Last updated on 2018-05-28 06:46:41 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.3 | 5.82 | 50.56 | 56.38 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3.3 | 4.39 | 43.33 | 47.72 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.3 | 79.50 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.3 | 75.44 | WARN | |||
| r-devel-windows-ix86+x86_64 | 0.3.3 | 8.00 | 242.00 | 250.00 | NOTE | |
| r-patched-linux-x86_64 | 0.3.3 | 5.75 | 54.70 | 60.45 | ERROR | |
| r-patched-solaris-x86 | 0.3.3 | 99.70 | WARN | |||
| r-release-linux-x86_64 | 0.3.3 | 4.48 | 54.53 | 59.01 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.3.3 | 14.00 | 303.00 | 317.00 | NOTE | |
| r-release-osx-x86_64 | 0.3.3 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.3.3 | 8.00 | 235.00 | 243.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.3.3 | NOTE |
Version: 0.3.3
Check: S3 generic/method consistency
Result: NOTE
Found the following apparent S3 methods exported but not registered:
plot.elbow plot.gmdm plot.gmdp plot.mhist plot.mhist.summary
print.gmdm print.gmdp summary.gmdp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 0.3.3
Check: R code for possible problems
Result: NOTE
.file_path_as_absolute: no visible global function definition for
‘file_test’
.plot.text: no visible global function definition for ‘par’
.plot.text: no visible global function definition for ‘plot’
.plot.text: no visible global function definition for ‘rect’
.plot.text: no visible global function definition for ‘text’
bedgraph.to.depth: no visible global function definition for
‘read.table’
ghist: no visible global function definition for ‘hist’
heatmap.3: no visible global function definition for ‘par’
heatmap.3: no visible global function definition for ‘flush.console’
heatmap.3: no visible global function definition for ‘layout’
heatmap.3: no visible global function definition for ‘image’
heatmap.3: no visible global function definition for ‘axis’
heatmap.3: no visible global function definition for ‘text’
heatmap.3: no visible global function definition for ‘mtext’
heatmap.3: no visible global function definition for ‘rect’
heatmap.3: no visible global function definition for ‘abline’
heatmap.3: no visible global function definition for ‘lines’
heatmap.3: no visible global function definition for ‘plot’
heatmap.3: no visible global function definition for ‘title’
heatmap.3: no visible global function definition for ‘hist’
legend: no visible global function definition for ‘par’
legend : rect2: no visible global function definition for ‘rect’
legend : segments2: no visible global function definition for
‘segments’
legend : points2: no visible global function definition for ‘points’
legend : text2: no visible global function definition for ‘text’
legend: no visible global function definition for ‘strwidth’
legend: no visible global function definition for ‘xinch’
legend: no visible global function definition for ‘yinch’
legend: no visible global function definition for ‘strheight’
plot.elbow: no visible global function definition for ‘par’
plot.elbow: no visible global function definition for ‘plot’
plot.elbow: no visible global function definition for ‘abline’
plot.elbow: no visible global function definition for ‘mtext’
plot.elbow: no visible global function definition for ‘text’
plot.elbow: no visible global function definition for ‘title’
plot.gmdm: no visible global function definition for ‘par’
plot.gmdm: no visible global function definition for ‘plot’
plot.gmdm: no visible global function definition for ‘text’
plot.gmdm: no visible global function definition for ‘rect’
plot.gmdm: no visible global function definition for ‘mtext’
plot.mhist: no visible global function definition for ‘plot’
plot.mhist: no visible global function definition for ‘abline’
plot.mhist: no visible global function definition for ‘mtext’
plot.mhist: no visible global function definition for ‘axis’
plot.mhist: no visible global function definition for ‘rect’
plot.mhist: no visible global function definition for ‘lines’
plot.mhist: no visible global function definition for ‘par’
plot.mhist.summary: no visible global function definition for ‘par’
ts2df: no visible global function definition for ‘is’
Undefined global functions or variables:
abline axis file_test flush.console hist image is layout lines mtext
par plot points read.table rect segments strheight strwidth text
title xinch yinch
Consider adding
importFrom("graphics", "abline", "axis", "hist", "image", "layout",
"lines", "mtext", "par", "plot", "points", "rect",
"segments", "strheight", "strwidth", "text", "title",
"xinch", "yinch")
importFrom("methods", "is")
importFrom("utils", "file_test", "flush.console", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 0.3.3
Check: compiled code
Result: NOTE
