These errors are typically caused by a mismatch between your version of > affy and your version of affyio. Given that you note that it works fine > using affy 1.12.0, this likely means you are uing an older affyio (not > the one from the current BioC 2.0 release) > > Ben > I installed the last affyio. It works now. Thanks. Julien.
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Dear Ben, would it be possible to use the "Depends" field of the DESCRIPTION in the affy package to safeguard better against such user confusions? (i.e. state the required versions of affyio etc. rather than just their name). Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Julien Gagneur ha scritto: > Ben Bolstad <bmb at="" ...=""> writes: > >> These errors are typically caused by a mismatch between your version of >> affy and your version of affyio. Given that you note that it works fine >> using affy 1.12.0, this likely means you are uing an older affyio (not >> the one from the current BioC 2.0 release) >> >> Ben >> > > > I installed the last affyio. It works now. > Thanks. > Julien.