trackViewer 1.13.8
Jianhong Ou
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/trackViewer | | Last Changed Rev: 131036 / Revision: 131943 | | Last Changed Date: 2017-07-07 10:00:37 -0400 (Fri, 07 Jul 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings trackViewer_1.13.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/trackViewer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
trackViewer-package 17.924 0.012 19.481
viewTracks 10.628 0.008 12.026
browseTracks 9.444 0.032 9.486
parseWIG 9.216 0.004 9.223
geneModelFromTxdb 8.820 0.096 9.147
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/home/biocbuild/bbs-3.6-bioc/meat/trackViewer.Rcheck/00check.log’
for details.