Last updated on 2024-12-22 10:50:33 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| hoardr | 3 | 2 | 8 |
| mulea | 4 | 9 | |
| webchem | 10 | 3 |
Current CRAN status: ERROR: 3, NOTE: 2, OK: 8
Version: 0.5.4
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
hoard.Rd: rappdirs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'hoardr-Ex.R' failed
The error most likely occurred in:
> ### Name: hoard
> ### Title: hoardr class
> ### Aliases: hoard
>
> ### ** Examples
>
> (x <- hoard())
<hoard>
path:
cache path:
> x$cache_path_set(path = "foobar", type = 'tempdir')
[1] "D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/R/foobar"
> x
<hoard>
path: foobar
cache path: D:\temp\2024_12_18_01_50_01_11818\Rtmpi28nvU/R/foobar
> x$path
[1] "foobar"
> x$cache_path_get()
[1] "D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/R/foobar"
>
> # Or you can set the full path directly with `full_path`
> mydir <- file.path(tempdir(), "foobar")
> x$cache_path_set(full_path = mydir)
[1] "D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar"
> x
<hoard>
path: foobar
cache path: D:\temp\2024_12_18_01_50_01_11818\Rtmpi28nvU/foobar
> x$path
[1] "foobar"
> x$cache_path_get()
[1] "D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar"
>
> # make the directory if doesn't exist already
> x$mkdir()
>
> # list files in dir
> x$list()
character(0)
> cat(1:10000L, file = file.path(x$cache_path_get(), "foo.txt"))
> x$list()
[1] "D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/foo.txt"
>
> # add more files
> cat(letters, file = file.path(x$cache_path_get(), "foo2.txt"))
> cat(LETTERS, file = file.path(x$cache_path_get(), "foo3.txt"))
>
> # see if files exist
> x$exists("foo.txt") # exists
files exists
1 D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/foo.txt TRUE
> x$exists(c("foo.txt", "foo3.txt")) # both exist
files exists
1 D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/foo.txt TRUE
2 D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/foo3.txt TRUE
> x$exists(c("foo.txt", "foo3.txt", "stuff.txt")) # one doesn't exist
files exists
1 D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/foo.txt TRUE
2 D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/foo3.txt TRUE
3 D:\\temp\\2024_12_18_01_50_01_11818\\Rtmpi28nvU/foobar/stuff.txt FALSE
>
> # cache details
> x$details()
<cached files>
directory: D:\temp\2024_12_18_01_50_01_11818\Rtmpi28nvU/foobar
Warning in sub(attr(x, "cpath"), "", x[[i]]$file) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(attr(x, "cpath"), "", x[[i]]$file) :
invalid regular expression 'D:\temp\2024_12_18_01_50_01_11818\Rtmpi28nvU/foobar', reason 'Invalid back reference'
Calls: <Anonymous> -> print.cache_info -> cat -> paste0 -> sub
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.5.4
Check: tests
Result: ERROR
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library("testthat")
> library("hoardr")
> test_check("hoardr")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HoardClient.R:155:3'): HoardClient works when files exist ──────
Error in `sub(attr(x, "cpath"), "", x[[i]]$file)`: invalid regular expression 'D:\temp\2024_12_18_01_50_01_11818\Rtmp2LafEm/R/test456', reason 'Invalid back reference'
Backtrace:
▆
1. ├─testthat::expect_output(print(deets1), "<cached files>") at test-HoardClient.R:155:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─base::print(deets1)
11. └─hoardr:::print.cache_info(deets1)
12. ├─base::cat(...)
