can't instal MetaData package "mouse4302"
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@gordon-smyth
Last seen 32 minutes ago
WEHI, Melbourne, Australia
I'm trying to update my copy of the 'mouse4302' annotation package. I have version 1.6.5, in the recent past version 1.6.8 was available, now I can't seem to get the package at all. I think the package used to be listed on the page http://www.bioconductor.org/data/metaData.html for the row 'moe430_2', but it's not there now. If I try install.packages2("mouse4302") under R 2.0.1 for Windows, the file 'mouse4302_1.6.8.zip' which is downloaded turns out to be of size zero. If I try install.packages2("mouse4302") under R 2.0.0 for linux (see the session below), a directory 'Rlibs/mouse4302' is created which seems at first sight to be a valid package, and even builds. However it will not load. The DESCRIPTION file is dated 6 Jan 2005. Can someone help me? Gordon > library(reposTools) Loading required package: tools Warning messages: 1: Incorrect permissions to edit package database, /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, curLib) 2: Incorrect permissions to edit package database, /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, curLib) > install.packages2("mouse4302",lib="Rlibs") Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download mouse4302 from http://www.bioconductor.org/data/metaData/" [1] "Download complete." [1] "Installing mouse4302" * Installing *source* package 'mouse4302' ... ** R ** data ** preparing package for lazy loading Error in .find.package("mouse4302") : none of the packages were found Execution halted ERROR: lazy loading failed for package 'mouse4302' From URL: http://www.bioconductor.org/data/metaData/ mouse4302 version 1.6.8 Warning message: Installation of package mouse4302 had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > install.packages2("mouse4302",lib="Rlibs",develOK=TRUE) Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download mouse4302 from http://www.bioconductor.org/data/metaData/" [1] "Download complete." [1] "Installing mouse4302" * Installing *source* package 'mouse4302' ... ** R ** data ** preparing package for lazy loading Error in .find.package("mouse4302") : none of the packages were found Execution halted ERROR: lazy loading failed for package 'mouse4302' ** Removing '/export/share/disk501/lab0605/smyth/gordon/Rlibs/mouse4302' ** Restoring previous '/export/share/disk501/lab0605/smyth/gordon/Rlibs/mouse4302' From URL: http://www.bioconductor.org/data/metaData/ mouse4302 version 1.6.8 Warning message: Installation of package mouse4302 had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 0.0 year 2004 month 10 day 04 language R > dir()
Annotation mouse4302 Annotation mouse4302 • 1.6k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Gordon, We've discovered a wide-spread issue with how the Windows metaData packages were built that makes the data very difficult to access. We are working on a fix and should have corrected packages posted soon. The Source packages, for Linux, are still available. From the transcript you sent, it would be helpful to know the value of the environment variable R_LIBS as well as the library package path, which you can get like this from inside R: path = .libPaths() This function returns invisibly, so you have to capture its return value in a variable in order to see it. On Mar 3, 2005, at 1:58 AM, Gordon Smyth wrote: > > library(reposTools) > Loading required package: tools > Warning messages: > 1: Incorrect permissions to edit package database, > /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, > curLib) > 2: Incorrect permissions to edit package database, > /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, > curLib) The above message indicates a permission problem with where you are installing your packages to. > [1] "Attempting to download mouse4302 from > http://www.bioconductor.org/data/metaData/" > [1] "Download complete." > [1] "Installing mouse4302" > * Installing *source* package 'mouse4302' ... > ** R > ** data > ** preparing package for lazy loading > Error in .find.package("mouse4302") : none of the packages were found > Execution halted > ERROR: lazy loading failed for package 'mouse4302' > From URL: http://www.bioconductor.org/data/metaData/ > mouse4302 version 1.6.8 > I've seen this error when the library path I was installing packages into was not the default R system path and I had not set and "exported" R_LIBS to my non-default path before running R. See the documentation for install.packages where there is a brief note about R_LIBS. Hope that helps, + seth
