Last updated on 2022-09-11 12:56:54 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| animint2 | 1 | 9 | 3 | |
| atime | 4 | 9 | ||
| aum | 13 | |||
| binsegRcpp | 13 | |||
| directlabels | 13 | |||
| inlinedocs | 1 | 12 | ||
| LOPART | 13 | |||
| namedCapture | 12 | 1 | ||
| nc | 12 | 1 | ||
| PeakError | 13 | |||
| PeakSegDisk | 13 | |||
| PeakSegDP | 13 | |||
| PeakSegJoint | 1 | 12 | ||
| PeakSegOptimal | 13 | |||
| penaltyLearning | 1 | 12 | ||
| plotHMM | 13 | |||
| WeightedROC | 13 |
Current CRAN status: WARN: 1, NOTE: 9, OK: 3
Version: 2022.1.25
Check: Rd files
Result: NOTE
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
checkRd: (-1) msleep.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) msleep.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) msleep.Rd:17: Escaped LaTeX specials: \_
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
Version: 2022.1.25
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-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2022.1.25
Check: Rd cross-references
Result: NOTE
Undeclared package ‘RColorBrewer’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2022.1.25
Check: for unstated dependencies in ‘tests’
Result: WARN
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: ERROR: 4, OK: 9
Version: 2022.8.25
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building 'PeakSegDisk.Rmd' using knitr
--- finished re-building 'PeakSegDisk.Rmd'
--- re-building 'binseg.Rmd' using knitr
--- finished re-building 'binseg.Rmd'
--- re-building 'cum_median.Rmd' using knitr
--- finished re-building 'cum_median.Rmd'
--- re-building 'data.table.Rmd' using knitr
--- finished re-building 'data.table.Rmd'
--- re-building 'git.Rmd' using knitr
Quitting from lines 72-80 (git.Rmd)
Error: processing vignette 'git.Rmd' failed with diagnostics:
! error in callr subprocess
Caused by error in `install.packages(sha.path, repos = NULL, type = "source", verbose = verbose)`:
! unable to install packages
--- failed re-building 'git.Rmd'
--- re-building 'optseg.Rmd' using knitr
--- finished re-building 'optseg.Rmd'
--- re-building 'regex.Rmd' using knitr
--- finished re-building 'regex.Rmd'
SUMMARY: processing the following file failed:
'git.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2022.8.25
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘PeakSegDisk.Rmd’ using knitr
--- finished re-building ‘PeakSegDisk.Rmd’
--- re-building ‘binseg.Rmd’ using knitr
Quitting from lines 127-153 (binseg.Rmd)
Error: processing vignette ‘binseg.Rmd’ failed with diagnostics:
‘from’ must be a finite number
--- failed re-building ‘binseg.Rmd’
--- re-building ‘cum_median.Rmd’ using knitr
--- finished re-building ‘cum_median.Rmd’
--- re-building ‘data.table.Rmd’ using knitr
--- finished re-building ‘data.table.Rmd’
--- re-building ‘git.Rmd’ using knitr
Quitting from lines 72-80 (git.Rmd)
Error: processing vignette ‘git.Rmd’ failed with diagnostics:
! error in callr subprocess
Caused by error in `install.packages(sha.path, repos = NULL, type = "source", verbose = verbose)`:
! unable to install packages
--- failed re-building ‘git.Rmd’
--- re-building ‘optseg.Rmd’ using knitr
--- finished re-building ‘optseg.Rmd’
--- re-building ‘regex.Rmd’ using knitr
--- finished re-building ‘regex.Rmd’
SUMMARY: processing the following files failed:
‘binseg.Rmd’ ‘git.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 1, OK: 12
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
Current CRAN status: OK: 13
Current CRAN status: NOTE: 12, OK: 1
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, 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
Current CRAN status: NOTE: 12, OK: 1
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, 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
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 2022.4.6
Check: running examples for arch ‘x64’
Result: ERROR
Running examples in 'PeakSegJoint-Ex.R' failed
The error most likely occurred in:
> ### Name: PeakSegJointError
> ### Title: PeakSegJointError
> ### Aliases: PeakSegJointError
>
> ### ** Examples
>
>
> library(PeakSegJoint)
> data(H3K36me3.TDH.other.chunk1, envir=environment())
> lims <- c(43000000, 43200000) # left
> some.counts <-
+ subset(H3K36me3.TDH.other.chunk1$counts,
+ lims[1] < chromEnd & chromStart < lims[2])
> some.regions <-
+ subset(H3K36me3.TDH.other.chunk1$regions,
+ lims[1] < chromEnd & chromStart < lims[2])
> fit <- PeakSegJointSeveral(some.counts)
Flavor: r-oldrel-windows-ix86+x86_64
Version: 2022.4.6
Check: running tests for arch ‘x64’
Result: ERROR
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> suite <- Sys.getenv("TEST_SUITE")
> if(suite=="")suite <- NULL
> test_check("PeakSegJoint", filter=suite)
Loading required package: PeakSegJoint
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 1, OK: 12
Version: 2020.5.13
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘jointseg’
Flavor: r-release-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: OK: 13