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Question: ABPkgBuilder Error;
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ADD COMMENTlink modified 12.3 years ago • written 12.3 years ago by Barry Henderson250
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12.3 years ago by
Barry Henderson250 wrote:
Reposted with sessionInfo() output: > library(AnnBuilder) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: XML Loading required package: annotate Warning message: package 'AnnBuilder' was built under R version 2.2.0 > myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") > myDir <- tempdir() > myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", "srcb")) > myBaseType="gb" > mySrcUrls <- getOption("AnnBuilderSourceUrls") > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, + organism = "Homo sapiens", version = "1.1.0", + author = list(author = "myname", maintainer = "myname at myemail.com"), + fromWeb = TRUE) Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder : GO Error in validObject(.Object) : invalid class "GO" object: invalid object for slot "srcUrl" in class "GO": got class "list", should be or extend class "character" > sessionInfo() R version 2.1.1, 2005-07-31, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" > -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Barry Henderson Sent: Wednesday, August 03, 2005 9:40 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] ABPkgBuilder Error; Hi All I am trying to build the test annotation package from the AnnBuilder primer but I keep getting an "invald class "GO" object" error. The code I am using is straight from the vignette with a couple of modifications for path and package naming >library(AnnBuilder) >datadir <- "/rc2/current project storage/RCAnnotation" >setwd(datadir) >myDir <- tempdir() >myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >myBaseType="gb" mySrcUrls <- getOption("AnnBuilderSourceUrls") >myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", "srcb")) >ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, +otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism = +"Homo sapiens", version = "1.1.0", author = list(author = "myname", +maintainer = "myname at myemail.com"), fromWeb = TRUE) >From here ABPkgBuilder downloads gene2accession.gz, runs gzip and dumps out with the following error: >Error in validObject(.Object) : invalid class "GO" object: invalid object for slot "srcUrl" in class "GO": got class "list", should be or extend class "character" System: Windows XP R 2.1.1 Current release of BioC packages (downloaded via getBioC yesterday) Any ideas? Thanks Barry [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.3 years ago by Barry Henderson250
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gravatar for Barry Henderson
12.3 years ago by
Barry Henderson250 wrote:
I just tried the same code on an linux system with the same results. R version 2.1.1, 2005-06-20, i686-pc-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.8.2" "1.5.31" "1.5.16" "0.97-7" "1.5.12" -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Barry Henderson Sent: Wednesday, August 03, 2005 10:27 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] ABPkgBuilder Error; Reposted with sessionInfo() output: > library(AnnBuilder) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: XML Loading required package: annotate Warning message: package 'AnnBuilder' was built under R version 2.2.0 > myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") > myDir <- tempdir() myOtherSrc <- c(srcone = > file.path(.path.package("AnnBuilder"), "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", "srcb")) > myBaseType="gb" > mySrcUrls <- getOption("AnnBuilderSourceUrls") ABPkgBuilder(baseName = > myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism = + "Homo sapiens", version = "1.1.0", author = list(author = "myname", + maintainer = "myname at myemail.com"), fromWeb = TRUE) Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder : GO Error in validObject(.Object) : invalid class "GO" object: invalid object for slot "srcUrl" in class "GO": got class "list", should be or extend class "character" > sessionInfo() R version 2.1.1, 2005-07-31, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" > -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Barry Henderson Sent: Wednesday, August 03, 2005 9:40 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] ABPkgBuilder Error; Hi All I am trying to build the test annotation package from the AnnBuilder primer but I keep getting an "invald class "GO" object" error. The code I am using is straight from the vignette with a couple of modifications for path and package naming >library(AnnBuilder) >datadir <- "/rc2/current project storage/RCAnnotation" >setwd(datadir) >myDir <- tempdir() >myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >myBaseType="gb" mySrcUrls <- getOption("AnnBuilderSourceUrls") >myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", "srcb")) >ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, +otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism = +"Homo sapiens", version = "1.1.0", author = list(author = "myname", +maintainer = "myname at myemail.com"), fromWeb = TRUE) >From here ABPkgBuilder downloads gene2accession.gz, runs gzip and dumps out with the following error: >Error in validObject(.Object) : invalid class "GO" object: invalid object for slot "srcUrl" in class "GO": got class "list", should be or extend class "character" System: Windows XP R 2.1.1 Current release of BioC packages (downloaded via getBioC yesterday) Any ideas? Thanks Barry [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.3 years ago by Barry Henderson250
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gravatar for John Zhang
12.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>>Error in validObject(.Object) : invalid class "GO" object: invalid >object for slot "srcUrl" in class "GO": got class "list", should be or >extend class "character" The return of getOption("AnnBuilderSourceUrls") does not work too well with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves the problem. However, KEGG changed some of the web pages that caused the code to fail. I have fixed the problem and will check in the fixes. It may take a few days for the revised version to be available though. > >System: > >Windows XP >R 2.1.1 >Current release of BioC packages (downloaded via getBioC yesterday) > >Any ideas? > >Thanks >Barry > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by John Zhang2.9k
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gravatar for Barry Henderson
12.3 years ago by
Barry Henderson250 wrote:
That helped a little but now I get the following error: ... > mySrcUrls <- getSrcUrl("all", "Homo sapiens") > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, + organism = "Homo sapiens", version = "1.1.0", + author = list(author = "myname", maintainer = "myname at myemail.com"), + fromWeb = TRUE) Error in if is.na(built) || is.null(built) || built == "") { : missing value where TRUE/FALSE needed In addition: Warning message: data length [932] is not a sub-multiple or multiple of the number of rows [311] in matrix > sessionInfo() R version 2.1.1, 2005-07-31, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" Barry -----Original Message----- From: John Zhang [mailto:jzhang@jimmy.harvard.edu] Sent: Wednesday, August 03, 2005 11:36 AM To: bioconductor at stat.math.ethz.ch; Barry Henderson Subject: Re: [BioC] ABPkgBuilder Error; >>Error in validObject(.Object) : invalid class "GO" object: invalid >object for slot "srcUrl" in class "GO": got class "list", should be or >extend class "character" The return of getOption("AnnBuilderSourceUrls") does not work too well with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves the problem. However, KEGG changed some of the web pages that caused the code to fail. I have fixed the problem and will check in the fixes. It may take a few days for the revised version to be available though. > >System: > >Windows XP >R 2.1.1 >Current release of BioC packages (downloaded via getBioC yesterday) > >Any ideas? > >Thanks >Barry > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by Barry Henderson250
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gravatar for John Zhang
12.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>That helped a little but now I get the following error: >... >> mySrcUrls <- getSrcUrl("all", "Homo sapiens") >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >myBaseType, >+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, >+ organism = "Homo sapiens", version = "1.1.0", >+ author = list(author = "myname", maintainer = "myname at myemail.com"), >+ fromWeb = TRUE) >Error in if is.na(built) || is.null(built) || built == "") { : > missing value where TRUE/FALSE needed Yes, that was because the code failed to get the built information from KEGG due to changes in the web interface. The fix has been checked in and a new version of AnnBuilder will be available when it is pushed out to the download site. >In addition: Warning message: >data length [932] is not a sub-multiple or multiple of the number of >rows [311] in matrix >> sessionInfo() >R version 2.1.1, 2005-07-31, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > >[7] "datasets" "base" > >other attached packages: > GO AnnBuilder annotate XML Biobase > "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" > >Barry > >-----Original Message----- >From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >Sent: Wednesday, August 03, 2005 11:36 AM >To: bioconductor at stat.math.ethz.ch; Barry Henderson >Subject: Re: [BioC] ABPkgBuilder Error; > > > >>>Error in validObject(.Object) : invalid class "GO" object: invalid >>object for slot "srcUrl" in class "GO": got class "list", should be or >>extend class "character" > >The return of getOption("AnnBuilderSourceUrls") does not work too well >with >ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves >the >problem. However, KEGG changed some of the web pages that caused the >code to >fail. I have fixed the problem and will check in the fixes. It may take >a few >days for the revised version to be available though. > >> >>System: >> >>Windows XP >>R 2.1.1 >>Current release of BioC packages (downloaded via getBioC yesterday) >> >>Any ideas? >> >>Thanks >>Barry >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by John Zhang2.9k
