CRAN Package Check Results for Maintainer ‘Toby Hocking <toby.hocking at r-project.org>’

Last updated on 2021-06-15 23:52:02 CEST.

Package ERROR NOTE OK
animint2 7 7
binsegRcpp 14
directlabels 14
inlinedocs 1 13
LOPART 14
namedCapture 11 3
nc 11 3
PeakError 4 10
PeakSegDisk 14
PeakSegDP 14
PeakSegJoint 14
PeakSegOptimal 14
penaltyLearning 1 13
WeightedROC 14

Package animint2

Current CRAN status: NOTE: 7, OK: 7

Version: 2020.9.18
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘lazyeval’ ‘tibble’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 2020.9.18
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘RColorBrewer’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2020.9.18
Check: installed package size
Result: NOTE
     installed size is 5.3Mb
     sub-directories of 1Mb or more:
     R 1.0Mb
     data 2.9Mb
Flavors: r-patched-solaris-x86, r-release-macos-arm64

Package binsegRcpp

Current CRAN status: OK: 14

Package directlabels

Current CRAN status: OK: 14

Package inlinedocs

Current CRAN status: NOTE: 1, OK: 13

Version: 2019.12.5
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘R.methodsS3’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Package LOPART

Current CRAN status: OK: 14

Package namedCapture

Current CRAN status: NOTE: 11, OK: 3

Version: 2020.4.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 're2r'
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-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Package nc

Current CRAN status: NOTE: 11, OK: 3

Version: 2020.8.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 're2r'
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-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Package PeakError

Current CRAN status: ERROR: 4, OK: 10

Version: 2017.06.19
Check: tests
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [2s]
    Running the tests in 'tests/script.R' failed.
    Complete output:
     > ## I initially tried writing these tests using testthat, but I got
     > ## errors when using the system() and system2() functions (bug in
     > ## testthat).
     > PeakError_compute.R <- system.file(
     + "exampleData", "PeakError_compute.R",
     + mustWork=TRUE,
     + package="PeakError")
     > Rscript <- R.home(file.path("bin", "Rscript"))
     > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
     > peaks.bed <- file.path(exampleData, "peaks.bed")
     > labels.bed <- file.path(exampleData, "labels.bed")
     > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
     >
     > ##test_that("PeakError_compute.R correct", {
     > out.file <- tempfile()
     > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
     > status <- system(cmd)
     Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
     Execution halted
     > errors <- read.table(out.file, sep="\t", header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file 'D:\temp\RtmpUVqwS0\file15620526f5267': No such file or directory
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 2017.06.19
Check: tests
Result: ERROR
     Running 'script.R'
    Running the tests in 'tests/script.R' failed.
    Last 13 lines of output:
     > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
     >
     > ##test_that("PeakError_compute.R correct", {
     > out.file <- tempfile()
     > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
     > status <- system(cmd)
     Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
     Execution halted
     > errors <- read.table(out.file, sep="\t", header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\PeakError\tmp\RtmpiOiY9S\file2a184eb5489': No such file or directory
     Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 2017.06.19
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [2s]
    Running the tests in 'tests/script.R' failed.
    Complete output:
     > ## I initially tried writing these tests using testthat, but I got
     > ## errors when using the system() and system2() functions (bug in
     > ## testthat).
     > PeakError_compute.R <- system.file(
     + "exampleData", "PeakError_compute.R",
     + mustWork=TRUE,
     + package="PeakError")
     > Rscript <- R.home(file.path("bin", "Rscript"))
     > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
     > peaks.bed <- file.path(exampleData, "peaks.bed")
     > labels.bed <- file.path(exampleData, "labels.bed")
     > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
     >
     > ##test_that("PeakError_compute.R correct", {
     > out.file <- tempfile()
     > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
     > status <- system(cmd)
     Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
     Execution halted
     > errors <- read.table(out.file, sep="\t", header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file 'D:\temp\RtmpSgvrex\file18c0c193f35f4': No such file or directory
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 2017.06.19
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [2s]
    Running the tests in 'tests/script.R' failed.
    Complete output:
     > ## I initially tried writing these tests using testthat, but I got
     > ## errors when using the system() and system2() functions (bug in
     > ## testthat).
     > PeakError_compute.R <- system.file(
     + "exampleData", "PeakError_compute.R",
     + mustWork=TRUE,
     + package="PeakError")
     > Rscript <- R.home(file.path("bin", "Rscript"))
     > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
     > peaks.bed <- file.path(exampleData, "peaks.bed")
     > labels.bed <- file.path(exampleData, "labels.bed")
     > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
     >
     > ##test_that("PeakError_compute.R correct", {
     > out.file <- tempfile()
     > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
     > status <- system(cmd)
     Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
     Execution halted
     > errors <- read.table(out.file, sep="\t", header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file 'D:\temp\RtmpiIOyIY\file164c426056bb4': No such file or directory
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 2017.06.19
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [2s]
    Running the tests in 'tests/script.R' failed.
    Complete output:
     > ## I initially tried writing these tests using testthat, but I got
     > ## errors when using the system() and system2() functions (bug in
     > ## testthat).
     > PeakError_compute.R <- system.file(
     + "exampleData", "PeakError_compute.R",
     + mustWork=TRUE,
     + package="PeakError")
     > Rscript <- R.home(file.path("bin", "Rscript"))
     > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
     > peaks.bed <- file.path(exampleData, "peaks.bed")
     > labels.bed <- file.path(exampleData, "labels.bed")
     > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
     >
     > ##test_that("PeakError_compute.R correct", {
     > out.file <- tempfile()
     > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
     > status <- system(cmd)
     Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
     Execution halted
     > errors <- read.table(out.file, sep="\t", header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file 'D:\temp\RtmpW0OxAs\file16d90722c541c': No such file or directory
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 2017.06.19
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [2s]
    Running the tests in 'tests/script.R' failed.
    Complete output:
     > ## I initially tried writing these tests using testthat, but I got
     > ## errors when using the system() and system2() functions (bug in
     > ## testthat).
     > PeakError_compute.R <- system.file(
     + "exampleData", "PeakError_compute.R",
     + mustWork=TRUE,
     + package="PeakError")
     > Rscript <- R.home(file.path("bin", "Rscript"))
     > exampleData <- system.file("exampleData", package="PeakError", mustWork=TRUE)
     > peaks.bed <- file.path(exampleData, "peaks.bed")
     > labels.bed <- file.path(exampleData, "labels.bed")
     > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
     >
     > ##test_that("PeakError_compute.R correct", {
     > out.file <- tempfile()
     > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
     > status <- system(cmd)
     Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
     Execution halted
     > errors <- read.table(out.file, sep="\t", header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file 'D:\temp\RtmpEfPhGk\file177406f9a19a4': No such file or directory
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Package PeakSegDisk

Current CRAN status: OK: 14

Package PeakSegDP

Current CRAN status: OK: 14

Package PeakSegJoint

Current CRAN status: OK: 14

Package PeakSegOptimal

Current CRAN status: OK: 14

Package penaltyLearning

Current CRAN status: NOTE: 1, OK: 13

Version: 2020.5.13
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘jointseg’
Flavor: r-release-macos-arm64

Package WeightedROC

Current CRAN status: OK: 14