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###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ToPASeq
###
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* checking for file ‘ToPASeq/DESCRIPTION’ ... OK
* preparing ‘ToPASeq’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: graphite
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Loading required package: gRbase
Loading required package: graph
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.0 (2015-02-19) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.19.0 (2015-02-27) successfully loaded. See ?R.oo for help.
Attaching package: ‘R.oo’
The following object is masked from ‘package:gRbase’:
compile
The following objects are masked from ‘package:methods’:
getClasses, getMethods
The following objects are masked from ‘package:base’:
attach, detach, gc, load, save
R.utils v2.1.0 (2015-05-27) successfully loaded. See ?R.utils for help.
Attaching package: ‘R.utils’
The following object is masked from ‘package:utils’:
timestamp
The following objects are masked from ‘package:base’:
cat, commandArgs, getOption, inherits, isOpen,
parse, warnings
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
0 pathways were filtered out
Found 40 differentially expressed genes
0 pathways were filtered out
0 pathways were filtered out
Found 40 differentially expressed genes
0 pathways were filtered out
22 pathways were filtered out
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.04209e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.20624e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.03265e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.3426e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.74003e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.35574e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.8963e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.00912e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.13642e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.78318e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.02427e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.29355e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.19868e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.8651e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.06489e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.1201e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.17736e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.25927e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.5807e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.66532e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.28439e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.20236e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.25381e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.30598e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.80894e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.25485e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.07039e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.85184e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.95235e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.4188e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.39229e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.73094e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.18421e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.48603e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.42036e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.22949e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.70487e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.36498e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.94191e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.64929e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.01875e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.32219e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.77092e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.41468e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.31626e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.19254e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.38681e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.66826e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.93545e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.53807e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.80742e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.56273e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.0363e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.73091e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.03114e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.885e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.42431e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.63332e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.53719e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.38632e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.94593e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.68915e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.8235e-19
Error in solve.default(V, xdiff) :
Lapack routine dgesv: system is exactly singular: U[47,47] = 0
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.21497e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.55658e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.30644e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.54818e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.37021e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.60139e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.15871e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.47251e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.12806e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.29889e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.33917e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.21906e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.25796e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.52675e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.42678e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.45876e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.54818e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.39984e-19
Error in solve.default(V, xdiff) :
Lapack routine dgesv: system is exactly singular: U[24,24] = 0
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.7119e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.06752e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.47794e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.12969e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.60141e-18
Error in solve.default(V, xdiff) :
Lapack routine dgesv: system is exactly singular: U[44,44] = 0
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.07955e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.92365e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.86928e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.56605e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.68081e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.4327e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.54818e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.04668e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.62636e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.98692e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.40489e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.86173e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.33611e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.89396e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.54818e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.68815e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.49136e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.04626e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.97995e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.18618e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.47382e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.33954e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.29367e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.13536e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.50522e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.34793e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.62313e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.33011e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.04028e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.00972e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.30598e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.64577e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.2747e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.25911e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.26706e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.36749e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.77248e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.75521e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.16743e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.10855e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.45684e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.17943e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.54235e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.49578e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.2017e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.73771e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.59439e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.79354e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.57817e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.73911e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.61244e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.58657e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.08632e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.61603e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.84263e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.55313e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.69305e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.18724e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.73058e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.28509e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.50473e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.66167e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.78852e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.71313e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.07473e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.60141e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.08859e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.72686e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.05463e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.5198e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.25166e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.1934e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.63169e-20
22 pathways were filtered out
22 pathways were filtered out
22 pathways were filtered out
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'ToPASeq.tex' failed.
LaTeX errors:
! Extra }, or forgotten \endgroup.
l.146 ...ng in one subset and ending in the other}
?
! Emergency stop.
! Emergency stop.
l.146 ...ng in one subset and ending in the other}
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted