Last updated on 2019-01-04 18:47:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.4 | 5.84 | 66.71 | 72.55 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.9.4 | 4.04 | 51.41 | 55.45 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.9.4 | 88.04 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.4 | 78.81 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 0.9.4 | 16.00 | 92.00 | 108.00 | WARN | |
| r-patched-linux-x86_64 | 0.9.4 | 5.94 | 61.41 | 67.35 | NOTE | |
| r-patched-solaris-x86 | 0.9.4 | 123.90 | NOTE | |||
| r-release-linux-x86_64 | 0.9.4 | 5.50 | 60.76 | 66.26 | NOTE | |
| r-release-windows-ix86+x86_64 | 0.9.4 | 11.00 | 80.00 | 91.00 | NOTE | |
| r-release-osx-x86_64 | 0.9.4 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 0.9.4 | 10.00 | 118.00 | 128.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.9.4 | WARN |
Version: 0.9.4
Check: package dependencies
Result: NOTE
Depends: includes the non-default packages:
'svmpath', 'kernlab', 'affy', 'Biobase', 'ROCR', 'igraph', 'lpSolve'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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
Version: 0.9.4
Check: dependencies in R code
Result: NOTE
'library' or 'require' call to ‘ROCR’ which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
‘Biobase’ ‘ROCR’ ‘affy’ ‘igraph’ ‘kernlab’ ‘lpSolve’ ‘svmpath’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘parallel:::detectCores’
See the note in ?`:::` about the use of this operator.
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: 0.9.4
Check: S3 generic/method consistency
Result: NOTE
Found the following apparent S3 methods exported but not registered:
plot.pathClassResult predict.graphSVM predict.networkBasedSVM
predict.rfe predict.rrfe
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: 0.9.4
Check: R code for possible problems
Result: NOTE
calc.auc: no visible global function definition for ‘prediction’
calc.auc: no visible global function definition for ‘performance’
calc.diffusionKernel: no visible global function definition for
‘graph.adjacency’
calc.diffusionKernel: no visible global function definition for
‘graph.laplacian’
calc.graph.svm: no visible global function definition for
‘as.kernelMatrix’
calc.graph.svm: no visible global function definition for ‘ksvm’
calc.graph.svm: no visible global function definition for ‘alphaindex’
calc.graph.svm: no visible global function definition for ‘coef’
calc.networkBasedSVM: no visible global function definition for ‘lp’
classify: no visible global function definition for ‘predict’
classify: no visible global function definition for ‘setTxtProgressBar’
classify: no visible global function definition for ‘getTxtProgressBar’
compare.auc: no visible global function definition for ‘prediction’
compare.auc: no visible global function definition for ‘performance’
compare.auc: no visible global function definition for ‘wilcox.test’
compare.auc: no visible global function definition for ‘pdf’
compare.auc: no visible global function definition for ‘par’
compare.auc: no visible global function definition for ‘plot’
compare.auc: no visible global function definition for ‘boxplot’
compare.auc: no visible global function definition for ‘dev.off’
crossval: no visible global function definition for ‘txtProgressBar’
crossval: no visible global function definition for ‘mclapply’
extractFeatures: no visible global function definition for ‘write.csv’
fit.networkBasedSVM: no visible binding for global variable ‘sd’
getRanking: no visible global function definition for
‘igraph.from.graphNEL’
getRanking: no visible global function definition for ‘get.adjacency’
plot.pathClassResult: no visible global function definition for ‘pdf’
plot.pathClassResult: no visible global function definition for
‘boxplot’
plot.pathClassResult: no visible global function definition for
‘stripchart’
plot.pathClassResult: no visible global function definition for
‘dev.new’
plot.pathClassResult: no visible global function definition for
‘prediction’
plot.pathClassResult: no visible global function definition for
‘performance’
plot.pathClassResult: no visible global function definition for ‘plot’
plot.pathClassResult: no visible global function definition for
‘dev.off’
predict.graphSVM: no visible global function definition for ‘coef’
predict.graphSVM: no visible global function definition for ‘b’
read.hprd: no visible global function definition for ‘read.delim’
spanbound: no visible global function definition for ‘alphaindex’
spanbound: no visible global function definition for ‘coef’
spanbound: no visible global function definition for ‘predict’
spanbound: no visible global function definition for ‘param’
spanbound: no visible global function definition for ‘error’
spanbound: no visible global function definition for ‘kernelMatrix’
spanbound: no visible global function definition for ‘kernelf’
spanbound: no visible global function definition for ‘b’
summarizeProbes : <anonymous>: no visible global function definition
for ‘median’
summarizeProbes : <anonymous>: no visible global function definition
for ‘rowMedians’
svm.fit: no visible global function definition for ‘kernelMatrix’
svm.fit: no visible global function definition for ‘vanilladot’
svm.fit: no visible global function definition for ‘as.kernelMatrix’
svm.fit: no visible global function definition for ‘ksvm’
svm.fit: no visible global function definition for ‘alphaindex’
svm.fit: no visible global function definition for ‘coef’
svm.predict: no visible global function definition for ‘kernelMatrix’
svm.predict: no visible global function definition for ‘vanilladot’
svm.predict: no visible global function definition for ‘rbfdot’
svm.predict: no visible global function definition for ‘coef’
svm.predict: no visible global function definition for ‘b’
Undefined global functions or variables:
alphaindex as.kernelMatrix b boxplot coef dev.new dev.off error
get.adjacency getTxtProgressBar graph.adjacency graph.laplacian
igraph.from.graphNEL kernelMatrix kernelf ksvm lp mclapply median par
param pdf performance plot predict prediction rbfdot read.delim
rowMedians sd setTxtProgressBar stripchart txtProgressBar vanilladot
wilcox.test write.csv
Consider adding
importFrom("grDevices", "dev.new", "dev.off", "pdf")
importFrom("graphics", "boxplot", "par", "plot", "stripchart")
importFrom("stats", "coef", "median", "predict", "sd", "wilcox.test")
importFrom("utils", "getTxtProgressBar", "read.delim",
"setTxtProgressBar", "txtProgressBar", "write.csv")
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: 0.9.4
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
Flavor: r-devel-windows-ix86+x86_64
Version: 0.9.4
Check: package dependencies
Result: NOTE
Depends: includes the non-default packages:
‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Flavors: r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.9.4
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’
Depends: includes the non-default packages:
‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.9.4
Check: running R code from vignettes
Result: WARN
Errors in running code in vignettes:
when running code in ‘pathClass.rnw’
...
union
Loading required package: lpSolve
> library(golubEsets)
When sourcing ‘pathClass.R’:
Error: there is no package called ‘golubEsets’
Execution halted
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.9.4
Check: re-building of vignette outputs
Result: NOTE
Error in re-building vignettes:
...
lowess
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:BiocGenerics’:
normalize, path, union
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: lpSolve
Error: processing vignette 'pathClass.rnw' failed with diagnostics:
chunk 2 (label = loadALLpackage)
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Flavor: r-release-osx-x86_64
Version: 0.9.4
Check: re-building of vignette outputs
Result: NOTE
Error in re-building vignettes:
...
lowess
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:BiocGenerics’:
normalize, union
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: lpSolve
Error: processing vignette 'pathClass.rnw' failed with diagnostics:
chunk 2 (label = loadALLpackage)
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Flavor: r-oldrel-osx-x86_64