Genominator 1.2.0
James Bullard
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/Genominator | | Last Changed Rev: 46401 / Revision: 49923 | | Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | [ ERROR ] | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for file 'Genominator/DESCRIPTION' ... OK
* preparing 'Genominator':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: DBI
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
Loading required package: biomaRt
Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Genominator)
* creating vignettes ... ERROR
Loading required package: RSQLite
Loading required package: DBI
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
Loading required package: GenomeGraphs
Loading required package: biomaRt
Loading required package: grid
writing regions table:
0.02 sec
SQL query: SELECT counts,feature FROM counts_tbl INNER JOIN __regions__ ON
__regions__.chr = counts_tbl.chr AND counts_tbl.location BETWEEN
__regions__.start AND __regions__.end AND (counts_tbl.strand =
__regions__.strand OR __regions__.strand = 0 OR counts_tbl.strand = 0)
fetching merge table:
0.03 sec
splitting by: feature:
0 sec
matplot: doing 1 plots with col= ("1") pch= ("1" "2" "3" "4" "5" "6" "7" "8" "9" "0" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z" "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z") ...
writing regions table:
0.01 sec
SQL query: SELECT __regions__.id, TOTAL(counts) FROM __regions__ LEFT OUTER
JOIN counts_tbl ON __regions__.chr = counts_tbl.chr AND counts_tbl.location
BETWEEN __regions__.start AND __regions__.end AND (counts_tbl.strand =
__regions__.strand OR __regions__.strand = 0 OR counts_tbl.strand = 0) GROUP BY
__regions__.id ORDER BY __regions__.id
fetching summary table:
0.05 sec
fetching summary:
0.01 sec
matplot: doing 1 plots with col= ("1") pch= ("1" "2" "3" "4" "5" "6" "7" "8" "9" "0" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z" "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z") ...
writing regions table:
0.02 sec
SQL query: SELECT __regions__.id, TOTAL(counts_1), TOTAL(counts_2) FROM
__regions__ LEFT OUTER JOIN allcounts ON __regions__.chr = allcounts.chr AND
allcounts.location BETWEEN __regions__.start AND __regions__.end AND
(allcounts.strand = __regions__.strand OR __regions__.strand = 0 OR
allcounts.strand = 0) GROUP BY __regions__.id ORDER BY __regions__.id
fetching summary table:
0.03 sec
Loading required package: ShortRead
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: yeastRNASeq
texi2dvi -q --pdf Genominator.tex
texi2dvi -q --pdf plotting.tex
texi2dvi -q --pdf withShortRead.tex
rm -rf Genominator.aux Genominator.log Genominator.tex Genominator.out \
plotting.aux plotting.log plotting.tex plotting.out \
withShortRead.aux withShortRead.log withShortRead.tex withShortRead.out \
plots_* Rplots.pdf auto my.db pmy.db
rm: cannot remove `Rplots.pdf': Device or resource busy
rm: cannot remove `my.db': Device or resource busy
rm: cannot remove `pmy.db': Device or resource busy
make: *** [all] Error 1
Error in buildVignettes(dir = ".") : running 'make' failed
Execution halted