xmapcore 1.10.0
Tim Yates
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/xmapcore | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| puck5 | Linux (Ubuntu 12.04) / x86_64 | [ ERROR ] | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for file 'xmapcore/DESCRIPTION' ... OK
* preparing 'xmapcore':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
/home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R --vanilla --verbose < ../cookbook/delia.R
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/methods/libs/methods.so") ...
R version 2.15.0 RC (2012-03-22 r58802)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
'verbose' and 'quietly' are both true; being verbose then ..
'verbose' and 'quietly' are both true; being verbose then ..
'verbose' and 'quietly' are both true; being verbose then ..
Garbage collection 1 = 0+0+1 (level 2) ...
3.7 Mbytes of cons cells used (20%)
2.4 Mbytes of vectors used (34%)
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/grDevices/libs/grDevices.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
'verbose' and 'quietly' are both true; being verbose then ..
Garbage collection 2 = 1+0+1 (level 0) ...
8.8 Mbytes of cons cells used (47%)
3.3 Mbytes of vectors used (47%)
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/stats/libs/stats.so") ...
>R_ReplConsole(): before "for(;;)" {main.c}
> # This script builds the cookbook if the correct DB name is set up
> # Or else does nothing, and leaves the PDF where it is...
> #
> # http://bit.ly/delia_smith
>
> library( "xmapcore" )
Loading required package: IRanges
Loading required package: BiocGenerics
Garbage collection 3 = 2+0+1 (level 0) ...
11.1 Mbytes of cons cells used (59%)
4.0 Mbytes of vectors used (58%)
Garbage collection 4 = 3+0+1 (level 0) ...
12.7 Mbytes of cons cells used (67%)
4.4 Mbytes of vectors used (63%)
Garbage collection 5 = 4+0+1 (level 0) ...
13.9 Mbytes of cons cells used (74%)
4.7 Mbytes of vectors used (67%)
Garbage collection 6 = 5+0+1 (level 0) ...
14.3 Mbytes of cons cells used (76%)
4.8 Mbytes of vectors used (68%)
Garbage collection 7 = 6+0+1 (level 0) ...
14.8 Mbytes of cons cells used (79%)
4.9 Mbytes of vectors used (70%)
Garbage collection 8 = 7+0+1 (level 0) ...
15.3 Mbytes of cons cells used (82%)
5.0 Mbytes of vectors used (72%)
Attaching package: 'BiocGenerics'
The following object(s) are masked from 'package:stats':
xtabs
The following object(s) are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
Garbage collection 9 = 7+1+1 (level 1) ...
15.2 Mbytes of cons cells used (81%)
3.4 Mbytes of vectors used (48%)
Garbage collection 10 = 7+1+2 (level 2) ...
15.3 Mbytes of cons cells used (70%)
3.4 Mbytes of vectors used (48%)
Garbage collection 11 = 8+1+2 (level 0) ...
16.0 Mbytes of cons cells used (73%)
3.4 Mbytes of vectors used (49%)
Garbage collection 12 = 9+1+2 (level 0) ...
17.1 Mbytes of cons cells used (78%)
3.7 Mbytes of vectors used (52%)
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/libs/IRanges.so") ...
Garbage collection 13 = 10+1+2 (level 0) ...
18.4 Mbytes of cons cells used (84%)
3.8 Mbytes of vectors used (54%)
Garbage collection 14 = 10+2+2 (level 1) ...
20.3 Mbytes of cons cells used (93%)
3.9 Mbytes of vectors used (56%)
Garbage collection 15 = 10+2+3 (level 2) ...
21.2 Mbytes of cons cells used (85%)
3.9 Mbytes of vectors used (49%)
Garbage collection 16 = 11+2+3 (level 0) ...
23.2 Mbytes of cons cells used (93%)
4.3 Mbytes of vectors used (55%)
Garbage collection 17 = 11+3+3 (level 1) ...
23.6 Mbytes of cons cells used (94%)
4.0 Mbytes of vectors used (51%)
Garbage collection 18 = 11+3+4 (level 2) ...
23.7 Mbytes of cons cells used (83%)
4.0 Mbytes of vectors used (51%)
Garbage collection 19 = 12+3+4 (level 0) ...