13. ├─base::paste0(" file: ", sub(attr(x, "cpath"), "", x[[i]]$file))
14. └─base::sub(attr(x, "cpath"), "", x[[i]]$file)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'hoardr_vignette.Rmd' using rmarkdown
Quitting from lines 91-92 [unnamed-chunk-10] (hoardr_vignette.Rmd)
Error: processing vignette 'hoardr_vignette.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2024_12_18_01_50_01_11818\RtmpsJTP3i/R/foobar', reason 'Invalid back reference'
--- failed re-building 'hoardr_vignette.Rmd'
SUMMARY: processing the following file failed:
'hoardr_vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'hoardr-Ex.R' failed
The error most likely occurred in:
> ### Name: hoard
> ### Title: hoardr class
> ### Aliases: hoard
>
> ### ** Examples
>
> (x <- hoard())
<hoard>
path:
cache path:
> x$cache_path_set(path = "foobar", type = 'tempdir')
[1] "D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/R/foobar"
> x
<hoard>
path: foobar
cache path: D:\temp\2024_12_08_01_50_01_8405\RtmpQPMiZQ/R/foobar
> x$path
[1] "foobar"
> x$cache_path_get()
[1] "D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/R/foobar"
>
> # Or you can set the full path directly with `full_path`
> mydir <- file.path(tempdir(), "foobar")
> x$cache_path_set(full_path = mydir)
[1] "D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar"
> x
<hoard>
path: foobar
cache path: D:\temp\2024_12_08_01_50_01_8405\RtmpQPMiZQ/foobar
> x$path
[1] "foobar"
> x$cache_path_get()
[1] "D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar"
>
> # make the directory if doesn't exist already
> x$mkdir()
>
> # list files in dir
> x$list()
character(0)
> cat(1:10000L, file = file.path(x$cache_path_get(), "foo.txt"))
> x$list()
[1] "D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/foo.txt"
>
> # add more files
> cat(letters, file = file.path(x$cache_path_get(), "foo2.txt"))
> cat(LETTERS, file = file.path(x$cache_path_get(), "foo3.txt"))
>
> # see if files exist
> x$exists("foo.txt") # exists
files exists
1 D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/foo.txt TRUE
> x$exists(c("foo.txt", "foo3.txt")) # both exist
files exists
1 D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/foo.txt TRUE
2 D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/foo3.txt TRUE
> x$exists(c("foo.txt", "foo3.txt", "stuff.txt")) # one doesn't exist
files exists
1 D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/foo.txt TRUE
2 D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/foo3.txt TRUE
3 D:\\temp\\2024_12_08_01_50_01_8405\\RtmpQPMiZQ/foobar/stuff.txt FALSE
>
> # cache details
> x$details()
<cached files>
directory: D:\temp\2024_12_08_01_50_01_8405\RtmpQPMiZQ/foobar
Warning in sub(attr(x, "cpath"), "", x[[i]]$file) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(attr(x, "cpath"), "", x[[i]]$file) :
invalid regular expression 'D:\temp\2024_12_08_01_50_01_8405\RtmpQPMiZQ/foobar', reason 'Invalid back reference'
Calls: <Anonymous> -> print.cache_info -> cat -> paste0 -> sub
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.5.4
Check: tests
Result: ERROR
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library("testthat")
> library("hoardr")
> test_check("hoardr")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HoardClient.R:155:3'): HoardClient works when files exist ──────
Error in `sub(attr(x, "cpath"), "", x[[i]]$file)`: invalid regular expression 'D:\temp\2024_12_08_01_50_01_8405\RtmpsvJmYX/R/test456', reason 'Invalid back reference'
Backtrace:
▆
1. ├─testthat::expect_output(print(deets1), "<cached files>") at test-HoardClient.R:155:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─base::print(deets1)
11. └─hoardr:::print.cache_info(deets1)
12. ├─base::cat(...)
