CRAN Package Check Results for Maintainer John Muschelli <muschellij2 at gmail.com>

CRAN Package Check Results for Maintainer ‘John Muschelli <muschellij2 at gmail.com>’

Last updated on 2026-10-24 01:52:15 CEST.

Package	OK	NOTE	ERROR
actibase	13
actimetrics	9	4
actinet	13
actiplot	13
actiquantiles	13
actiread	13
actisensorlog	13
actisomni	13
actiwalkability	13
asleep	13
brainR	11	2
cforward	12		1
cifti	12		1
diffr	13
freesurfer	13
fslr	11	2
gcite	13
gifti	13
glassdoor	13
kirby21.base	11	2
kirby21.fmri	11	2
kirby21.t1	11	2
mapnhanespa	13
matlabr	13
mscstts	13
neurobase	8	5
neurohcp	13
rscopus	8	5
sleeper	13
stapler	11	2
stepcount	13
text2speech	13
walking	13
WhiteStripe	11	2

Version: 0.9.0
Check: dependencies in R code
Result: NOTE warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy` cause: Can't use Python at `/usr/sbin/pypy` cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.9.0
Check: dependencies in R code
Result: NOTE Downloading cpython-3.13.16-macos-aarch64-none (download) (24.1MiB) Downloaded cpython-3.13.16-macos-aarch64-none (download) Downloading numpy (5.2MiB) Downloaded numpy Installed 1 package in 7ms Flavor: r-release-macos-arm64

Version: 0.9.0
Check: dependencies in R code
Result: NOTE Downloading cpython-3.13.16-macos-aarch64-none (download) (24.1MiB) Downloaded cpython-3.13.16-macos-aarch64-none (download) Downloading numpy (11.5MiB) Downloaded numpy Installed 1 package in 15ms Flavor: r-oldrel-macos-arm64

Package actinet

Current CRAN status: OK: 13

Package actiplot

Current CRAN status: OK: 13

Package actiquantiles

Current CRAN status: OK: 13

Package actiread

Current CRAN status: OK: 13

Package actisensorlog

Current CRAN status: OK: 13

Package actisomni

Current CRAN status: OK: 13

Package actiwalkability

Current CRAN status: OK: 13

Package asleep

Current CRAN status: OK: 13

Package brainR

Current CRAN status: OK: 11, NOTE: 2

Version: 1.7.0
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘John Muschelli <muschellij2@gmail.com>’ Problems when reading CITATION file: Replacing special names ‘.Names’ is deprecated; use ‘names’ instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package cforward

