[BioC] ABPkgBuilder Error; Again: Solved
Barry Henderson
barry.henderson at ribonomics.com
Wed Aug 17 18:44:09 CEST 2005
Problem solved based on a little more info using Rterm. Perl does not like the use of "\\" in path statements. Use "/" instead. Duh.
> llMapping <- parseData(eg, eg at accession)
Unrecognized escape \R passed through at C:\PROGRA~1\R\RW2011~1\library\AnnBuild
er\temp\tempPerl7276.pl line 4.
Unrecognized escape \R passed through at C:\PROGRA~1\R\RW2011~1\library\AnnBuild
er\temp\tempPerl7276.pl line 4.
Scalar value @vals[1] better written as $vals[1] at C:\PROGRA~1\R\RW2011~1\libra
ry\AnnBuilder\temp\tempPerl7276.pl line 16.
c2§rren~1RCAnno~1/RC2baseName.txt at C:\PROGRA~1\R\RW2011~1\library\AnnBuilder\t
emp\tempPerl7276.pl line 4.
Error in file(file, "r") : unable to open connection
In addition: Warning message:
cannot open file 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut3384'
>
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Barry Henderson
Sent: Wednesday, August 17, 2005 12:06 PM
To: John Zhang; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ABPkgBuilder Error; Again
Hi John
Just getting back to AnnBuilder after vacation. 1.6.8.5 worked like a champ on Linux with ABPkgBuilder. But I need/would prefer the package on a windows xp system. When I tried the same process on XP, ABPkgBuilder dies complaining about not finding a temp file. I think it may be related to the parser/perl based on the information below. ActiveState Perl v5.8.7 is installed, in the path and runs. Can you offer any suggestions as to why this might be failing and how to proceed?
Thanks Barry
After AnnPkgBuilder failed I tried to manually build the package on XP based on code derived from the vignette. The srcfiles download and unzip ok. But when I call parseData on the EG object it fails with the same error I get with ABPkgBuilder:
> llMapping <- parseData(eg, eg at accession)
+ Error in file(file, "r") : unable to open connection
+ In addition: Warning message:
+ cannot open file
+ 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut24672'
The above command downloads gene2accession.gz, launches a cmd window and unzips the archive, then launches another cmd window and exits. The final cmd window closes so fast I can not see what is returned.
SessionInfo, full code/errors, traceback and debug runs are pasted below.
> 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" "1.6.8-5" "1.5.16" "0.97-7" "1.5.12"
>
##################################Beginning of Code block
> datadir <- "c:\\rc2\\curren~1\\RCAnno~1"
> setwd(datadir)
> 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
> #
> #
> # First create a text file called baseName with two columns
> # col1 = ProbeID
> # col2 = GB
> #
> # call that file RC2baseName.txt#
> #
> #
> # Actually, first is to download the XML package from
cran.r-project.org
> # and install into windows R
> #
>
########################################################################
####
>
> myBase <- file.path(datadir, "RC2baseName.txt")
> myDir <- datadir
> showmyBase <- read.table(myBase)
> myBaseType="gbNRef"
> mySrcUrls <- getSrcUrl("all", "Homo sapiens")
#
############Predownloaded src files to speed the process
#
> mySrcUrls["EG"] <- "ftp://192.168.0.4/pub/data/" mySrcUrls["UG"] <-
> "ftp://192.168.0.4/pub/data/Hs.data.gz"
> mySrcUrls["HG"] <- "ftp://192.168.0.4/pub/data/hmlg.ftp"
> mySrcUrls["GO"] <-
"ftp://192.168.0.4/pub/data/go_200507-termdb.rdf-xml"
> baseName = myBase
> srcUrls = mySrcUrls
> baseMapType = myBaseType
> pkgName = "hsRCv2"
> pkgPath = datadir
> organism = "Homo sapiens"
> version = "1.0.0"
> author = list(author = "Barry Henderson", maintainer =
"barry.henderson at ribonomics.com")
> fromWeb = TRUE
> otherSrc = NULL
> pkgpath <- .find.package("AnnBuilder")
> # Begin disecting BPPkgBuilder
>
> require("GO", quietly = TRUE) || stop("GO is needed to build data
package")
Attaching package: 'GO'
The following object(s) are masked from package:AnnBuilder :
GO
[1] TRUE
>
> makeSrcInfo()
> srcObjs <- list()
> eg <- EG(srcUrl = mySrcUrls["EG"], parser = file.path(pkgpath,
"scripts",
+ "gbLLParser"), baseFile = baseName, accession = "gene2accession.gz",
+ built = "N/A", fromWeb = TRUE)
> ug <- UG(srcUrl = mySrcUrls["UG"], parser = file.path(pkgpath,
+ "scripts", "gbUGParser"), baseFile = baseName,
+ organism = "Homo sapiens", built = "N/A", fromWeb = TRUE)
>
> srcObjs[["eg"]] <- eg
> srcObjs[["ug"]] <- ug
>
> llMapping <- parseData(eg, eg at accession)
Error in file(file, "r") : unable to open connection
In addition: Warning message:
cannot open file 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut12498'
> traceback()
7: file(file, "r")
6: scan(fileMuncher(tempOut, baseFile(object), srcData, parser(object)),
what = "character", sep = sep, quote = "", quiet = TRUE,
strip.white = TRUE, comment.char = "")
5: as.vector(data)
4: matrix(scan(fileMuncher(tempOut, baseFile(object), srcData, parser(object)),
what = "character", sep = sep, quote = "", quiet = TRUE,
strip.white = TRUE, comment.char = ""), ncol = ncol, byrow =
TRUE)
3: .local(object, ...)
2: parseData(eg, eg at accession)
1: parseData(eg, eg at accession)
> ?fileMuncher
> debug(parseData)
> llMapping <- parseData(eg, eg at accession)
debugging in: parseData(eg, eg at accession)
debug: standardGeneric("parseData")
Browse[1]>
Error in file(file, "r") : unable to open connection
In addition: Warning message:
cannot open file 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut4328'
-----Original Message-----
From: John Zhang [mailto:jzhang at jimmy.harvard.edu]
Sent: Friday, August 05, 2005 9:43 AM
To: Barry Henderson
Subject: RE: [BioC] ABPkgBuilder Error;
Hi Barry,
1.6.8-4 should work for Linux but did have problems for Windows. I have fixed
the bug and am attaching both the zip and gz files. I have tested the code under
both platforms.
John
>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
>
>
>
Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
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