Hi Seth,
The possibility of caching computations would be a great boon when
one is iteratively refining a paper; so I'm most grateful for your
work on this. Unfortunately I have a problem to report:
******************installing******************
> source("http://bioconductor.org/biocLite.R")
> biocLite("weaver")
Running getBioC version 0.1.8 with R version 2.4.0
Running biocinstall version 1.9.8 with R version 2.4.0
Your version of R requires version 1.9 of Bioconductor.
trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/macosx/
universal/contrib/2.4/weaver_1.0.0.tgz'
Content type 'application/x-gzip' length 101153 bytes
opened URL
=================================================downloaded 98Kb
The downloaded packages are in
/tmp/RtmpO6uHHW/downloaded_packages
******************loading weaver******************
> library(weaver)
Loading required package: digest
Loading required package: tools
Loading required package: codetools
******************testing Sweave******************
> testfile <- system.file("Sweave",
"Sweave-test-1.Rnw", package =
"utils")
>
> ## enforce par(ask=FALSE)
> options(par.ask.default=FALSE)
>
> ## create a LaTeX file
> Sweave(testfile)
Writing to file Sweave-test-1.tex
Processing code chunks ...
1 : print term verbatim
2 : term hide
3 : echo print term verbatim
4 : term verbatim
5 : echo term verbatim
6 : echo term verbatim eps pdf
7 : echo term verbatim eps pdf
You can now run LaTeX on 'Sweave-test-1.tex'
******************testing weaver******************
> weaver(testfile)
Error in weaver(testfile) : unused argument(s) ("/Library/Frameworks/
R.framework/Resources/library/utils/Sweave/Sweave-test-1.Rnw")
******************session info******************
R version 2.4.0 (2006-10-03)
powerpc-apple-darwin8.7.0
locale:
C
attached base packages:
[1] "tools" "grid" "splines"
"datasets" "methods"
"stats" "graphics" "grDevices"
[9] "utils" "base"
other attached packages:
weaver codetools digest effects Hmisc
chron xtable geepack glmmML
"1.0.0" "0.0-3" "0.2.2"
"1.0-9" "3.1-1" "2.3-8"
"1.3-2" "1.0-10" "0.65-3"
nlme lme4 Matrix lattice MASS
JGR iplots JavaGD rJava
"3.1-77" "0.9975-1" "0.9975-2"
"0.14-9" "7.2-29" "1.4-11"
"1.0-4" "0.3-5" "0.4-10"
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
Hi Michael, Michael Kubovy <kubovy at virginia.edu> writes:> Hi Seth, > > The possibility of caching computations would be a great boon when > one is iteratively refining a paper; so I'm most grateful for your > work on this. Unfortunately I have a problem to report:> ******************testing Sweave****************** >> testfile <- system.file("Sweave", "Sweave-test-1.Rnw", package = > "utils") >> > ******************testing weaver****************** >> weaver(testfile) > Error in weaver(testfile) : unused argument(s) ("/Library/Frameworks/ > R.framework/Resources/library/utils/Sweave/Sweave-test-1.Rnw")Actually, you want: Sweave(testfile, driver=weaver()) I will add something to the man page for weaver to make this more clear. You might want to have a look at the vignette included with the package: library("Biobase") library("weaver") openVignette("weaver") + seth
Michael Kubovy <kubovy at virginia.edu> writes:> Hi Seth, > > The possibility of caching computations would be a great boon when > one is iteratively refining a paper; so I'm most grateful for your > work on this. Unfortunately I have a problem to report: > > ******************installing****************** > > source("http://bioconductor.org/biocLite.R") > > biocLite("weaver") > Running getBioC version 0.1.8 with R version 2.4.0 > Running biocinstall version 1.9.8 with R version 2.4.0 > Your version of R requires version 1.9 of Bioconductor. > trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/macosx/ > universal/contrib/2.4/weaver_1.0.0.tgz' > Content type 'application/x-gzip' length 101153 bytes > opened URL > =================================================> downloaded 98Kb > > > The downloaded packages are in > /tmp/RtmpO6uHHW/downloaded_packages > > ******************loading weaver****************** > > library(weaver) > Loading required package: digest > Loading required package: tools > Loading required package: codetools > > ******************testing Sweave****************** > > testfile <- system.file("Sweave", "Sweave-test-1.Rnw", package = > "utils") > > > > ## enforce par(ask=FALSE) > > options(par.ask.default=FALSE) > > > > ## create a LaTeX file > > Sweave(testfile) > Writing to file Sweave-test-1.tex > Processing code chunks ... > 1 : print term verbatim > 2 : term hide > 3 : echo print term verbatim > 4 : term verbatim > 5 : echo term verbatim > 6 : echo term verbatim eps pdf > 7 : echo term verbatim eps pdf > > You can now run LaTeX on 'Sweave-test-1.tex' > > ******************testing weaver****************** > > weaver(testfile) > Error in weaver(testfile) : unused argument(s) ("/Library/Frameworks/ > R.framework/Resources/library/utils/Sweave/Sweave-test-1.Rnw")Er, that would not appear to be the intended usage, as per http://www.bioconductor.org/packages/1.9/bioc/vignettes/weaver/inst/doc/weaver_howTo.pdf#search=%22weaver%20bioconductor%22 -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907