makecdfenv problem
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colin clarke ▴ 30
@colin-clarke-3282
Last seen 9.6 years ago
Hi all, R is returning the following error when attempting to load the makecdfenv > library("makecdfenv") Error : package 'affy' does not have a name space Error in as.environment(pos) : no item called "newtable" on the search list Error: package/namespace load failed for 'makecdfenv' My version info: platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 8.1 year 2008 month 12 day 22 svn rev 47281 language R version.string R version 2.8.1 (2008-12-22) Any help would be greatly appriciated, Colin [[alternative HTML version deleted]]
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
United States
Hi Colin, Using R 2.8.1 I can't reproduce this. Could you please tell us a little more about what packages you had loaded (sessionInfo()), when this happened? For example what version of affy are you using? Have you run update.packages() lately? source("http://bioconductor.org/biocLite.R") update.packages(repos=biocinstallRepos(), ask=FALSE) Marc colin clarke wrote: > Hi all, > > R is returning the following error when attempting to load the makecdfenv > > >> library("makecdfenv") >> > Error : package 'affy' does not have a name space > Error in as.environment(pos) : > no item called "newtable" on the search list > Error: package/namespace load failed for 'makecdfenv' > > My version info: > > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 8.1 > year 2008 > month 12 > day 22 > svn rev 47281 > language R > version.string R version 2.8.1 (2008-12-22) > > Any help would be greatly appriciated, > > Colin > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Hi Colin, A sessionInfo() would be helpful, as would the output from packageDescription("makecdfenv")$V and packageDescription("affy")$V as this works for me: > library(makecdfenv) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affy Loading required package: affyio > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices datasets utils methods [8] base other attached packages: [1] makecdfenv_1.20.0 affyio_1.10.0 affy_1.21.6 Biobase_2.2.0 loaded via a namespace (and not attached): [1] preprocessCore_1.4.0 Best, Jim colin clarke wrote: > Hi all, > > R is returning the following error when attempting to load the makecdfenv > >> library("makecdfenv") > Error : package 'affy' does not have a name space > Error in as.environment(pos) : > no item called "newtable" on the search list > Error: package/namespace load failed for 'makecdfenv' > > My version info: > > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 8.1 > year 2008 > month 12 > day 22 > svn rev 47281 > language R > version.string R version 2.8.1 (2008-12-22) > > Any help would be greatly appriciated, > > Colin > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Hi Colin, Please don't take things off-list. The intent is that the list archives might be a useful thing for people to search for answers. colin clarke wrote: > Hi James, > > sessionInfo() > > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] pls_2.1-0 affy_1.14.2 affyio_1.10.1 Biobase_2.2.2 > plsgenomics_1.2-2 MASS_7.2-45 > > > packageDescription("makecdfenv")$V > [1] "1.20.0" > > packageDescription("affy")$V > [1] "1.14.2" This is your problem. You have a very out of date version of affy. No idea how you got such a beast, but using biocLite() to install packages should make such a thing impossible. So biocLite("affy") should get you fixed up. Best, Jim > > Thank you, > > Colin > > > > > On Thu, Feb 12, 2009 at 4:20 PM, James W. MacDonald > <jmacdon at="" med.umich.edu="">wrote: > >> Hi Colin, >> >> A sessionInfo() would be helpful, as would the output from >> >> packageDescription("makecdfenv")$V >> and >> packageDescription("affy")$V >> >> as this works for me: >> >>> library(makecdfenv) >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: affy >> Loading required package: affyio >>> sessionInfo() >> R version 2.8.0 (2008-10-20) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] tools stats graphics grDevices datasets utils methods >> [8] base >> >> other attached packages: >> [1] makecdfenv_1.20.0 affyio_1.10.0 affy_1.21.6 Biobase_2.2.0 >> >> loaded via a namespace (and not attached): >> [1] preprocessCore_1.4.0 >> >> Best, >> >> Jim >> >> >> >> colin clarke wrote: >> >>> Hi all, >>> >>> R is returning the following error when attempting to load the makecdfenv >>> >>> library("makecdfenv") >>> Error : package 'affy' does not have a name space >>> Error in as.environment(pos) : >>> no item called "newtable" on the search list >>> Error: package/namespace load failed for 'makecdfenv' >>> >>> My version info: >>> >>> platform i386-pc-mingw32 >>> arch i386 >>> os mingw32 >>> system i386, mingw32 >>> status >>> major 2 >>> minor 8.1 >>> year 2008 >>> month 12 >>> day 22 >>> svn rev 47281 >>> language R >>> version.string R version 2.8.1 (2008-12-22) >>> >>> Any help would be greatly appriciated, >>> >>> Colin >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >> Hildebrandt Lab >> 8220D MSRB III >> 1150 W. Medical Center Drive >> Ann Arbor MI 48109-0646 >> 734-936-8662 >> > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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Hi James, That worked a treat! Thanks a million for your help, Cheers, Colin On Thu, Feb 12, 2009 at 5:11 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Colin, > > Please don't take things off-list. The intent is that the list archives > might be a useful thing for people to search for answers. > > colin clarke wrote: > >> Hi James, >> >> sessionInfo() >> >> R version 2.8.1 (2008-12-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] pls_2.1-0 affy_1.14.2 affyio_1.10.1 Biobase_2.2.2 >> plsgenomics_1.2-2 MASS_7.2-45 >> >> >> packageDescription("makecdfenv")$V >> [1] "1.20.0" >> >> packageDescription("affy")$V >> [1] "1.14.2" >> > > This is your problem. You have a very out of date version of affy. No idea > how you got such a beast, but using biocLite() to install packages should > make such a thing impossible. > > So biocLite("affy") should get you fixed up. > > Best, > > Jim > > > > >> Thank you, >> >> Colin >> >> >> >> >> On Thu, Feb 12, 2009 at 4:20 PM, James W. MacDonald >> <jmacdon@med.umich.edu>wrote: >> >> Hi Colin, >>> >>> A sessionInfo() would be helpful, as would the output from >>> >>> packageDescription("makecdfenv")$V >>> and >>> packageDescription("affy")$V >>> >>> as this works for me: >>> >>> library(makecdfenv) >>>> >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: affy >>> Loading required package: affyio >>> >>>> sessionInfo() >>>> >>> R version 2.8.0 (2008-10-20) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices datasets utils methods >>> [8] base >>> >>> other attached packages: >>> [1] makecdfenv_1.20.0 affyio_1.10.0 affy_1.21.6 Biobase_2.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] preprocessCore_1.4.0 >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> colin clarke wrote: >>> >>> Hi all, >>>> >>>> R is returning the following error when attempting to load the >>>> makecdfenv >>>> >>>> library("makecdfenv") >>>> Error : package 'affy' does not have a name space >>>> Error in as.environment(pos) : >>>> no item called "newtable" on the search list >>>> Error: package/namespace load failed for 'makecdfenv' >>>> >>>> My version info: >>>> >>>> platform i386-pc-mingw32 >>>> arch i386 >>>> os mingw32 >>>> system i386, mingw32 >>>> status >>>> major 2 >>>> minor 8.1 >>>> year 2008 >>>> month 12 >>>> day 22 >>>> svn rev 47281 >>>> language R >>>> version.string R version 2.8.1 (2008-12-22) >>>> >>>> Any help would be greatly appriciated, >>>> >>>> Colin >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@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 >>> Hildebrandt Lab >>> 8220D MSRB III >>> 1150 W. Medical Center Drive >>> Ann Arbor MI 48109-0646 >>> 734-936-8662 >>> >>> >> > -- > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662 > [[alternative HTML version deleted]]
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