BioC 3.6: CHECK report for trackViewer on tokay1

Package: trackViewer

Version: 1.13.8

Command: rm -rf trackViewer.buildbin-libdir trackViewer.Rcheck && mkdir trackViewer.buildbin-libdir trackViewer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trackViewer.buildbin-libdir trackViewer_1.13.8.tar.gz >trackViewer.Rcheck\00install.out 2>&1 && cp trackViewer.Rcheck\00install.out trackViewer-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=trackViewer.buildbin-libdir --install="check:trackViewer-install.out" --force-multiarch --no-vignettes --timings trackViewer_1.13.8.tar.gz

StartedAt: 2017-08-16 02:53:43 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:03:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 601.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: trackViewer.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf trackViewer.buildbin-libdir trackViewer.Rcheck && mkdir trackViewer.buildbin-libdir trackViewer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trackViewer.buildbin-libdir trackViewer_1.13.8.tar.gz >trackViewer.Rcheck\00install.out 2>&1 && cp trackViewer.Rcheck\00install.out trackViewer-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=trackViewer.buildbin-libdir --install="check:trackViewer-install.out" --force-multiarch --no-vignettes --timings trackViewer_1.13.8.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/trackViewer.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trackViewer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trackViewer' version '1.13.8'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'trackViewer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'filterTracks'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'ideogramPlot':
ideogramPlot
  Code: function(ideo, dataList, layout = NULL, horiz = TRUE,
                 parameterList = list(vp = plotViewport(margins =
                 c(0.1, 4.1, 0.3, 0.1)), ideoHeight = unit(1/(1 +
                 length(dataList)), "npc"), vgap = unit(0.3, "lines"),
                 ylabs = "auto", ylabsRot = ifelse(horiz, 0, 90),
                 ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis =
                 FALSE, xlab = "", types = "barplot", heights = NULL,
                 dataColumn = "score", gps = gpar(col = "black", fill =
                 "gray")), colorSheme = gieStain(), gp = gpar(fill =
                 NA, lwd = 2), ...)
  Docs: function(ideo, dataList, layout = NULL, horiz = TRUE,
                 parameterList = list(vp = plotViewport(margins =
                 c(0.1, 4.1, 0.3, 0.1)), ideoHeight = unit(0.5, "npc"),
                 vgap = unit(0.3, "lines"), ylabs = "auto", ylabsRot =
                 ifelse(horiz, 0, 90), ylabsPos = unit(2.5, "lines"),
                 xaxis = FALSE, yaxis = FALSE, xlab = "", types =
                 "barplot", heights = NULL, dataColumn = "score", gps =
                 gpar(col = "black", fill = "gray")), colorSheme =
                 gieStain(), gp = gpar(fill = NA, lwd = 2), ...)
  Mismatches in argument default values:
    Name: 'parameterList'
    Code: list(vp = plotViewport(margins = c(0.1, 4.1, 0.3, 0.1)), ideoHeight = unit(1/(1 + 
          length(dataList)), "npc"), vgap = unit(0.3, "lines"), ylabs = "auto", 
          ylabsRot = ifelse(horiz, 0, 90), ylabsPos = unit(2.5, "lines"), 
          xaxis = FALSE, yaxis = FALSE, xlab = "", types = "barplot", 
          heights = NULL, dataColumn = "score", gps = gpar(col = "black", 
              fill = "gray"))
    Docs: list(vp = plotViewport(margins = c(0.1, 4.1, 0.3, 0.1)), ideoHeight = unit(0.5, 
          "npc"), vgap = unit(0.3, "lines"), ylabs = "auto", ylabsRot = ifelse(horiz, 
          0, 90), ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis = FALSE, 
          xlab = "", types = "barplot", heights = NULL, dataColumn = "score", 
          gps = gpar(col = "black", fill = "gray"))

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 20.22   0.13   20.59
browseTracks        13.09   0.26   13.47
viewTracks          11.97   0.00   11.97
parseWIG            11.40   0.01   11.58
geneModelFromTxdb   10.59   0.33   10.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 18.24   0.09   18.33
viewTracks          12.33   0.02   12.35
browseTracks        12.05   0.02   12.06
parseWIG             9.47   0.00    9.46
geneModelFromTxdb    8.11   0.23    8.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/trackViewer.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'trackViewer' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'trackViewer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trackViewer' as trackViewer_1.13.8.zip
* DONE (trackViewer)

name	user	system	elapsed
GRoperator	3.25	0.05	3.29
addArrowMark	0.02	0.00	0.02
addGuideLine	0.02	0.00	0.02
browseTracks	13.09	0.26	13.47
coverageGR	0.22	0.00	0.22
dandelion.plot	1.47	0.06	1.53
geneModelFromTxdb	10.59	0.33	10.92
getCurTrackViewport	0.11	0.00	0.11
ideogramPlot	0	0	0
importBam	0.58	0.00	0.57
importData	2.40	0.00	2.97
importScore	0.71	0.00	0.71
loadIdeogram	0	0	0
lolliplot	1.28	0.00	1.28
optimizeStyle	0.86	0.02	0.87
parse2GRanges	0	0	0
parseWIG	11.40	0.01	11.58
plotGRanges	1.77	0.00	1.77
track	0.06	0.00	0.06
trackViewer-package	20.22	0.13	20.59
trackViewerStyle	0	0	0
viewTracks	11.97	0.00	11.97

name	user	system	elapsed
GRoperator	2.54	0.00	2.55
addArrowMark	0	0	0
addGuideLine	0	0	0
browseTracks	12.05	0.02	12.06
coverageGR	0.24	0.00	0.24
dandelion.plot	1.55	0.00	1.55
geneModelFromTxdb	8.11	0.23	8.34
getCurTrackViewport	0.05	0.00	0.05
ideogramPlot	0.00	0.02	0.02
importBam	0.37	0.00	0.37
importData	2.47	0.00	2.47
importScore	0.83	0.00	0.83
loadIdeogram	0	0	0
lolliplot	1.17	0.01	1.19
optimizeStyle	1.08	0.00	1.07
parse2GRanges	0.01	0.00	0.02
parseWIG	9.47	0.00	9.46
plotGRanges	1.29	0.00	1.30
track	0.04	0.00	0.03
trackViewer-package	18.24	0.09	18.33
trackViewerStyle	0.01	0.00	0.01
viewTracks	12.33	0.02	12.35