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

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

Last updated on 2020-08-07 01:50:35 CEST.

Package	ERROR	NOTE	OK
directlabels			12
inlinedocs		1	11
LOPART			12
namedCapture		8	4
nc	9	2	1
PeakError	2		10
PeakSegDisk			12
PeakSegDP			12
PeakSegJoint			12
PeakSegOptimal			12
penaltyLearning			12
WeightedROC			12

Package inlinedocs

Current CRAN status: NOTE: 1, OK: 11

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: 12

Package namedCapture

Current CRAN status: NOTE: 8, OK: 4

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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64

Package nc

Current CRAN status: ERROR: 9, NOTE: 2, OK: 1

Version: 2020.5.13
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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64

Version: 2020.5.13
Check: tests
Result: ERROR
     Running 'testthat.R' [14s/12s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     -- 1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) -
     children$dob inherits from `IDate/Date` not `character`.

     == testthat results ===========================================================
     [ OK: 355 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
     1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2020.5.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [8s/12s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     ── 1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) ─────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ──
     children$dob inherits from `IDate/Date` not `character`.

     ── 4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ─
     children$dob inherits from `IDate/Date` not `character`.

     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 355 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
     1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2020.5.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [12s/12s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     ── 1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) ─────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ──
     children$dob inherits from `IDate/Date` not `character`.

     ── 4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ─
     children$dob inherits from `IDate/Date` not `character`.

     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 355 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
     1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2020.5.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [11s/13s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     ── 1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) ─────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ──
     children$dob inherits from `IDate/Date` not `character`.

     ── 4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ─
     children$dob inherits from `IDate/Date` not `character`.

     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 355 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
     1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2020.5.13
Check: tests
Result: ERROR
     Running 'testthat.R' [15s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     -- 1. Failure: RE2 gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 2. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 3. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 4. Failure: RE2 gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 5. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 6. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) -
     children$dob inherits from `IDate/Date` not `character`.

     == testthat results ===========================================================
     [ OK: 530 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 6 ]
     1. Failure: RE2 gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     4. Failure: RE2 gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     5. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     6. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2020.5.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/12s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     ── 1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) ─────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ──
     children$dob inherits from `IDate/Date` not `character`.

     ── 4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ─
     children$dob inherits from `IDate/Date` not `character`.

     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 355 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
     1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 2020.5.13
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/11s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     ── 1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) ─────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ────────────
     na.children$dob inherits from `IDate/Date` not `character`.

     ── 3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ──
     children$dob inherits from `IDate/Date` not `character`.

     ── 4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) ─
     children$dob inherits from `IDate/Date` not `character`.

     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 355 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
     1. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     4. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-linux-x86_64

Version: 2020.5.13
Check: tests
Result: ERROR
     Running 'testthat.R' [8s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     -- 1. Failure: RE2 gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 2. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 3. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 4. Failure: RE2 gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 5. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 6. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) -
     children$dob inherits from `IDate/Date` not `character`.

     == testthat results ===========================================================
     [ OK: 530 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 6 ]
     1. Failure: RE2 gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     4. Failure: RE2 gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     5. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     6. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 2020.5.13
Check: tests
Result: ERROR
     Running 'testthat.R' [12s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > if(require(testthat))test_check("nc")
     Loading required package: testthat
     Loading required package: nc
     -- 1. Failure: RE2 gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 2. Failure: ICU gender dob example (@test-CRAN-multiple.R#115) -------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 3. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115) ------------
     na.children$dob inherits from `IDate/Date` not `character`.

     -- 4. Failure: RE2 gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 5. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) --
     children$dob inherits from `IDate/Date` not `character`.

     -- 6. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174) -
     children$dob inherits from `IDate/Date` not `character`.

     == testthat results ===========================================================
     [ OK: 530 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 6 ]
     1. Failure: RE2 gender dob example (@test-CRAN-multiple.R#115)
     2. Failure: ICU gender dob example (@test-CRAN-multiple.R#115)
     3. Failure: PCRE gender dob example (@test-CRAN-multiple.R#115)
     4. Failure: RE2 gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     5. Failure: ICU gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)
     6. Failure: PCRE gender dob example na.rm=TRUE (@test-CRAN-multiple.R#174)

     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Package PeakError

Current CRAN status: ERROR: 2, OK: 10

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\Rtmp2nN1hB\file2ada044a42b9': No such file or directory
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2017.06.19
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [3s]
    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\RtmpoTvzZ6\file1473040e752c2': No such file or directory
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2017.06.19
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'script.R' [1s]
     Running 'testthat.R' [3s]
    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\Rtmp4wjZ3M\file170c8774931c8': 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' [3s]
    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\RtmpsdLxXZ\file26b9818264b11': No such file or directory
     Execution halted
Flavor: r-release-windows-ix86+x86_64