File ‘GMD/libs/GMD.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.3.3
Check: examples
Result: ERROR
Running examples in ‘GMD-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmdp
> ### Title: Generalized Minimum Distance between a pair of distributions
> ### Aliases: gmdp print.gmdp summary.gmdp
> ### Keywords: classes
>
> ### ** Examples
>
> require(GMD)
> gmdp(c(4,1,1,0,0,0,3,1),c(2,1,1,0,0,0,3,3),sliding=FALSE)
[1] 1.4
attr(,"class")
[1] "gmdp" "numeric"
attr(,"meta")
attr(,"meta")$labels
[1] "v1" "v2"
attr(,"meta")$v1.ori
[1] 0.4 0.1 0.1 0.0 0.0 0.0 0.3 0.1
attr(,"meta")$v2.ori
[1] 0.2 0.1 0.1 0.0 0.0 0.0 0.3 0.3
attr(,"meta")$resolution
[1] 1
attr(,"meta")$v1
[1] 0.4 0.1 0.1 0.0 0.0 0.0 0.3 0.1
attr(,"meta")$v2
[1] 0.2 0.1 0.1 0.0 0.0 0.0 0.3 0.3
attr(,"meta")$sliding
[1] FALSE
attr(,"meta")$pseudocount
[1] 0
attr(,"meta")$gap.pair
[,1] [,2]
[1,] 0 0
attr(,"meta")$n.hit
[1] 1
> x <- gmdp(c(4,1,1,0,0,0,3,1), c(1,1,2,1,1,0,0,0,3,3,5,5),
+ pseudocount=1, sliding=TRUE)
> print(x)
[1] 1.156863
attr(,"class")
[1] "gmdp" "numeric"
attr(,"meta")
attr(,"meta")$labels
[1] "v1" "v2"
attr(,"meta")$v1.ori
[1] 5 2 2 1 1 1 4 2
attr(,"meta")$v2.ori
[1] 2 2 3 2 2 1 1 1 4 4 6 6
attr(,"meta")$resolution
[1] 1
attr(,"meta")$v1
[1] 0.27777778 0.11111111 0.11111111 0.05555556 0.05555556 0.05555556 0.22222222
[8] 0.11111111
attr(,"meta")$v2
[1] 0.05882353 0.05882353 0.08823529 0.05882353 0.05882353 0.02941176
[7] 0.02941176 0.02941176 0.11764706 0.11764706 0.17647059 0.17647059
attr(,"meta")$sliding
[1] TRUE
attr(,"meta")$pseudocount
[1] 1
attr(,"meta")$gap.pair
[,1] [,2]
[1,] 4 0
attr(,"meta")$n.hit
[1] 1
> print(x, "full")
Warning in print.default(x, "full") : NAs introduced by coercion
Error in print.default(x, "full") : invalid 'digits' argument
Calls: print -> print.default
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.3.3
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: GMD
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: row dendrogram is asked; Rowv is set to `TRUE'.
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: col dendrogram is asked; Colv is set to `TRUE'.
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
heatmap.3 | From GMD 0.3.3, please use relative values for cexRow.
heatmap.3 | From GMD 0.3.3, please use relative values for cexCol.
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Warning in plot.window(...) : "cex.text" is not a graphical parameter
Warning in plot.window(...) :
"if.plot.new" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
plot type ‘polygon’ will be truncated to first character
Warning in plot.xy(xy, type, ...) :
"cex.text" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
"if.plot.new" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
"cex.text" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
"if.plot.new" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
"cex.text" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
"if.plot.new" is not a graphical parameter
Warning in box(...) : "cex.text" is not a graphical parameter
Warning in box(...) : "if.plot.new" is not a graphical parameter
Warning in title(...) : "cex.text" is not a graphical parameter
Warning in title(...) : "if.plot.new" is not a graphical parameter
Error: processing vignette ‘GMD-vignette.Rnw’ failed with diagnostics:
chunk 6
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' is a list, but does not have components 'x' and 'y'
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.3.3
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: GMD
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: row dendrogram is asked; Rowv is set to `TRUE'.
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: col dendrogram is asked; Colv is set to `TRUE'.
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
heatmap.3 | From GMD 0.3.3, please use relative values for cexRow.
heatmap.3 | From GMD 0.3.3, please use relative values for cexCol.
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'GMD-vignette.tex' failed.
LaTeX errors:
! Package inputenc Error: Unicode character <c2><8a> (U+8A)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character <c2><9a> (U+9A)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86
Version: 0.3.3
Check: DESCRIPTION meta-information
Result: NOTE
NeedsCompilation field should likely be 'yes'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.3.3
Check: re-building of vignette outputs
Result: NOTE
Error in re-building vignettes:
...
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Warning in as.mhist(tmp.x) :
`bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'GMD-data-processing.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.10 ^^M
! ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Flavor: r-oldrel-osx-x86_64