Last updated on 2024-04-23 05:59:01 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| anndata | 7 | 6 | |
| babelwhale | 13 | ||
| diffusionMap | 13 | ||
| dyndimred | 13 | ||
| dyngen | 7 | 6 | |
| dynparam | 13 | ||
| dynutils | 13 | ||
| dynwrap | 13 | ||
| funkyheatmap | 2 | 11 | |
| GillespieSSA | 13 | ||
| GillespieSSA2 | 4 | 9 | |
| lmds | 13 | ||
| princurve | 13 | ||
| qsub | 13 | ||
| SCORPIUS | 1 | 6 | 6 |
Current CRAN status: NOTE: 7, OK: 6
Version: 0.7.5.6
Check: Rd files
Result: NOTE
checkRd: (-1) concat.Rd:35: Lost braces; missing escapes or markup?
35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
| ^
checkRd: (-1) concat.Rd:35: Lost braces
35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
| ^
checkRd: (-1) concat.Rd:35: Lost braces
35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
| ^
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-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 13
Version: 1.0.4
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘lle’
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-prerel-macos-arm64, r-prerel-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-windows-x86_64
Version: 1.0.4
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-prerel-macos-arm64, r-prerel-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-windows-x86_64
Current CRAN status: NOTE: 7, OK: 6
Version: 1.0.5
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'SingleCellExperiment', 'SummarizedExperiment'
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.5
Check: Rd files
Result: NOTE
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
| ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
| ^
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-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64
Current CRAN status: NOTE: 13
Version: 1.0.2
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-prerel-macos-arm64, r-prerel-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-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 0.5.0
Check: data for non-ASCII characters
Result: NOTE
Note: found 36 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: NOTE: 4, OK: 9
Version: 0.3.0
Check: installed package size
Result: NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
doc 1.7Mb
libs 3.4Mb
Flavors: r-prerel-macos-arm64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Current CRAN status: NOTE: 13
Version: 0.1.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
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-prerel-macos-arm64, r-prerel-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-windows-x86_64
Version: 0.1.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘Matrix’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 6, OK: 6
Version: 1.0.9
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘SingleCellExperiment’
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.9
Check: Rd files
Result: NOTE
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
| ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
| ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
| ^
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-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64
Version: 1.0.9
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘anndata.Rmd’ using rmarkdown
--- finished re-building ‘anndata.Rmd’
--- re-building ‘ginhoux.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/show_dimred-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19199 bytes
Input file size = 19301 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14187
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14187
Output IDAT size = 14187 bytes (5012 bytes decrease)
Output file size = 14265 bytes (5036 bytes = 26.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/plot_trajectory-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20139 bytes
Input file size = 20241 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15180
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15180
Output IDAT size = 15180 bytes (4959 bytes decrease)
Output file size = 15258 bytes (4983 bytes = 24.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/visualise_tafs-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15021 bytes
Input file size = 15111 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11452
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11452
Output IDAT size = 11452 bytes (3569 bytes decrease)
Output file size = 11530 bytes (3581 bytes = 23.70% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/moduled_tafs-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15692 bytes
Input file size = 15782 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11492
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11492
Output IDAT size = 11492 bytes (4200 bytes decrease)
Output file size = 11570 bytes (4212 bytes = 26.69% decrease)
--- finished re-building ‘ginhoux.Rmd’
--- re-building ‘simulated-data.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/show_dimred-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18081 bytes
Input file size = 18183 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13317
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13317
Output IDAT size = 13317 bytes (4764 bytes decrease)
Output file size = 13395 bytes (4788 bytes = 26.33% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/plot_trajectory-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19472 bytes
Input file size = 19574 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14652
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14652
Output IDAT size = 14652 bytes (4820 bytes decrease)
Output file size = 14730 bytes (4844 bytes = 24.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/visualise_tafs-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16253 bytes
Input file size = 16343 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11827
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11827
Output IDAT size = 11827 bytes (4426 bytes decrease)
Output file size = 11905 bytes (4438 bytes = 27.16% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/moduled_tafs-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17734 bytes
Input file size = 17836 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12733
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12733
Output IDAT size = 12733 bytes (5001 bytes decrease)
Output file size = 12811 bytes (5025 bytes = 28.17% decrease)
--- finished re-building ‘simulated-data.Rmd’
--- re-building ‘singlecellexperiment.Rmd’ using rmarkdown
Quitting from lines at lines 26-40 [load_data] (singlecellexperiment.Rmd)
Error: processing vignette 'singlecellexperiment.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed re-building ‘singlecellexperiment.Rmd’
SUMMARY: processing the following file failed:
‘singlecellexperiment.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang