problem with loading affyQCReport

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Tuomas Raitila ▴ 10

@tuomas-raitila-1539

Last seen 10.2 years ago

Hello I'm having some trouble with loading affyQCReport package. I'm using RGui 2.2.0 (windows). The error message I got looks like this: > library(affyQCReport) Loading required package: simpleaffy Loading required package: genefilter Loading required package: survival Loading required package: splines Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : ReadItem: unknown type 241 In addition: Warning message: package 'simpleaffy' was built under R version 2.3.0 Error in .getGeneric(f, as.environment(where)) : recursive default argument reference > At first I accidentally downloaded affyQCReport from BioC 1.8 Devel source which gave error message. After this I removed that version and installed version from 1.7. Simpleaffy is 2.4.1 version from 1.7 release. Does anyone know what is the problem? Thanks Tuomas

simpleaffy affyQCReport simpleaffy affyQCReport • 1.3k views

ADD COMMENT • link updated 18.9 years ago by Seth Falcon ★ 7.4k • written 18.9 years ago by Tuomas Raitila ▴ 10

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 10.2 years ago

Hi Tuomas, On 14 Dec 2005, tuomas.raitila at helsinki.fi wrote: > Hello > > I'm having some trouble with loading affyQCReport package. I'm using > RGui > 2.2.0 (windows). The error message I got looks like this: > >> library(affyQCReport) > Loading required package: simpleaffy > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : > ReadItem: unknown type 241 > In addition: Warning message: > package 'simpleaffy' was built under R version 2.3.0 > Error in .getGeneric(f, as.environment(where)) : > recursive default argument reference >> > > At first I accidentally downloaded affyQCReport from BioC 1.8 Devel > source which gave error message. After this I removed that version > and installed version from 1.7. That was a good catch and should have resolved the problem. > Simpleaffy is 2.4.1 version from 1.7 release. Does anyone know what > is the problem? I believe so: Since the release, a few bug fixes have gone into the simpleaffy package. It seems that a mistake was made on our end during the latest update and the package was rebuilt with the wrong version of R. We will correct this *today* and repost. Thanks for the report and sorry for the inconvenience. + seth PS: You are using Windows, right? PPS: You did read the posting guide: http://www.bioconductor.org/docs/postingGuide.html

ADD COMMENT • link 18.9 years ago Seth Falcon ★ 7.4k

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Hi Tuomas, Thanks for telling us! Due to recent minor fixes in packages "GeneR", "DEDS" and "simpleaffy", I recently had to rebuild them in order to provide updated source and binary (Windows) packages on our BioC 1.7 repository. But given the error message you got while trying to load the "simpleaffy" package, I guess I probably used R-2.3 instead of R-2.2 to rebuild. My mistake, sorry! Packages affected by this mistake are: GeneR (1.4.1), DEDS (1.2.1) and simpleaffy (2.4.1). Today I rebuilt them with R-2.2 and pushed them to our repository (http://bioconductor.org). The new (and hopefully working *) packages are: GeneR (1.4.2), DEDS (1.2.2) and simpleaffy (2.4.2). Regards, Herv? (*) I only tested with "install.packages(pkg)" and "library(pkg)" on our Linux and Windows machines and it looked OK. Tell me if it doesn't work for you. Seth Falcon wrote: >Hi Tuomas, > >On 14 Dec 2005, tuomas.raitila at helsinki.fi wrote: > > >>Hello >> >>I'm having some trouble with loading affyQCReport package. I'm using >>RGui >>2.2.0 (windows). The error message I got looks like this: >> >> >> >>>library(affyQCReport) >>> >>> >>Loading required package: simpleaffy >>Loading required package: genefilter >>Loading required package: survival >>Loading required package: splines >>Error in lazyLoadDBfetch(key, datafile, compressed, envhook) : >>ReadItem: unknown type 241 >>In addition: Warning message: >>package 'simpleaffy' was built under R version 2.3.0 >>Error in .getGeneric(f, as.environment(where)) : >>recursive default argument reference >> >> >>At first I accidentally downloaded affyQCReport from BioC 1.8 Devel >>source which gave error message. After this I removed that version >>and installed version from 1.7. >> >> > >That was a good catch and should have resolved the problem. > > > >>Simpleaffy is 2.4.1 version from 1.7 release. Does anyone know what >>is the problem? >> >> > >I believe so: Since the release, a few bug fixes have gone into the >simpleaffy package. It seems that a mistake was made on our end >during the latest update and the package was rebuilt with the wrong >version of R. We will correct this *today* and repost. > >Thanks for the report and sorry for the inconvenience. > >+ seth > >PS: You are using Windows, right? >PPS: You did read the posting guide: >http://www.bioconductor.org/docs/postingGuide.html > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