24.3 Mbytes of cons cells used (85%)
4.1 Mbytes of vectors used (51%)
Garbage collection 20 = 12+4+4 (level 1) ...
24.7 Mbytes of cons cells used (87%)
4.3 Mbytes of vectors used (54%)
Garbage collection 21 = 12+4+5 (level 2) ...
24.5 Mbytes of cons cells used (77%)
4.2 Mbytes of vectors used (52%)
Garbage collection 22 = 13+4+5 (level 0) ...
24.8 Mbytes of cons cells used (77%)
4.2 Mbytes of vectors used (53%)
Garbage collection 23 = 14+4+5 (level 0) ...
24.8 Mbytes of cons cells used (78%)
4.2 Mbytes of vectors used (53%)
Garbage collection 24 = 15+4+5 (level 0) ...
25.1 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 25 = 16+4+5 (level 0) ...
25.2 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 26 = 17+4+5 (level 0) ...
25.2 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 27 = 18+4+5 (level 0) ...
25.3 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 28 = 19+4+5 (level 0) ...
25.4 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 29 = 20+4+5 (level 0) ...
25.4 Mbytes of cons cells used (80%)
4.3 Mbytes of vectors used (53%)
Garbage collection 30 = 20+5+5 (level 1) ...
25.1 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 31 = 21+5+5 (level 0) ...
25.2 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 32 = 22+5+5 (level 0) ...
25.2 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 33 = 23+5+5 (level 0) ...
25.3 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 34 = 24+5+5 (level 0) ...
25.3 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 35 = 25+5+5 (level 0) ...
25.4 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 36 = 26+5+5 (level 0) ...
25.4 Mbytes of cons cells used (79%)
4.2 Mbytes of vectors used (53%)
Garbage collection 37 = 27+5+5 (level 0) ...
25.5 Mbytes of cons cells used (80%)
4.3 Mbytes of vectors used (53%)
Garbage collection 38 = 28+5+5 (level 0) ...
25.5 Mbytes of cons cells used (80%)
4.3 Mbytes of vectors used (54%)
Garbage collection 39 = 29+5+5 (level 0) ...
25.6 Mbytes of cons cells used (80%)
4.3 Mbytes of vectors used (54%)
Garbage collection 40 = 30+5+5 (level 0) ...
25.6 Mbytes of cons cells used (80%)
4.3 Mbytes of vectors used (54%)
Garbage collection 41 = 30+5+6 (level 2) ...
25.4 Mbytes of cons cells used (71%)
4.2 Mbytes of vectors used (53%)
Garbage collection 42 = 31+5+6 (level 0) ...
25.5 Mbytes of cons cells used (71%)
4.2 Mbytes of vectors used (53%)
Garbage collection 43 = 32+5+6 (level 0) ...
25.5 Mbytes of cons cells used (71%)
4.2 Mbytes of vectors used (53%)
Garbage collection 44 = 33+5+6 (level 0) ...
25.6 Mbytes of cons cells used (72%)
4.3 Mbytes of vectors used (53%)
Garbage collection 45 = 34+5+6 (level 0) ...
25.9 Mbytes of cons cells used (72%)
4.3 Mbytes of vectors used (54%)
Garbage collection 46 = 35+5+6 (level 0) ...
27.7 Mbytes of cons cells used (78%)
4.5 Mbytes of vectors used (56%)
Garbage collection 47 = 36+5+6 (level 0) ...
28.5 Mbytes of cons cells used (80%)
4.5 Mbytes of vectors used (57%)
Garbage collection 48 = 37+5+6 (level 0) ...
29.2 Mbytes of cons cells used (82%)
4.6 Mbytes of vectors used (58%)
Garbage collection 49 = 37+6+6 (level 1) ...
30.7 Mbytes of cons cells used (86%)
4.6 Mbytes of vectors used (58%)
Garbage collection 50 = 37+6+7 (level 2) ...
31.2 Mbytes of cons cells used (79%)
4.7 Mbytes of vectors used (53%)
Garbage collection 51 = 38+6+7 (level 0) ...
31.4 Mbytes of cons cells used (79%)
4.8 Mbytes of vectors used (53%)
Garbage collection 52 = 39+6+7 (level 0) ...