13. ├─base::paste0(" file: ", sub(attr(x, "cpath"), "", x[[i]]$file))
14. └─base::sub(attr(x, "cpath"), "", x[[i]]$file)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'hoardr_vignette.Rmd' using rmarkdown
Quitting from lines 91-92 [unnamed-chunk-10] (hoardr_vignette.Rmd)
Error: processing vignette 'hoardr_vignette.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2024_12_08_01_50_01_8405\RtmpaYOcWT/R/foobar', reason 'Invalid back reference'
--- failed re-building 'hoardr_vignette.Rmd'
SUMMARY: processing the following file failed:
'hoardr_vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'hoardr-Ex.R' failed
The error most likely occurred in:
> ### Name: hoard
> ### Title: hoardr class
> ### Aliases: hoard
>
> ### ** Examples
>
> (x <- hoard())
<hoard>
path:
cache path:
> x$cache_path_set(path = "foobar", type = 'tempdir')
[1] "D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/R/foobar"
> x
<hoard>
path: foobar
cache path: D:\temp\2024_12_20_01_50_00_19051\RtmpAjXwBE/R/foobar
> x$path
[1] "foobar"
> x$cache_path_get()
[1] "D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/R/foobar"
>
> # Or you can set the full path directly with `full_path`
> mydir <- file.path(tempdir(), "foobar")
> x$cache_path_set(full_path = mydir)
[1] "D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar"
> x
<hoard>
path: foobar
cache path: D:\temp\2024_12_20_01_50_00_19051\RtmpAjXwBE/foobar
> x$path
[1] "foobar"
> x$cache_path_get()
[1] "D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar"
>
> # make the directory if doesn't exist already
> x$mkdir()
>
> # list files in dir
> x$list()
character(0)
> cat(1:10000L, file = file.path(x$cache_path_get(), "foo.txt"))
> x$list()
[1] "D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/foo.txt"
>
> # add more files
> cat(letters, file = file.path(x$cache_path_get(), "foo2.txt"))
> cat(LETTERS, file = file.path(x$cache_path_get(), "foo3.txt"))
>
> # see if files exist
> x$exists("foo.txt") # exists
files exists
1 D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/foo.txt TRUE
> x$exists(c("foo.txt", "foo3.txt")) # both exist
files exists
1 D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/foo.txt TRUE
2 D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/foo3.txt TRUE
> x$exists(c("foo.txt", "foo3.txt", "stuff.txt")) # one doesn't exist
files exists
1 D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/foo.txt TRUE
2 D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/foo3.txt TRUE
3 D:\\temp\\2024_12_20_01_50_00_19051\\RtmpAjXwBE/foobar/stuff.txt FALSE
>
> # cache details
> x$details()
<cached files>
directory: D:\temp\2024_12_20_01_50_00_19051\RtmpAjXwBE/foobar
Warning in sub(attr(x, "cpath"), "", x[[i]]$file) :
TRE pattern compilation error 'Invalid back reference'
Error in sub(attr(x, "cpath"), "", x[[i]]$file) :
invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpAjXwBE/foobar', reason 'Invalid back reference'
Calls: <Anonymous> -> print.cache_info -> cat -> paste0 -> sub
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.5.4
Check: tests
Result: ERROR
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library("testthat")
> library("hoardr")
> test_check("hoardr")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HoardClient.R:155:3'): HoardClient works when files exist ──────
Error in `sub(attr(x, "cpath"), "", x[[i]]$file)`: invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpUVEoRe/R/test456', reason 'Invalid back reference'
Backtrace:
▆
1. ├─testthat::expect_output(print(deets1), "<cached files>") at test-HoardClient.R:155:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─base::print(deets1)
11. └─hoardr:::print.cache_info(deets1)
12. ├─base::cat(...)
13. ├─base::paste0(" file: ", sub(attr(x, "cpath"), "", x[[i]]$file))
14. └─base::sub(attr(x, "cpath"), "", x[[i]]$file)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'hoardr_vignette.Rmd' using rmarkdown
Quitting from lines 91-92 [unnamed-chunk-10] (hoardr_vignette.Rmd)
Error: processing vignette 'hoardr_vignette.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\Rtmp42M8VK/R/foobar', reason 'Invalid back reference'
--- failed re-building 'hoardr_vignette.Rmd'
SUMMARY: processing the following file failed:
'hoardr_vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 4, OK: 9
Version: 1.1.1
Check: package dependencies
Result: ERROR
Package required but not available: ‘fgsea’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Current CRAN status: NOTE: 10, OK: 3
Version: 1.3.0
Check: Rd files
Result: NOTE
checkRd: (-1) get_cid.Rd:58-59: Lost braces
58 | <structure search> is assembled as "{\code{substructure} |
| ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
| ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
| ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
| ^
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