Last updated on 2022-04-24 03:52:55 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| DRviaSPCN | 2 | 10 | |
| ICDS | 2 | 10 | |
| LncPath | 6 | 6 | |
| MiRSEA | 12 | ||
| PAGI | 12 | ||
| pathwayTMB | 12 | ||
| PMAPscore | 6 | 6 | |
| PriorCD | 8 | 4 | |
| psSubpathway | 2 | 10 | |
| SMDIC | 6 | 6 | |
| SubtypeDrug | 2 | 10 |
Current CRAN status: NOTE: 2, OK: 10
Version: 0.1.2
Check: installed package size
Result: NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 5.0Mb
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64
Current CRAN status: ERROR: 2, OK: 10
Version: 0.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ICDS.Rmd’ using rmarkdown
Loading required package: graphite
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Quitting from lines 150-156 (ICDS.Rmd)
Error: processing vignette ‘ICDS.Rmd’ failed with diagnostics:
cannot download pathway data: are you using the latest graphite version?
--- failed re-building ‘ICDS.Rmd’
SUMMARY: processing the following file failed:
‘ICDS.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Current CRAN status: NOTE: 6, OK: 6
Version: 1.1
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'tTestTable.rda'
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
Current CRAN status: OK: 12
Current CRAN status: NOTE: 12
Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Title field: should not end in a period.
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, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0
Check: R code for possible problems
Result: NOTE
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible global function definition for 'p.adjust'
PAGI.Main: no visible global function definition for 'pt'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Undefined global functions or variables:
ExampleData PAGIData p.adjust pt
Consider adding
importFrom("stats", "p.adjust", "pt")
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-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0
Check: Rd line widths
Result: NOTE
Rd file 'CalGIF.Rd':
\examples lines wider than 100 characters:
###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
Rd file 'PAGI.Main.Rd':
\examples lines wider than 100 characters:
#Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
#"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
#Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
#"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
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: 1.0
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 1.6Mb
localdata 3.1Mb
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 12
Current CRAN status: NOTE: 6, OK: 6
Version: 0.1.1
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘base’ ‘grDevices’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: NOTE: 8, OK: 4
Version: 0.1.0
Check: package vignettes
Result: NOTE
Package vignette with placeholder title 'Vignette Title':
'priorcd.Rmd'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.1.0
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'network.html' 'network_files'
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
Current CRAN status: NOTE: 2, OK: 10
Version: 0.1.1
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 4.6Mb
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64
Current CRAN status: NOTE: 6, OK: 6
Version: 0.1.3
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘quadprog’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: NOTE: 2, OK: 10
Version: 0.1.5
Check: installed package size
Result: NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 4.6Mb
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64