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@kasper-daniel-hansen-459
Last seen 10.2 years ago
Seth wrote yesterday that he is working on fixing the windows build of the metadata packages, so that part of the site has been taking ofline. He expected to be finished around noon pacific time. So I would try again tomorrow. Kasper On Thu, Mar 03, 2005 at 08:58:14PM +1100, Gordon Smyth wrote: > I'm trying to update my copy of the 'mouse4302' annotation package. I have > version 1.6.5, in the recent past version 1.6.8 was available, now I can't > seem to get the package at all. I think the package used to be listed on > the page http://www.bioconductor.org/data/metaData.html for the row > 'moe430_2', but it's not there now. > > If I try install.packages2("mouse4302") under R 2.0.1 for Windows, the file > 'mouse4302_1.6.8.zip' which is downloaded turns out to be of size zero. > > If I try install.packages2("mouse4302") under R 2.0.0 for linux (see the > session below), a directory 'Rlibs/mouse4302' is created which seems at > first sight to be a valid package, and even builds. However it will not > load. The DESCRIPTION file is dated 6 Jan 2005. > > Can someone help me? > Gordon > > > library(reposTools) > Loading required package: tools > Warning messages: > 1: Incorrect permissions to edit package database, > /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, curLib) > 2: Incorrect permissions to edit package database, > /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, curLib) > > install.packages2("mouse4302",lib="Rlibs") > Note: You did not specify a download type. Using a default value of: Source > This will be fine for almost all users > > [1] "Attempting to download mouse4302 from > http://www.bioconductor.org/data/metaData/" > [1] "Download complete." > [1] "Installing mouse4302" > * Installing *source* package 'mouse4302' ... > ** R > ** data > ** preparing package for lazy loading > Error in .find.package("mouse4302") : none of the packages were found > Execution halted > ERROR: lazy loading failed for package 'mouse4302' > From URL: http://www.bioconductor.org/data/metaData/ > mouse4302 version 1.6.8 > > Warning message: > Installation of package mouse4302 had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > > install.packages2("mouse4302",lib="Rlibs",develOK=TRUE) > Note: You did not specify a download type. Using a default value of: Source > This will be fine for almost all users > > [1] "Attempting to download mouse4302 from > http://www.bioconductor.org/data/metaData/" > [1] "Download complete." > [1] "Installing mouse4302" > * Installing *source* package 'mouse4302' ... > ** R > ** data > ** preparing package for lazy loading > Error in .find.package("mouse4302") : none of the packages were found > Execution halted > ERROR: lazy loading failed for package 'mouse4302' > ** Removing '/export/share/disk501/lab0605/smyth/gordon/Rlibs/mouse4302' > ** Restoring previous > '/export/share/disk501/lab0605/smyth/gordon/Rlibs/mouse4302' > From URL: http://www.bioconductor.org/data/metaData/ > mouse4302 version 1.6.8 > > Warning message: > Installation of package mouse4302 had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > > version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 2 > minor 0.0 > year 2004 > month 10 > day 04 > language R > > dir() > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
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@gordon-smyth
Last seen 32 minutes ago
WEHI, Melbourne, Australia
I guess that things have changed since the MetaData packages were re- built earlier today, but the mouse4302 problem hasn't been solved, so I provide more info below as requested. >Date: Thu, 3 Mar 2005 07:28:09 -0800 >From: Seth Falcon <sfalcon@fhcrc.org> >Subject: Re: [BioC] can't instal MetaData package "mouse4302" >To: BioC Mailing List <bioconductor@stat.math.ethz.ch> > >Hi Gordon, > >We've discovered a wide-spread issue with how the Windows metaData >packages were built that makes the data very difficult to access. > >We are working on a fix and should have corrected packages posted soon. > >The Source packages, for Linux, are still available. From the >transcript you sent, it would be helpful to know the value of the >environment variable R_LIBS as well as the library package path, which >you can get like this from inside R: > >path = .libPaths() I'm using a plain vanilla R 2.0.0 for unix