31.5 Mbytes of cons cells used (79%)
4.8 Mbytes of vectors used (53%)
Garbage collection 53 = 40+6+7 (level 0) ...
32.1 Mbytes of cons cells used (81%)
4.8 Mbytes of vectors used (54%)
Garbage collection 54 = 40+7+7 (level 1) ...
33.3 Mbytes of cons cells used (84%)
5.1 Mbytes of vectors used (56%)
Garbage collection 55 = 40+7+8 (level 2) ...
33.2 Mbytes of cons cells used (76%)
5.0 Mbytes of vectors used (55%)
Garbage collection 56 = 40+8+8 (level 1) ...
33.8 Mbytes of cons cells used (77%)
5.0 Mbytes of vectors used (56%)
Garbage collection 57 = 41+8+8 (level 0) ...
34.8 Mbytes of cons cells used (79%)
5.1 Mbytes of vectors used (57%)
Garbage collection 58 = 42+8+8 (level 0) ...
35.5 Mbytes of cons cells used (81%)
5.2 Mbytes of vectors used (58%)
Garbage collection 59 = 42+9+8 (level 1) ...
36.5 Mbytes of cons cells used (83%)
5.3 Mbytes of vectors used (59%)
Garbage collection 60 = 42+9+9 (level 2) ...
37.9 Mbytes of cons cells used (79%)
5.4 Mbytes of vectors used (54%)
Garbage collection 61 = 43+9+9 (level 0) ...
38.5 Mbytes of cons cells used (80%)
5.5 Mbytes of vectors used (55%)
Garbage collection 62 = 43+10+9 (level 1) ...
39.4 Mbytes of cons cells used (82%)
5.6 Mbytes of vectors used (56%)
Garbage collection 63 = 43+10+10 (level 2) ...
40.2 Mbytes of cons cells used (76%)
5.7 Mbytes of vectors used (57%)
Garbage collection 64 = 44+10+10 (level 0) ...
41.0 Mbytes of cons cells used (78%)
5.8 Mbytes of vectors used (58%)
Garbage collection 65 = 45+10+10 (level 0) ...
41.4 Mbytes of cons cells used (79%)
5.9 Mbytes of vectors used (59%)
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RMySQL/libs/RMySQL.so") ...
Garbage collection 66 = 46+10+10 (level 0) ...
42.3 Mbytes of cons cells used (80%)
6.1 Mbytes of vectors used (60%)
Garbage collection 67 = 46+10+11 (level 2) ...
43.3 Mbytes of cons cells used (75%)
6.1 Mbytes of vectors used (55%)
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/digest/libs/digest.so") ...
now dyn.load("/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biobase/libs/Biobase.so") ...
Garbage collection 68 = 47+10+11 (level 0) ...
45.5 Mbytes of cons cells used (79%)
6.4 Mbytes of vectors used (58%)
Garbage collection 69 = 48+10+11 (level 0) ...
45.5 Mbytes of cons cells used (79%)
6.4 Mbytes of vectors used (58%)
Garbage collection 70 = 49+10+11 (level 0) ...
46.6 Mbytes of cons cells used (81%)
6.6 Mbytes of vectors used (59%)
Garbage collection 71 = 49+11+11 (level 1) ...
48.2 Mbytes of cons cells used (84%)
6.9 Mbytes of vectors used (62%)
Garbage collection 72 = 49+11+12 (level 2) ...
48.2 Mbytes of cons cells used (77%)
6.8 Mbytes of vectors used (56%)
Garbage collection 73 = 50+11+12 (level 0) ...
48.2 Mbytes of cons cells used (77%)
6.8 Mbytes of vectors used (56%)
Garbage collection 74 = 51+11+12 (level 0) ...
48.3 Mbytes of cons cells used (77%)
6.8 Mbytes of vectors used (56%)
Warning messages:
1: In find.package(package, lib.loc, quiet = TRUE, verbose = verbose) :
package 'xmapcore' found more than once,
using the one found in '/tmp/RtmpbvzdAE/Rinst42365896a53c/xmapcore'
2: In sillyname(methods) : package 'methods' already present in search()
3: In find.package(package, lib.loc, quiet = TRUE) :
package 'xmapcore' found more than once,
using the one found in '/tmp/RtmpbvzdAE/Rinst42365896a53c/xmapcore'
>
> data = tryCatch( xmap.connect( "hs-test" ), error=function(e) { FALSE } )
Using /home/hpages/.xmapcore as our configuration directory
> if( length( data ) == 1 ) {
+ # The here's one I prepared earlier shortcut
+ message( "Cannot find datasource 'hs-test', I'm not going to build the cookbook." )
+ } else {
+ message( "Generating cookbook..." )
+ # First, we'll disconnect, so the Rnw gets a fresh start
+ xmap.disconnect()
+
+ current.path = getwd()
+ path <- file.path( getwd(), "..", "cookbook" )
+ setwd( path )
+ # Parse the Rnw
+ library(tools)
+ utils::Sweave( 'cookbook.Rnw' )
+
+ # Generate the PDF
+ texi2dvi( 'cookbook.tex', pdf=T, clean=T )
+
+ # Copy it to the docs
+ file.copy( 'cookbook.pdf', file.path( path, '..', 'doc' ), overwrite=T )
+
+ # cleanup
+ unlink( 'cookbook.pdf' )
+ unlink( 'cookbook.tex' )
+ unlink( 'fig1.pdf' )
+ unlink( 'fig2.pdf' )
+ unlink( 'fig3.pdf' )
+ unlink( 'fig4.pdf' )
+ unlink( 'fig5.pdf' )
+ unlink( 'fig6.pdf' )
+
+ message( "Generating Splicing Index Documentation" )
+ utils::Sweave( 'SplicingIndexExample.Rnw' )
+ # Generate the PDF
+ texi2dvi( 'SplicingIndexExample.tex', pdf=T, clean=T )
+ # Copy it to the docs
+ file.copy( 'SplicingIndexExample.pdf', file.path( path, '..', 'doc' ), overwrite=T )
+ # cleanup
+ unlink( 'SplicingIndexExample.pdf' )
+ unlink( 'SplicingIndexExample.tex' )
+
+ setwd( current.path )
+ }
Cannot find datasource 'hs-test', I'm not going to build the cookbook.
>
>
texi2dvi --pdf xmapcore.tex
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
entering extended mode
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(./xmapcore.tex (/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size12.clo))
(/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty
(/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty))
(/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty))
(/usr/share/texmf-texlive/tex/latex/pstricks/pstricks.sty
(/usr/share/texmf-texlive/tex/generic/pstricks/pstricks.tex
`PSTricks' v1.29 <2009/05/19> (tvz)
(/usr/share/texmf-texlive/tex/generic/pstricks/pstricks.con))
(/usr/share/texmf/tex/latex/xcolor/xcolor.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)))
(/usr/share/texmf-texlive/tex/latex/auto-pst-pdf/auto-pst-pdf.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texmf-texlive/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texmf-texlive/tex/generic/xkeyval/keyval.tex)))
(/usr/share/texmf-texlive/tex/latex/ifplatform/ifplatform.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))
(/usr/share/texmf-texlive/tex/generic/oberdiek/catchfile.sty)
Package ifplatform Warning:
shell escape is disabled, so I can only detect \ifwindows.
)
/usr/share/texmf-texlive/tex/latex/auto-pst-pdf/auto-pst-pdf.sty:134: Package a
uto-pst-pdf Error:
"shell escape" (or "write18") is not enabled:
auto-pst-pdf will not work!
.
See the auto-pst-pdf package documentation for explanation.
Type H <return> for immediate help.
...
l.134 Or turn off auto-pst-pdf.}
%
?
/usr/share/texmf-texlive/tex/latex/auto-pst-pdf/auto-pst-pdf.sty:134: Emergency
stop.
...
l.134 Or turn off auto-pst-pdf.}
%
/usr/share/texmf-texlive/tex/latex/auto-pst-pdf/auto-pst-pdf.sty:134: ==> Fata
l error occurred, no output PDF file produced!
Transcript written on xmapcore.log.
/usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
make: *** [pdf] Error 1
Error in tools::buildVignettes(dir = ".") : running 'make' failed
Execution halted