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gravatar for Barry Henderson
12.3 years ago by
Barry Henderson250 wrote:
John et al. I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error but it still fails building the package. Results from windows install is below (same results on linux): > library(AnnBuilder) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: XML Loading required package: annotate Warning message: package 'AnnBuilder' was built under R version 2.2.0 > myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") > datadir <- "c:/rc2/curren~1/RCAnno~1" > myDir <- tempdir() > myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", "srcb")) > myBaseType="gb" > mySrcUrls <- getSrcUrl("all", "Homo sapiens") > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, + pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo sapiens", + version = "1.0.0", + author = list(author = "Barry Henderson", maintainer = "barry.henderson at ribonomics.com"), + fromWeb = TRUE) Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder : GO Error in if is.na(built) || is.null(built) || built == "") { : missing value where TRUE/FALSE needed In addition: Warning message: data length [932] is not a sub-multiple or multiple of the number of rows [311] in matrix > sessionInfo() R version 2.1.1, 2005-07-31, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [8] "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" > -----Original Message----- From: John Zhang [mailto:jzhang@jimmy.harvard.edu] Sent: Wednesday, August 03, 2005 11:36 AM To: bioconductor at stat.math.ethz.ch; Barry Henderson Subject: Re: [BioC] ABPkgBuilder Error; >>Error in validObject(.Object) : invalid class "GO" object: invalid >object for slot "srcUrl" in class "GO": got class "list", should be or >extend class "character" The return of getOption("AnnBuilderSourceUrls") does not work too well with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves the problem. However, KEGG changed some of the web pages that caused the code to fail. I have fixed the problem and will check in the fixes. It may take a few days for the revised version to be available though. > >System: > >Windows XP >R 2.1.1 >Current release of BioC packages (downloaded via getBioC yesterday) > >Any ideas? > >Thanks >Barry > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by Barry Henderson250
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gravatar for John Zhang
12.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
Are you sure you have installed AnnBuilder 1.6.8-4 as your sessionInfo still showed 1.6.8? >John et al. > >I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error but >it still fails building the package. Results from windows install is >below (same results on linux): > >> library(AnnBuilder) >Loading required package: Biobase >Loading required package: tools >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Loading required package: XML >Loading required package: annotate >Warning message: >package 'AnnBuilder' was built under R version 2.2.0 >> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >> datadir <- "c:/rc2/curren~1/RCAnno~1" >> myDir <- tempdir() >> myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), >"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data", >"srcb")) >> myBaseType="gb" >> mySrcUrls <- getSrcUrl("all", "Homo sapiens") >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >myBaseType, >+ pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo >sapiens", >+ version = "1.0.0", >+ author = list(author = "Barry Henderson", maintainer = >"barry.henderson at ribonomics.com"), >+ fromWeb = TRUE) > >Attaching package: 'GO' > > > The following object(s) are masked from package:AnnBuilder : > > GO > >Error in if is.na(built) || is.null(built) || built == "") { : > missing value where TRUE/FALSE needed >In addition: Warning message: >data length [932] is not a sub-multiple or multiple of the number of >rows [311] in matrix >> sessionInfo() >R version 2.1.1, 2005-07-31, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >"datasets" >[8] "base" > >other attached packages: > GO AnnBuilder annotate XML Biobase > "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" >> > > > > >-----Original Message----- >From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >Sent: Wednesday, August 03, 2005 11:36 AM >To: bioconductor at stat.math.ethz.ch; Barry Henderson >Subject: Re: [BioC] ABPkgBuilder Error; > > > >>>Error in validObject(.Object) : invalid class "GO" object: invalid >>object for slot "srcUrl" in class "GO": got class "list", should be or >>extend class "character" > >The return of getOption("AnnBuilderSourceUrls") does not work too well >with >ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves >the >problem. However, KEGG changed some of the web pages that caused the >code to >fail. I have fixed the problem and will check in the fixes. It may take >a few >days for the revised version to be available though. > >> >>System: >> >>Windows XP >>R 2.1.1 >>Current release of BioC packages (downloaded via getBioC yesterday) >> >>Any ideas? >> >>Thanks >>Barry >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by John Zhang2.9k
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12.3 years ago by
Barry Henderson250 wrote:
Yes I am sure. The sessionInfo from the linux installation (using the zip you emailed) is: R version 2.1.1, 2005-06-20, i686-pc-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder annotate XML Biobase "1.6.8-4" "1.5.16" "0.97-7" "1.5.12" I installed 1.6.8-4 listed on the developers page form bioconductor (I just re-downloaded and re-installed it to make sure). The session info there is: R version 2.1.1, 2005-07-31, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder annotate XML Biobase "1.6.8" "1.5.16" "0.97-7" "1.5.12" Note that there were a couple of warnings on windows installation: >package 'AnnBuilder' successfully unpacked and MD5 sums checked >updating HTML package descriptions >Warning messages: >1: no package 'file15700' was found in: packageDescription(i, fields = "Title", lib.loc = lib) >2: no package 'file27003' was found in: packageDescription(i, fields = "Title", lib.loc = lib) -----Original Message----- From: John Zhang [mailto:jzhang@jimmy.harvard.edu] Sent: Thursday, August 04, 2005 7:57 AM To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry Henderson Subject: Re: [BioC] ABPkgBuilder Error; Are you sure you have installed AnnBuilder 1.6.8-4 as your sessionInfo still showed 1.6.8? >John et al. > >I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error >but it still fails building the package. Results from windows install >is below (same results on linux): > >> library(AnnBuilder) >Loading required package: Biobase >Loading required package: tools >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Loading required package: XML >Loading required package: annotate >Warning message: >package 'AnnBuilder' was built under R version 2.2.0 >> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >> datadir <- "c:/rc2/curren~1/RCAnno~1" myDir <- tempdir() >> myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), >"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), >"data", >"srcb")) >> myBaseType="gb" >> mySrcUrls <- getSrcUrl("all", "Homo sapiens") ABPkgBuilder(baseName = >> myBase, srcUrls = mySrcUrls, baseMapType = >myBaseType, >+ pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo >sapiens", >+ version = "1.0.0", >+ author = list(author = "Barry Henderson", maintainer = >"barry.henderson at ribonomics.com"), >+ fromWeb = TRUE) > >Attaching package: 'GO' > > > The following object(s) are masked from package:AnnBuilder : > > GO > >Error in if is.na(built) || is.null(built) || built == "") { : > missing value where TRUE/FALSE needed >In addition: Warning message: >data length [932] is not a sub-multiple or multiple of the number of >rows [311] in matrix >> sessionInfo() >R version 2.1.1, 2005-07-31, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >"datasets" >[8] "base" > >other attached packages: > GO AnnBuilder annotate XML Biobase > "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" >> > > > > >-----Original Message----- >From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >Sent: Wednesday, August 03, 2005 11:36 AM >To: bioconductor at stat.math.ethz.ch; Barry Henderson >Subject: Re: [BioC] ABPkgBuilder Error; > > > >>>Error in validObject(.Object) : invalid class "GO" object: invalid >>object for slot "srcUrl" in class "GO": got class "list", should be or >>extend class "character" > >The return of getOption("AnnBuilderSourceUrls") does not work too well >with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls >solves the >problem. However, KEGG changed some of the web pages that caused the >code to >fail. I have fixed the problem and will check in the fixes. It may take >a few >days for the revised version to be available though. > >> >>System: >> >>Windows XP >>R 2.1.1 >>Current release of BioC packages (downloaded via getBioC yesterday) >> >>Any ideas? >> >>Thanks >>Barry >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by Barry Henderson250