system, installed by our IT staff just after the last release of Bioconductor on a multi-user linux system with default everything. The default library tree is > .libPaths() [1] "/usr/local/lib/R/library" All environment variables are at default settings, meaning that R_LIBS is not set: > system("echo $R_RLIBS") >This function returns invisibly, so you have to capture its return >value in a variable in order to see it. I didn't find this necessary -- .libPaths() has an invisible name, but the value it returns is just a character value, not wrapped in a call to invisible(). >On Mar 3, 2005, at 1:58 AM, Gordon Smyth wrote: > > > library(reposTools) > > Loading required package: tools > > Warning messages: > > 1: Incorrect permissions to edit package database, > > /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, > > curLib) > > 2: Incorrect permissions to edit package database, > > /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, > > curLib) > >The above message indicates a permission problem with where you are >installing your packages to. This is such a familiar warning message, and the reasons for it are well known, so I didn't comment on it in my original post. In my opinion, the problem is not with the permissions on our system, which are perfectly standard, but rather with the insistance by reposTools in trying to write to a directory which it really has no right to expect to be able to write to. I doubt that there are many unix systems administrators around the world concerned with security and system stability who would want all the users on a multiuser system having write privileges to system directories like /usr/lib and /usr/local/lib. Note also that there is actually no permission problem. I don't have write privileges to /usr/local/lib, but I am also not trying to install any packages there. The whole point of the 'lib' argument in my call to install.packages2() was to re-direct installation to another library tree where I do have write privileges. Finally, note that there is actually no reason for reposTools to be writing to disk at all. There is an existing and up-to-date file /usr/local/lib/R/library/liblisting.Rda already, created when the IT staff ran getBioC() back in October. There is no reason to re-write this file every time any user loads up reposTools, especially as no request has been made by the user to install packages to this directory. It would be much better if reposTools wrote to disk only when necessary, and in those cases wrote to the library tree when installation was actually to take place. > > [1] "Attempting to download mouse4302 from > > http://www.bioconductor.org/data/metaData/" > > [1] "Download complete." > > [1] "Installing mouse4302" > > * Installing *source* package 'mouse4302' ... > > ** R > > ** data > > ** preparing package for lazy loading > > Error in .find.package("mouse4302") : none of the packages were found > > Execution halted > > ERROR: lazy loading failed for package 'mouse4302' > > From URL: http://www.bioconductor.org/data/metaData/ > > mouse4302 version 1.6.8 > >I've seen this error when the library path I was installing packages >into was not the default R system path and I had not set and >"exported" R_LIBS to my non-default path before running R. See the >documentation for install.packages where there is a brief note about >R_LIBS. I don't think that the problem is to do with R_LIBS. Firstly, the use of the 'lib' argument to install.packages2() should provide a working library tree value, obviating the need for R_LIBS. Secondly, the problem is specific to the "mouse4302" package. Two days ago, > install.packages("hgu95av2",lib="Rlibs") and > install.packages("mouse4302",lib="/home/users/lab0605/smyth/gordon/ Rlibs") both worked, while > install.packages("mouse4302",lib="Rlibs") failed. Today, both of the last two commands fail. Hope this extra information helps to track something down. Cheers Gordon >Hope that helps, > >+ seth
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Gordon, The mouse4302 annotation package is again available. The version is 1.6.9. The data is the same as version 1.6.8, the packaging was modified so that the package is usable on Windows. Sorry for the delay. Best, + seth Gordon Smyth <smyth@wehi.edu.au> writes: > I'm trying to update my copy of the 'mouse4302' annotation package. I > have version 1.6.5, in the recent past version 1.6.8 was available, > now I can't seem to get the package at all. I think the package used > to be listed on the page > http://www.bioconductor.org/data/metaData.html for the row 'moe430_2', > but it's not there now. > > If I try install.packages2("mouse4302") under R 2.0.1 for Windows, the > file 'mouse4302_1.6.8.zip' which is downloaded turns out to be of size > zero. > > If I try install.packages2("mouse4302") under R 2.0.0 for linux (see > the session below), a directory 'Rlibs/mouse4302' is created which > seems at first sight to be a valid package, and even builds. However > it will not load. The DESCRIPTION file is dated 6 Jan 2005. > > Can someone help me? > Gordon >
