CRAN Package Check Results for Maintainer ‘Tamás Stirling <stirling.tamas at gmail.com>’

Last updated on 2024-12-23 12:49:53 CET.

Package ERROR NOTE OK
hoardr 3 2 8
mulea 4 9
webchem 10 3

Package hoardr

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

Package mulea

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

Package webchem

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