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12.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>I installed 1.6.8-4 listed on the developers page form bioconductor (I >just re-downloaded and re-installed it to make sure). The session info >there is: 1.6.8-4 is not even available from the web and this still gives you 1.6.8 as shown below. That was why I sent you the package I built. > >R version 2.1.1, 2005-07-31, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > >[7] "datasets" "base" > >other attached packages: >AnnBuilder annotate XML Biobase > "1.6.8" "1.5.16" "0.97-7" "1.5.12" > >Note that there were a couple of warnings on windows installation: > >>package 'AnnBuilder' successfully unpacked and MD5 sums checked >>updating HTML package descriptions >>Warning messages: >>1: no package 'file15700' was found in: packageDescription(i, fields = >"Title", lib.loc = lib) >>2: no package 'file27003' was found in: packageDescription(i, fields = >"Title", lib.loc = lib) > > > >-----Original Message----- >From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >Sent: Thursday, August 04, 2005 7:57 AM >To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry >Henderson >Subject: Re: [BioC] ABPkgBuilder Error; > > >Are you sure you have installed AnnBuilder 1.6.8-4 as your sessionInfo >still >showed 1.6.8? > > > >>John et al. >> >>I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error >>but it still fails building the package. Results from windows install >>is below (same results on linux): >> >>> library(AnnBuilder) >>Loading required package: Biobase >>Loading required package: tools >>Welcome to Bioconductor >> Vignettes contain introductory material. To view, >> simply type: openVignette() >> For details on reading vignettes, see >> the openVignette help page. >>Loading required package: XML >>Loading required package: annotate >>Warning message: >>package 'AnnBuilder' was built under R version 2.2.0 >>> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >>> datadir <- "c:/rc2/curren~1/RCAnno~1" myDir <- tempdir() >>> myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), >>"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), >>"data", >>"srcb")) >>> myBaseType="gb" >>> mySrcUrls <- getSrcUrl("all", "Homo sapiens") ABPkgBuilder(baseName = > >>> myBase, srcUrls = mySrcUrls, baseMapType = >>myBaseType, >>+ pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo >>sapiens", >>+ version = "1.0.0", >>+ author = list(author = "Barry Henderson", maintainer = >>"barry.henderson at ribonomics.com"), >>+ fromWeb = TRUE) >> >>Attaching package: 'GO' >> >> >> The following object(s) are masked from package:AnnBuilder : >> >> GO >> >>Error in if is.na(built) || is.null(built) || built == "") { : >> missing value where TRUE/FALSE needed >>In addition: Warning message: >>data length [932] is not a sub-multiple or multiple of the number of >>rows [311] in matrix >>> sessionInfo() >>R version 2.1.1, 2005-07-31, i386-pc-mingw32 >> >>attached base packages: >>[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >>"datasets" >>[8] "base" >> >>other attached packages: >> GO AnnBuilder annotate XML Biobase >> "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" >>> >> >> >> >> >>-----Original Message----- >>From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >>Sent: Wednesday, August 03, 2005 11:36 AM >>To: bioconductor at stat.math.ethz.ch; Barry Henderson >>Subject: Re: [BioC] ABPkgBuilder Error; >> >> >> >>>>Error in validObject(.Object) : invalid class "GO" object: invalid >>>object for slot "srcUrl" in class "GO": got class "list", should be or >>>extend class "character" >> >>The return of getOption("AnnBuilderSourceUrls") does not work too well >>with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls >>solves the >>problem. However, KEGG changed some of the web pages that caused the >>code to >>fail. I have fixed the problem and will check in the fixes. It may take >>a few >>days for the revised version to be available though. >> >>> >>>System: >>> >>>Windows XP >>>R 2.1.1 >>>Current release of BioC packages (downloaded via getBioC yesterday) >>> >>>Any ideas? >>> >>>Thanks >>>Barry >>> >>> [[alternative HTML version deleted]] >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>Jianhua Zhang >>Department of Medical Oncology >>Dana-Farber Cancer Institute >>44 Binney Street >>Boston, MA 02115-6084 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by John Zhang2.9k
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gravatar for Barry Henderson
12.3 years ago by
Barry Henderson250 wrote:
I installed the version you sent me on the linux system. Same error. >From the web site: Package: AnnBuilder Description: Processing annotation date from public data repositories and building annoation data packages or XML data documents using the source data. Version: 1.6.8-4 Author: J. Zhang Maintainer: J. Zhang Dependencies: R (>= 2.1.0), methods, Biobase, XML, annotate, utils Suggests: None SystemRequirements: None License: LGPL URL: None available -----Original Message----- From: John Zhang [mailto:jzhang at jimmy.harvard.edu] Sent: Thu 8/4/2005 10:38 AM To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry Henderson Cc: Subject: RE: [BioC] ABPkgBuilder Error; >I installed 1.6.8-4 listed on the developers page form bioconductor (I >just re-downloaded and re-installed it to make sure). The session info >there is: 1.6.8-4 is not even available from the web and this still gives you 1.6.8 as shown below. That was why I sent you the package I built. > >R version 2.1.1, 2005-07-31, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > >[7] "datasets" "base" > >other attached packages: >AnnBuilder annotate XML Biobase > "1.6.8" "1.5.16" "0.97-7" "1.5.12" > >Note that there were a couple of warnings on windows installation: > >>package 'AnnBuilder' successfully unpacked and MD5 sums checked >>updating HTML package descriptions >>Warning messages: >>1: no package 'file15700' was found in: packageDescription(i, fields = >"Title", lib.loc = lib) >>2: no package 'file27003' was found in: packageDescription(i, fields = >"Title", lib.loc = lib) > > > >-----Original Message----- >From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >Sent: Thursday, August 04, 2005 7:57 AM >To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry >Henderson >Subject: Re: [BioC] ABPkgBuilder Error; > > >Are you sure you have installed AnnBuilder 1.6.8-4 as your sessionInfo >still >showed 1.6.8? > > > >>John et al. >> >>I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error >>but it still fails building the package. Results from windows install >>is below (same results on linux): >> >>> library(AnnBuilder) >>Loading required package: Biobase >>Loading required package: tools >>Welcome to Bioconductor >> Vignettes contain introductory material. To view, >> simply type: openVignette() >> For details on reading vignettes, see >> the openVignette help page. >>Loading required package: XML >>Loading required package: annotate >>Warning message: >>package 'AnnBuilder' was built under R version 2.2.0 >>> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >>> datadir <- "c:/rc2/curren~1/RCAnno~1" myDir <- tempdir() >>> myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), >>"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), >>"data", >>"srcb")) >>> myBaseType="gb" >>> mySrcUrls <- getSrcUrl("all", "Homo sapiens") ABPkgBuilder(baseName = > >>> myBase, srcUrls = mySrcUrls, baseMapType = >>myBaseType, >>+ pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo >>sapiens", >>+ version = "1.0.0", >>+ author = list(author = "Barry Henderson", maintainer = >>"barry.henderson at ribonomics.com"), >>+ fromWeb = TRUE) >> >>Attaching package: 'GO' >> >> >> The following object(s) are masked from package:AnnBuilder : >> >> GO >> >>Error in if is.na(built) || is.null(built) || built == "") { : >> missing value where TRUE/FALSE needed >>In addition: Warning message: >>data length [932] is not a sub-multiple or multiple of the number of >>rows [311] in matrix >>> sessionInfo() >>R version 2.1.1, 2005-07-31, i386-pc-mingw32 >> >>attached base packages: >>[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >>"datasets" >>[8] "base" >> >>other attached packages: >> GO AnnBuilder annotate XML Biobase >> "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" >>> >> >> >> >> >>-----Original Message----- >>From: John Zhang [mailto:jzhang at jimmy.harvard.edu] >>Sent: Wednesday, August 03, 2005 11:36 AM >>To: bioconductor at stat.math.ethz.ch; Barry Henderson >>Subject: Re: [BioC] ABPkgBuilder Error; >> >> >> >>>>Error in validObject(.Object) : invalid class "GO" object: invalid >>>object for slot "srcUrl" in class "GO": got class "list", should be or >>>extend class "character" >> >>The return of getOption("AnnBuilderSourceUrls") does not work too well >>with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls >>solves the >>problem. However, KEGG changed some of the web pages that caused the >>code to >>fail. I have fixed the problem and will check in the fixes. It may take >>a few >>days for the revised version to be available though. >> >>> >>>System: >>> >>>Windows XP >>>R 2.1.1 >>>Current release of BioC packages (downloaded via getBioC yesterday) >>> >>>Any ideas? >>> >>>Thanks >>>Barry >>> >>> [[alternative HTML version deleted]] >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>Jianhua Zhang >>Department of Medical Oncology >>Dana-Farber Cancer Institute >>44 Binney Street >>Boston, MA 02115-6084 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.3 years ago by Barry Henderson250
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