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At 01:11 PM 12/03/2005, Seth Falcon wrote: >Hi Gordon, > >The mouse4302 annotation package is again available. The version is >1.6.9. The data is the same as version 1.6.8, the packaging was >modified so that the package is usable on Windows. > >Sorry for the delay. >Best, >+ seth Hi Seth, Many thanks for this. I'll update my recent Mouse 430 2.0 analyses with this package. I've compared versions 1.6.5 and 1.6.9 of the mouse4302 annotation package and found somewhat more differences than I expected. 3758 probe sets have symbols now which didn't before, and 166 probe sets which previously had symbols have no symbol now. More surprisingly, a further 3940 probe sets have different symbols than before. That makes 7864 probe sets in total for which the gene symbols have changed. Are these changes just a reflection of changes in the public databases, or have there also been changes in how the content of the annotation package is assembled? It seems that there have. Many of the changes from version 1.6.5 to 1.6.9 look like improvements, but there are also some which seem clearly wrong. For example, consider probe set 1460164_at. This probe set is identified by NETAFFX as being gene "Spin" with LocusLinkID 20729, and that was the information given in version 1.6.5 of the mouse4302 package. In version 1.6.9, this probe set has been re-assigned to LocusLink 102420 which, according to Entrez Gene, is an obsolete identifier. What information is being used by the package builder which could cause the LocusLinkID given by Affymetrix to be over-ruled? Many thanks for your help Gordon > library("mouse4302") > packageDescription("mouse4302")$Version [1] "1.6.5" > packageDescription("mouse4302")$Created [1] "Thu Oct 21 16:13:45 2004" > mouse4302.v165 <- as.list(mouse4302SYMBOL) > detach(2) > library(reposTools) > install.packages2("mouse4302") Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users [1] "Attempting to download mouse4302 from http://www.bioconductor.org/data/metaData/" [1] "Download complete." [1] "Installing mouse4302" [1] "Installation complete" From URL: http://www.bioconductor.org/data/metaData/ mouse4302 version 1.6.9 > library("mouse4302") > packageDescription("mouse4302")$Version [1] "1.6.9" > packageDescription("mouse4302")$Created [1] "Fri Mar 11 13:54:41 PST 2005" > mouse4302.v169 <- as.list(mouse4302SYMBOL) > o165 <- order(names(mouse4302.v165)) > o169 <- order(names(mouse4302.v169)) > mouse4302.v165.symbol <- unlist(mouse4302.v165)[o165] > mouse4302.v169.symbol <- unlist(mouse4302.v169)[o169] > table(v165=is.na(mouse4302.v165.symbol),v169=is.na(mouse4302.v169.s ymbol)) v169 v165 FALSE TRUE FALSE 36489 166 TRUE 3758 4688 > notna <- !is.na(mouse4302.v165.symbol) & !is.na(mouse4302.v169.symbol) > noteq <- (mouse4302.v165.symbol[notna] != mouse4302.v169.symbol[notna]) > sum(noteq) [1] 3940 > tab.noteq <- data.frame(v165=mouse4302.v165.symbol[notna][noteq],v169=mouse4302.v16 9.symbol[notna][noteq]) > tab.noteq[1:20,] v165 v169 1415692_s_at Canx AI316784 1415693_at 1110021N07Rik Derl1 1415703_at Ureb1 C430014N20Rik 1415711_at D130059B05Rik Arfgef1 1415712_at Zranb1 Ctbp2 1415715_at Slbp 2410015J15Rik 1415719_s_at Arcp Armc1 1415720_s_at 2510031P20Rik Mad2l1bp 1415725_at E130302O19Rik Rrn3 1415726_at BC038311 AU017193 1415758_at 2510002A14Rik 2010313D22Rik 1415765_at Bscl2 AI465155 1415793_at AI415282 Pnpo 1415937_s_at Pdcd6ip AI197427 1415948_at Pappa2 Creg1 1415953_s_at Mark2 AU024026 1415954_at Try4 1810049H19Rik 1416043_at Nasp A430091L06Rik 1416046_a_at 0610025O11Rik Fuca2 1416047_at 0610025O11Rik Fuca2 > library(annotate) > getSYMBOL("1460164_at",data="mouse4302") [1] NA > getLL("1460164_at",data="mouse4302") [1] 102420 > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 0.1 year 2004 month 11 day 15 language R
