maSigPro 1.41.0
Maria Jose Nueda
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maSigPro | | Last Changed Rev: 106786 / Revision: 107696 | | Last Changed Date: 2015-07-27 03:07:56 -0700 (Mon, 27 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/maSigPro.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maSigPro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maSigPro’ version ‘1.41.0’
* 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 ‘maSigPro’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘stats’ ‘MASS’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
see.genes: warning in mfuzz(signif, c = k, m = m): partial argument
match of 'c' to 'centers'
* 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 'PlotGroups':
PlotGroups
Code: function(data, edesign = NULL, time = edesign[, 1], groups =
edesign[, c(3:ncol(edesign))], repvect = edesign[, 2],
show.fit = FALSE, dis = NULL, step.method =
"backward", min.obs = 2, alfa = 0.05, nvar.correction
= FALSE, summary.mode = "median", show.lines = TRUE,
groups.vector = NULL, xlab = "Time", ylab =
"Expression value", cex.xaxis = 1, ylim = NULL, main =
NULL, cexlab = 0.8, legend = TRUE, sub = NULL)
Docs: function(data, edesign = NULL, time = edesign[, 1], groups =
edesign[, c(3:ncol(edesign))], repvect = edesign[, 2],
show.fit = FALSE, dis = NULL, step.method =
"backward", min.obs = 2, alfa = 0.05, nvar.correction
= FALSE, summary.mode = "median", show.lines = TRUE,
groups.vector = NULL, xlab = "time", cex.xaxis = 1,
ylim = NULL, main = NULL, cexlab = 0.8, legend = TRUE,
sub = NULL)
Argument names in code not in docs:
ylab
Mismatches in argument names (first 3):
Position: 16 Code: ylab Docs: cex.xaxis
Position: 17 Code: cex.xaxis Docs: ylim
Position: 18 Code: ylim Docs: main
Mismatches in argument default values:
Name: 'xlab' Code: "Time" Docs: "time"
Codoc mismatches from documentation object 'see.genes':
see.genes
Code: function(data, edesign = data$edesign, time.col = 1, repl.col =
2, group.cols = c(3:ncol(edesign)), names.groups =
colnames(edesign)[3:ncol(edesign)], cluster.data = 1,
groups.vector = data$groups.vector, k = 9, m = 1.45,
cluster.method = "hclust", distance = "cor",
agglo.method = "ward.D", show.fit = FALSE, dis = NULL,
step.method = "backward", min.obs = 3, alfa = 0.05,
nvar.correction = FALSE, show.lines = TRUE, iter.max =
500, summary.mode = "median", color.mode = "rainbow",
cexlab = 1, legend = TRUE, newX11 = TRUE, ylim = NULL,
main = NULL, ...)
Docs: function(data, edesign = data$edesign, time.col = 1, repl.col =
2, group.cols = c(3:ncol(edesign)), names.groups =
colnames(edesign)[3:ncol(edesign)], cluster.data = 1,
groups.vector = data$groups.vector, k = 9, m = 1.45,
cluster.method = "hclust", distance = "cor",
agglo.method = "ward", show.fit = FALSE, dis = NULL,
step.method = "backward", min.obs = 3, alfa = 0.05,
nvar.correction = FALSE, show.lines = TRUE, iter.max =
500, summary.mode = "median", color.mode = "rainbow",
cexlab = 1, legend = TRUE, newX11 = TRUE, ylim = NULL,
main = NULL, ...)
Mismatches in argument default values:
Name: 'agglo.method' Code: "ward.D" Docs: "ward"
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
T.fit 10.305 0.892 11.051
maSigPro 7.264 0.644 7.825
get.siggenes 5.231 0.446 5.713
* 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/maSigPro.Rcheck/00check.log’
for details.