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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/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 = 1.31247e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.91502e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.43233e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.56341e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.72179e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.77236e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.06115e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.83199e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.62837e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.38592e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.98844e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.11401e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.66179e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.47751e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.30005e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.90924e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.36085e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.97013e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.33675e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.82405e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.70047e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.1608e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.38673e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.21036e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.19195e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.78397e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.37932e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.59939e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.62146e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.08364e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.15401e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.73426e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.21686e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.10874e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.97295e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.07364e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.60917e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.21865e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.06921e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.5449e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.04406e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.08148e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.06451e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.8864e-23
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.46712e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.3595e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.70974e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.77901e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.28171e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.60707e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.1698e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.37172e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.33772e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.99964e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.41928e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.04256e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.07968e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.16058e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.70481e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.23231e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.31343e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.50341e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.29357e-18
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 = 9.24607e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.448e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.2853e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.23378e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.20393e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.84066e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.64533e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.28942e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.3849e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.18995e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.61763e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.14993e-17
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.72179e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.20698e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.38433e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.60834e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.23378e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.46242e-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 = 4.58891e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.03772e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.03277e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.92997e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.12335e-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 = 3.66895e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.62455e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.7504e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.50618e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.30897e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.07994e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.23378e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.49257e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.6116e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.97187e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.51105e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.12626e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.86059e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.24499e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.23378e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.85146e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.50988e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.93076e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.58008e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.34137e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.01663e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.66433e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.98793e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.05078e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.45908e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.28238e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.5561e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.0885e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.19184e-22
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.83779e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.21036e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.31329e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.94202e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.96282e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.5502e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.44597e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.33892e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.77805e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.05143e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.82952e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.7486e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.07453e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.66267e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.26793e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 8.52431e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.43225e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.55508e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.5519e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.23005e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.90838e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.68592e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.10856e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.50254e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.29788e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.61817e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.57477e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.58906e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 4.08899e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.49123e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.41924e-20
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.02735e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.72831e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.2748e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.77103e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.58868e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.12335e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 9.47731e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 7.55976e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 3.99671e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 5.76098e-21
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 1.55514e-18
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 6.11439e-19
Error in solve.default(V, xdiff) :
system is computationally singular: reciprocal condition number = 2.45611e-21
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}
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.159 ...in a pathway: \texttt{directed}, \textttt
{undirected} or both
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted