[Bioc-devel] Error in Biobase docs

Keith Satterley keith at wehi.EDU.AU
Tue Oct 17 07:51:16 CEST 2006


thanks for all the extra info. I'm learning more about this as time goes on. 
Sweave is a great tool.

I'm wondering if you missed something in my message.
the line at fault in the pdf is

"updateObject(experimentData(+ annotation = ...."

Note that it should be

"updateObject(experimentData(object)+ annotation = ...."

Some text is actually missing from the pdf, it's not just a visual problem as 
you suggest below.

Two other points, possibly related.
1. When I move from page 10 to page 11 in Adobe Acrobat Reader(version 7.0.8 on 
Win XP) I get an information message saying "Could not find a font in the 
Resources dictionary - using Helvetica instead". I press OK and I see the page, 
with of course the text as described above.

2. When I open the pdf in GSView, I get the following message when I view page 1 
and then goto Page 11. Other pages OK.
========== Start GSView Message Box ===========
GSview 4.8 2006-02-25
AFPL Ghostscript 8.00 (2002-11-21)
Copyright (C) 2002 artofcode LLC, Benicia, CA.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Scanning PDF file
%GSVIEW_PDF_MARK: /OUT /Title (Introduction)
%GSVIEW_PDF_MARK: /OUT /Title (Comparing old and new)
%GSVIEW_PDF_MARK: /OUT /Title (A quick tour) /Count -3
%GSVIEW_PDF_MARK: /OUT /Title (The eSet object: high-throughput experiments) 
/Count -5
%GSVIEW_PDF_MARK: /OUT /Title (assayData: high-throughput data)
%GSVIEW_PDF_MARK: /OUT /Title (phenoData: sample covariates)
%GSVIEW_PDF_MARK: /OUT /Title (featureData: feature covariates)
%GSVIEW_PDF_MARK: /OUT /Title (experimentData: experiment description)
%GSVIEW_PDF_MARK: /OUT /Title (annotation: assay description)
%GSVIEW_PDF_MARK: /OUT /Title (Important eSet methods) /Count -1
%GSVIEW_PDF_MARK: /OUT /Title (Additional eSet methods)
%GSVIEW_PDF_MARK: /OUT /Title (Subclasses of eSet) /Count -2
%GSVIEW_PDF_MARK: /OUT /Title (ExpressionSet)
%GSVIEW_PDF_MARK: /OUT /Title (MultiSet and SnpSet)
%GSVIEW_PDF_MARK: /OUT /Title (Comments on assayData: high-throughput data storage)
%GSVIEW_PDF_MARK: /OUT /Title (Extending eSet) /Count -1
%GSVIEW_PDF_MARK: /OUT /Title (Implementing a new class: a SwirlSet example)
%GSVIEW_PDF_MARK: /OUT /Title (Versioned) /Count -2
%GSVIEW_PDF_MARK: /OUT /Title (Versioned versus VersionedBiobase)
%GSVIEW_PDF_MARK: /OUT /Title (Adding Versioned information to your own classes)
%GSVIEW_PDF_MARK: /OUT /Title (Summary)
%GSVIEW_PDF_MARK: /OUT /Title (Session Information)
Displaying PDF page 1
%GSVIEW_PDF_MEDIA: [0 0 612 792]
%GSVIEW_PDF_MARK: /LNK /A -dict- /Border [0.0 0.0 1.0] /Rect [254.319 614.875 
350.482 630.816] /Color [0 1 1]
Displaying PDF page 11
%GSVIEW_PDF_MEDIA: [0 0 612 792]
    **** Warning: reference to free object: 192 0 R
Error: /invalidfont in /F93
Operand stack:
    --dict:5/5(L)--   F93   9.963
Execution stack:
    %interp_exit   .runexec2   --nostringval--   --nostringval-- 
--nostringval--   2   %stopped_push   --nostringval--   --nostringval--   false 
   1   %stopped_push   1   3   %oparray_pop   1   3   %oparray_pop   1   3 
%oparray_pop   1   3   %oparray_pop   .runexec2   --nostringval-- 
--nostringval--   --nostringval--   2   %stopped_push   --nostringval-- 
--nostringval--   --nostringval--   --nostringval--   --nostringval-- 
%array_continue   --nostringval--   false   1   %stopped_push   --nostringval-- 
   %loop_continue   --nostringval--   --nostringval--   --nostringval--
Dictionary stack:
    --dict:1055/1123(ro)(G)--   --dict:0/20(G)--   --dict:78/200(L)-- 
--dict:100/127(ro)(G)--   --dict:230/230(ro)(G)--   --dict:20/24(L)-- 
--dict:4/6(L)--   --dict:23/31(L)--
Current allocation mode is local
pdf_page failed
========== End GSView Message Box ===========

I also viewed the pdf on another Windows XP computer with Acrobat Reader ver. 
7.0.8 and received the same error message regarding the font resource.

Also I have viewed the pdf using Preview on a Mac, it doesn't complain about the 
not finding a font, but is does display the same as Windows AR, but when I copy 
and paste the relevant line into a text editor the right bracket after 
"experimentData" and before "+ annotation" seems to be replaced by a linefeed.

Does any of this point to a bug in whatever (Sweave?)is producing the pdf document?



Martin Morgan wrote:
> Thanks Keith for the report. The pdf file is created (like other
> vignettes) by some R code called Sweave, from a document written in
> the markup language LaTeX. The document is actually 'computed', that
> is, I wrote the R code, but Sweave performed the calculations that
> appear in the document. This is quite amazing for many reasons (e.g.,
> providing documentation of, and a repeatable way for conducting, a
> complicated analysis), but in the present case it means that there is
> no syntax error in the R code used to generate the document.
> The problem is a visual one. Sweave provides some control over how
> output looks, but some lines of code (especially with very long names
> and no clear places to insert breaks) can be hard to format correctly
> -- inserting cues like line breaks doesn't help, because Sweave parses
> the blank lines as though they didn't exist. I'll try to arrange for
> this to be formatted better.
> In the mean time, you can find the original source for the document by
> looking at the location returned by
>>system.file("doc", package="Biobase")
> In fact, you can extract the exact R code in the document by using
> 'setwd()' or on windows under the 'File' menu choose "Change dir" to
> move to a directory where you can safely write a file, and then type
> the command
>>Stangle(system.file("doc", "BiobaseDevelopment.Rnw",
> + package="Biobase"))
> This will create a file BiobaseDevelopment.R, and in that file you'll
> find each of the 'chunks' of code used to generate the PDF. See below
> for the problematic line you mention!
> Hope that helps,
> Martin
> Keith Satterley <keith at wehi.EDU.AU> writes:
>>To Biobase authors, in particular Martin Morgan,
>>I was looking at Vignette no. 2 in the Biobase package which displays a pdf 
>>entitled "Biobase development and the new eSet"
>>The author is Martin T. Morgan, and it is dated 7 August, 2006 and the revision 
>>text is "Revised 4 September, 2006 √ featureData slot".
>>On Page 11 of this document, you have
>>and add code to update to the new version
>> > setMethod("updateObject", signature(object = "MySet"), function(object,
>>+ ..., verbose = FALSE) {
>>+ if (verbose)
>>+ message("updateObject(object = MySet )")
>>+ object <- callNextMethod()
>>+ if (isCurrent(object)["MySet"])
>>+ return(object)
>>+ if (!isVersioned(object))
>>+ new("MySet", assayData = updateObject(assayData(object)),
>>+ phenoData = updateObject(phenoData(object)), experimentData = 
>>updateObject(experimentData(+ annotation = updateObject(annotation(object)))
>>+ else {
>>+ classVersion(object)["MySet"] <- classVersion("MySet")["MySet"]
>>+ object
>>+ }
>>+ })
>>[1] "updateObject"
>>One doesn't see the error in the pdf as it is past the right margin. When copied 
>>and pasted into an R console there is an error message because of the following 
>>"updateObject(experimentData(+ annotation = updateObject(annotation(object)))"
>>I can see this is meant to be
>>+ annotation = updateObject(annotation(object)))"
> experimentData = updateObject(experimentData(object)),
>>Perhaps another line break before "experimentData =" in the line before this 
>>would also avoid the text going beyond the right margin.
>>Thanks for all the work you put into R package development,
>> > sessionInfo()
>>R version 2.4.0 (2006-10-03)
>>attached base packages:
>>[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
>>"datasets"  "base"
>>other attached packages:
>>  Biobase
>> >
>>Keith Satterley
>>Bioinformatics Division
>>The Walter and Eliza Hall Institute of Medical Research
>>Parkville, Melbourne,
>>Victoria, Australia
>>Bioc-devel at stat.math.ethz.ch mailing list



Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
ph: +61 3 9345 2628
mob:+61 4 2570 0419
email:keith at wehi.edu.au

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