Last updated on 2019-01-26 15:47:23 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1-0 | 4.69 | 60.32 | 65.01 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1-0 | 3.72 | 44.68 | 48.40 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.1-0 | 78.13 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1-0 | 71.01 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.1-0 | 8.00 | 89.00 | 97.00 | NOTE | |
| r-patched-linux-x86_64 | 1.1-0 | 4.47 | 54.17 | 58.64 | NOTE | |
| r-patched-solaris-x86 | 1.1-0 | 123.70 | NOTE | |||
| r-release-linux-x86_64 | 1.1-0 | 4.51 | 54.38 | 58.89 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.1-0 | 12.00 | 66.00 | 78.00 | NOTE | |
| r-release-osx-x86_64 | 1.1-0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1-0 | 11.00 | 91.00 | 102.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.1-0 | NOTE |
Version: 1.1-0
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
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: 1.1-0
Check: dependencies in R code
Result: NOTE
'library' or 'require' call to ‘vegan’ which was already attached by Depends.
Please remove these calls from your code.
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: 1.1-0
Check: S3 generic/method consistency
Result: NOTE
Found the following apparent S3 methods exported but not registered:
cca.pertables plot.adonis.pertables plot.cca.pertables
plot.mantel.pertables plot.rda.pertables print.adonis.pertables
print.cca.pertables print.mantel.pertables print.pertables
print.rda.pertables rda.pertables
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: 1.1-0
Check: R code for possible problems
Result: NOTE
adonis.pertables: no visible binding for global variable ‘quantile’
cca.pertables : cca.var: no visible binding for global variable
‘cca.formula’
cca.pertables : cca.var: no visible global function definition for
‘anova’
cca.pertables: no visible binding for global variable ‘quantile’
cca.pertables: no visible binding for global variable ‘cca.formula’
cca.pertables: no visible global function definition for ‘anova’
mantel.pertables : mantel.test: no visible global function definition
for ‘dist’
mantel.pertables: no visible binding for global variable ‘quantile’
mantel.pertables: no visible global function definition for ‘dist’
plot.adonis.pertables: no visible global function definition for
‘layout’
plot.adonis.pertables: no visible global function definition for ‘par’
plot.adonis.pertables: no visible global function definition for ‘hist’
plot.adonis.pertables: no visible global function definition for
‘mtext’
plot.adonis.pertables: no visible global function definition for ‘plot’
plot.adonis.pertables: no visible global function definition for
‘density’
plot.adonis.pertables: no visible global function definition for
‘abline’
plot.adonis.pertables: no visible global function definition for
‘median’
plot.cca.pertables: no visible global function definition for ‘plot’
plot.cca.pertables : <anonymous> : <anonymous>: no visible global
function definition for ‘arrows’
plot.cca.pertables : <anonymous>: no visible global function definition
for ‘points’
plot.cca.pertables: no visible global function definition for ‘points’
plot.cca.pertables: no visible global function definition for ‘text’
plot.mantel.pertables: no visible global function definition for
‘layout’
plot.mantel.pertables: no visible global function definition for ‘par’
plot.mantel.pertables: no visible global function definition for ‘hist’
plot.mantel.pertables: no visible global function definition for ‘plot’
plot.mantel.pertables: no visible global function definition for
‘density’
plot.mantel.pertables: no visible global function definition for
‘abline’
plot.mantel.pertables: no visible global function definition for
‘median’
plot.mantel.pertables : <anonymous>: no visible global function
definition for ‘lines’
plot.mantel.pertables : <anonymous>: no visible global function
definition for ‘lowess’
plot.mantel.pertables: no visible global function definition for
‘lines’
plot.mantel.pertables: no visible global function definition for
‘lowess’
plot.rda.pertables: no visible global function definition for ‘plot’
plot.rda.pertables : <anonymous> : <anonymous>: no visible global
function definition for ‘arrows’
plot.rda.pertables : <anonymous>: no visible global function definition
for ‘points’
plot.rda.pertables: no visible global function definition for ‘points’
plot.rda.pertables: no visible global function definition for ‘text’
rda.pertables : rda.var: no visible binding for global variable
‘rda.formula’
rda.pertables : rda.var: no visible global function definition for
‘anova’
rda.pertables: no visible binding for global variable ‘quantile’
rda.pertables: no visible binding for global variable ‘rda.formula’
rda.pertables: no visible global function definition for ‘anova’
Undefined global functions or variables:
abline anova arrows cca.formula density dist hist layout lines lowess
median mtext par plot points quantile rda.formula text
Consider adding
importFrom("graphics", "abline", "arrows", "hist", "layout", "lines",
"mtext", "par", "plot", "points", "text")
importFrom("stats", "anova", "density", "dist", "lowess", "median",
"quantile")
to your NAMESPACE file.
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: 1.1-0
Check: Rd line widths
Result: NOTE
Rd file 'adonis.pertables.Rd':
\examples lines wider than 100 characters:
# Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
#Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
# Assess the effects of taxonomic uncertainty on a Mantel test of biological dissimilarity correlated to soil dissimilarity among site ... [TRUNCATED]
Rd file 'cca.pertables.Rd':
\examples lines wider than 100 characters:
# Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined
#Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
# Assess the effects of taxonomic uncertainty on a CCA analysis of biological data explained by all the
Rd file 'mantel.pertables.Rd':
\usage lines wider than 90 characters:
mantel.pertables(pertab, env, dist.method = "bray", binary = FALSE, cor.method = "pearson", permutations = 100)
plot(x, xlab = "Environmental distance", ylab = "Sorensen's similarity index", pch = 19, ...)
\examples lines wider than 100 characters:
# Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
#Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
# Assess the effects of taxonomic uncertainty on a Mantel test of biological dissimilarity correlated to soil dissimilarity among site ... [TRUNCATED]
Rd file 'pertables.Rd':
\examples lines wider than 100 characters:
# Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
#Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
Rd file 'rda.pertables.Rd':
\examples lines wider than 100 characters:
# Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
#Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
# Assess the effects of taxonomic uncertainty on a RDA analysis of biological data explained by all the environmental variables of the ... [TRUNCATED]
These lines will be truncated in the PDF 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: 1.1-0
Check: Rd \usage sections
Result: NOTE
S3 methods shown with full name in documentation object 'cca.pertables':
‘cca.pertables’
S3 methods shown with full name in documentation object 'rda.pertables':
‘rda.pertables’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ 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-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