ADD REPLY • link 18.9 years ago Hervé Pagès 16k

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Hi Herve, I'm relaying on a problem about downloading simpleaffy for Macs; thought it might be related what happened before. Adrienne was able to download and install other Bioconductor packages, but not simpleaffy. Hello Jenny, Thank you! Well, I managed to get almost everything to install okay on my Mac (OS X, PowerPC G4, 512 MB SDRAM). I figured out that there is a Package Installer in the menu bar. By selecting Bioconductor (binaries), I was able to get a long list that included all of the packages listed in #7 of your instructions. I selected each of them and clicked install. This worked for all of the packages except simpleaffy. The error message** popped up in the R console. It also said: Warning: unable to access index for repository http://www.bioconductor.org/ packages/data/experiment/stable/bin/macosx/powerpc/contrib/2.2 trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/macosx/ powerpc/contrib/2.2/simpleaffy_2.2.0.tgz' but I think it said that even when it was able to download/install the other packages. **Here's the error message: Error in download.file(url, destfile, method, mode = "wb") : cannot open URL 'http://www.bioconductor.org/packages/bioc/stable/ bin/macosx/powerpc/contrib/2.2/simpleaffy_2.2.0.tgz' Here's her sessionInfo(): R version 2.2.0, 2005-10-06, powerpc-apple-darwin7.9.0 attached base packages: [1] "tcltk" "tools" "methods" "stats" "graphics" [6] "grDevices" "utils" "datasets" "base" other attached packages: plier affy tkWidgets DynDoc reposTools "1.2.0" "1.8.1" "1.8.0" "1.8.0" "1.8.0" widgetTools convert marray Biobase made4 "1.6.0" "1.4.0" "1.8.0" "1.8.0" "1.4.0" scatterplot3d ade4 limma "0.3-24" "1.4-0" "2.4.4" At 06:10 PM 12/14/2005, Herve Pages wrote: >Hi Tuomas, > >Thanks for telling us! >Due to recent minor fixes in packages "GeneR", "DEDS" and "simpleaffy", >I recently had to rebuild them in order to provide updated source and binary >(Windows) packages on our BioC 1.7 repository. >But given the error message you got while trying to load the "simpleaffy" >package, I guess I probably used R-2.3 instead of R-2.2 to rebuild. >My mistake, sorry! >Packages affected by this mistake are: GeneR (1.4.1), DEDS (1.2.1) and >simpleaffy (2.4.1). > >Today I rebuilt them with R-2.2 and pushed them to our repository >(http://bioconductor.org). The new (and hopefully working *) packages >are: GeneR (1.4.2), DEDS (1.2.2) and simpleaffy (2.4.2). > >Regards, > >Herv? Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

ADD REPLY • link 18.9 years ago Jenny Drnevich ★ 2.2k

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Hi Jenny, Concerning the first problem you had: Warning: unable to access index for repository http://www.bioconductor.org/packages/data/experiment/stable/bin/macosx /powerpc/contrib/2.2 since the data/experiment repository doesn't contain Mac OS X packages, what you can do if you need to install a package from this repository is try to install the source package: > install.packages("package_name", > repos="http://bioconductor.org/packages/data/experiment/stable", > type="source") Concerning the simpleaffy_2.2.0.tgz package missing from our Mac OS X repository, I don't know what happened but I'm almost sure that we used to have this package here. However when I checked this morning it was missing. I restored it so yoou should be able to install it now. Let me know if you run into any other problem. Regards, H. Jenny Drnevich wrote: > Hi Herve, > > I'm relaying on a problem about downloading simpleaffy for Macs; > thought it might be related what happened before. Adrienne was able to > download and install other Bioconductor packages, but not simpleaffy. > > Hello Jenny, > Thank you! Well, I managed to get almost everything to install okay on > my Mac > (OS X, PowerPC G4, 512 MB SDRAM). I figured out that there is a Package > Installer in the menu bar. By selecting Bioconductor (binaries), I was > able to get > a long list that included all of the packages listed in #7 of your > instructions. I > selected each of them and clicked install. This worked for all of the > packages > except simpleaffy. The error message** popped up in the R console. It > also said: > > Warning: unable to access index for repository > http://www.bioconductor.org/ > packages/data/experiment/stable/bin/macosx/powerpc/contrib/2.2 > trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/macosx/ > powerpc/contrib/2.2/simpleaffy_2.2.0.tgz' > > but I think it said that even when it was able to download/install the > other > packages. > > **Here's the error message: > > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL > 'http://www.bioconductor.org/packages/bioc/stable/ > bin/macosx/powerpc/contrib/2.2/simpleaffy_2.2.0.tgz' > > > Here's her sessionInfo(): > > R version 2.2.0, 2005-10-06, powerpc-apple-darwin7.9.0 > > attached base packages: > [1] "tcltk" "tools" "methods" "stats" "graphics" > [6] "grDevices" "utils" "datasets" "base" > > other attached packages: > plier affy tkWidgets DynDoc reposTools > "1.2.0" "1.8.1" "1.8.0" "1.8.0" "1.8.0" > widgetTools convert marray Biobase made4 > "1.6.0" "1.4.0" "1.8.0" "1.8.0" "1.4.0" > scatterplot3d ade4 limma > "0.3-24" "1.4-0" "2.4.4" > > > > > > At 06:10 PM 12/14/2005, Herve Pages wrote: > >> Hi Tuomas, >> >> Thanks for telling us! >> Due to recent minor fixes in packages "GeneR", "DEDS" and "simpleaffy", >> I recently had to rebuild them in order to provide updated source and >> binary >> (Windows) packages on our BioC 1.7 repository. >> But given the error message you got while trying to load the >> "simpleaffy" >> package, I guess I probably used R-2.3 instead of R-2.2 to rebuild. >> My mistake, sorry! >> Packages affected by this mistake are: GeneR (1.4.1), DEDS (1.2.1) and >> simpleaffy (2.4.1). >> >> Today I rebuilt them with R-2.2 and pushed them to our repository >> (http://bioconductor.org). The new (and hopefully working *) packages >> are: GeneR (1.4.2), DEDS (1.2.2) and simpleaffy (2.4.2). >> >> Regards, >> >> Herv? > > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

ADD REPLY • link 18.9 years ago Hervé Pagès 16k

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