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Hi Gordon, Thanks for the careful report - we will be looking in to this and see what can be resolved. Some issues are due to the move to Seattle (hopefully that is mostly resolved now), and some due to the change from LocusLink to EntrezGene - and that is more problematic as our basic data sources have changed completely. Best wishes, Robert On Mar 11, 2005, at 10:40 PM, Gordon Smyth wrote: > At 01:11 PM 12/03/2005, Seth Falcon wrote: >> Hi Gordon, >> >> The mouse4302 annotation package is again available. The version is >> 1.6.9. The data is the same as version 1.6.8, the packaging was >> modified so that the package is usable on Windows. >> >> Sorry for the delay. >> Best, >> + seth > > Hi Seth, > > Many thanks for this. I'll update my recent Mouse 430 2.0 analyses > with this package. > > I've compared versions 1.6.5 and 1.6.9 of the mouse4302 annotation > package and found somewhat more differences than I expected. 3758 > probe sets have symbols now which didn't before, and 166 probe sets > which previously had symbols have no symbol now. More surprisingly, a > further 3940 probe sets have different symbols than before. That > makes 7864 probe sets in total for which the gene symbols have > changed. > > Are these changes just a reflection of changes in the public > databases, or have there also been changes in how the content of the > annotation package is assembled? It seems that there have. > > Many of the changes from version 1.6.5 to 1.6.9 look like > improvements, but there are also some which seem clearly wrong. For > example, consider probe set 1460164_at. This probe set is identified > by NETAFFX as being gene "Spin" with LocusLinkID 20729, and that was > the information given in version 1.6.5 of the mouse4302 package. In > version 1.6.9, this probe set has been re-assigned to LocusLink 102420 > which, according to Entrez Gene, is an obsolete identifier. What > information is being used by the package builder which could cause the > LocusLinkID given by Affymetrix to be over-ruled? > > Many thanks for your help > Gordon > > > library("mouse4302") > > packageDescription("mouse4302")$Version > [1] "1.6.5" > > packageDescription("mouse4302")$Created > [1] "Thu Oct 21 16:13:45 2004" > > mouse4302.v165 <- as.list(mouse4302SYMBOL) > > detach(2) > > library(reposTools) > > install.packages2("mouse4302") > Note: You did not specify a download type. Using a default value of: > Win32 > This will be fine for almost all users > > [1] "Attempting to download mouse4302 from > http://www.bioconductor.org/data/metaData/" > [1] "Download complete." > [1] "Installing mouse4302" > [1] "Installation complete" > From URL: http://www.bioconductor.org/data/metaData/ > mouse4302 version 1.6.9 > > > library("mouse4302") > > packageDescription("mouse4302")$Version > [1] "1.6.9" > > packageDescription("mouse4302")$Created > [1] "Fri Mar 11 13:54:41 PST 2005" > > mouse4302.v169 <- as.list(mouse4302SYMBOL) > > o165 <- order(names(mouse4302.v165)) > > o169 <- order(names(mouse4302.v169)) > > mouse4302.v165.symbol <- unlist(mouse4302.v165)[o165] > > mouse4302.v169.symbol <- unlist(mouse4302.v169)[o169] > > > table(v165=is.na(mouse4302.v165.symbol),v169=is.namouse4302.v169.sy mbo > l)) > v169 > v165 FALSE TRUE > FALSE 36489 166 > TRUE 3758 4688 > > notna <- !is.na(mouse4302.v165.symbol) & > !is.na(mouse4302.v169.symbol) > > noteq <- (mouse4302.v165.symbol[notna] != > mouse4302.v169.symbol[notna]) > > sum(noteq) > [1] 3940 > > tab.noteq <- > data.frame(v165=mouse4302.v165.symbol[notna][noteq],v169=mouse4302.v 169 > .symbol[notna][noteq]) > > tab.noteq[1:20,] > v165 v169 > 1415692_s_at Canx AI316784 > 1415693_at 1110021N07Rik Derl1 > 1415703_at Ureb1 C430014N20Rik > 1415711_at D130059B05Rik Arfgef1 > 1415712_at Zranb1 Ctbp2 > 1415715_at Slbp 2410015J15Rik > 1415719_s_at Arcp Armc1 > 1415720_s_at 2510031P20Rik Mad2l1bp > 1415725_at E130302O19Rik Rrn3 > 1415726_at BC038311 AU017193 > 1415758_at 2510002A14Rik 2010313D22Rik > 1415765_at Bscl2 AI465155 > 1415793_at AI415282 Pnpo > 1415937_s_at Pdcd6ip AI197427 > 1415948_at Pappa2 Creg1 > 1415953_s_at Mark2 AU024026 > 1415954_at Try4 1810049H19Rik > 1416043_at Nasp A430091L06Rik > 1416046_a_at 0610025O11Rik Fuca2 > 1416047_at 0610025O11Rik Fuca2 > > library(annotate) > > getSYMBOL("1460164_at",data="mouse4302") > [1] NA > > getLL("1460164_at",data="mouse4302") > [1] 102420 > > version > _ > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 0.1 > year 2004 > month 11 > day 15 > language R > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+
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