Current CRAN status: OK: 12, ERROR: 1

Version: 0.2.0
Check: examples
Result: ERROR Running examples in ‘cforward-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cforward > ### Title: Forward Selection Based on C-Index/Concordance > ### Aliases: cforward cforward_one make_folds > > ### ** Examples > > variables = c("gender", + "age_years_interview", "education_adult") > > res = cforward(nhanes_example, + event_time = "event_time_years", + event_status = "mortstat", + weight_column = "WTMEC4YR_norm", + variables = variables, + included_variables = NULL, + n_folds = 5, + c_threshold = 0.02, + seed = 1989, + max_model_size = 50, + verbose = TRUE) Creating 5 Folds # A tibble: 5 × 2 fold_number n <int> <int> 1 1 731 2 2 730 3 3 731 4 4 729 5 5 732 Error in a$specials[[i]] : subscript out of bounds Calls: cforward ... estimate_concordance -> predict -> predict.coxph -> delete.response -> off Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(cforward) > > test_check("cforward") # A tibble: 5 × 2 fold_number n <int> <int> 1 1 731 2 2 730 3 3 731 4 4 729 5 5 732 Saving _problems/test-nhanes-15.R # A tibble: 10 × 2 fold_number n <int> <int> 1 1 367 2 2 367 3 3 363 4 4 365 5 5 364 6 6 366 7 7 365 8 8 365 9 9 365 10 10 366 # A tibble: 10 × 2 fold_number n <int> <int> 1 1 367 2 2 367 3 3 363 4 4 365 5 5 364 6 6 366 7 7 365 8 8 365 9 9 365 10 10 366 Saving _problems/test-nhanes-95.R # A tibble: 5 × 2 fold_number n <int> <int> 1 1 731 2 2 730 3 3 731 4 4 729 5 5 732 Saving _problems/test-nhanes-126.R # A tibble: 5 × 2 fold_number n <int> <int> 1 1 731 2 2 730 3 3 731 4 4 729 5 5 732 Saving _problems/test-nhanes-146.R Saving _problems/test-wrong_arguments-15.R [ FAIL 5 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-nhanes.R:6:3'): Example for cforward ─────────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─cforward::cforward(...) at test-nhanes.R:6:3 2. └─cforward::cforward_one(...) 3. └─cforward::estimate_concordance(...) 4. ├─stats::predict(fit_k, type = "lp", newdata = test) 5. └─survival:::predict.coxph(fit_k, type = "lp", newdata = test) 6. └─stats::delete.response(Terms) 7. └─stats (local) off(a$specials[[i]]) ── Error ('test-nhanes.R:86:7'): Variables and included have overlap ─────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-nhanes.R:84:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─testthat::expect_message(...) at test-nhanes.R:85:5 7. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) 8. │ ├─testthat (local) .capture(...) 9. │ │ └─base::withCallingHandlers(...) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─cforward::cforward(...) at test-nhanes.R:86:7 12. └─cforward::cforward_one(...) 13. └─cforward::estimate_concordance(...) 14. ├─stats::predict(fit_k, type = "lp", newdata = test) 15. └─survival:::predict.coxph(fit_k, type = "lp", newdata = test) 16. └─stats::delete.response(Terms) 17. └─stats (local) off(a$specials[[i]]) ── Error ('test-nhanes.R:117:3'): Restrict maximum size ──────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─cforward::cforward(...) at test-nhanes.R:117:3 2. └─cforward::cforward_one(...) 3. └─cforward::estimate_concordance(...) 4. ├─stats::predict(fit_k, type = "lp", newdata = test) 5. └─survival:::predict.coxph(fit_k, type = "lp", newdata = test) 6. └─stats::delete.response(Terms) 7. └─stats (local) off(a$specials[[i]]) ── Error ('test-nhanes.R:135:3'): Restrict c_threshold ───────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─cforward::cforward(...) at test-nhanes.R:135:3 2. └─cforward::cforward_one(...) 3. └─cforward::estimate_concordance(...) 4. ├─stats::predict(fit_k, type = "lp", newdata = test) 5. └─survival:::predict.coxph(fit_k, type = "lp", newdata = test) 6. └─stats::delete.response(Terms) 7. └─stats (local) off(a$specials[[i]]) ── Error ('test-wrong_arguments.R:6:3'): Passing in weights and data arguments ── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─cforward::cforward(...) at test-wrong_arguments.R:6:3 2. └─cforward::cforward_one(...) 3. └─cforward::estimate_concordance(...) 4. ├─stats::predict(fit_k, type = "lp", newdata = test) 5. └─survival:::predict.coxph(fit_k, type = "lp", newdata = test) 6. └─stats::delete.response(Terms) 7. └─stats (local) off(a$specials[[i]]) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 1 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Package cifti

Current CRAN status: OK: 12, ERROR: 1

Version: 0.5.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'cifti_work.Rmd' using rmarkdown --- finished re-building 'cifti_work.Rmd' --- re-building 'test_dims_MSC.Rmd' using rmarkdown trying URL 'https://www.nitrc.org/frs/download.php/8541' Quitting from test_dims_MSC.Rmd:24-27 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `download.file()`: ! cannot open URL 'https://www.nitrc.org/frs/download.php/8541' --- Backtrace: ▆ 1. └─cifti::download_cifti_data(outdir = install_dir) 2. └─utils::download.file(url = url, destfile = destfile, mode = "wb") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'test_dims_MSC.Rmd' failed with diagnostics: cannot open URL 'https://www.nitrc.org/frs/download.php/8541' --- failed re-building 'test_dims_MSC.Rmd' SUMMARY: processing the following file failed: 'test_dims_MSC.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-windows-x86_64

Package diffr

Current CRAN status: OK: 13

Package freesurfer

Current CRAN status: OK: 13

Package fslr

Current CRAN status: OK: 11, NOTE: 2

Version: 2.27.0
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘John Muschelli <muschellij2@gmail.com>’ Problems when reading CITATION file: Replacing special names ‘.Names’ is deprecated; use ‘names’ instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package gcite

Current CRAN status: OK: 13

Package gifti

Current CRAN status: OK: 13

Package glassdoor

Current CRAN status: OK: 13

Package kirby21.base

Current CRAN status: OK: 11, NOTE: 2

Version: 1.7.3
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘John Muschelli <muschellij2@gmail.com>’ No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: person(given = "John", family = "Muschelli", role = c("aut", "cre"), email = "muschellij2@gmail.com") as necessary. Problems when reading CITATION file: Replacing special names ‘.Names’ is deprecated; use ‘names’ instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package kirby21.fmri

Current CRAN status: OK: 11, NOTE: 2

Version: 1.8.0
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘John Muschelli <muschellij2@gmail.com>’ Problems when reading CITATION file: Replacing special names ‘.Names’ is deprecated; use ‘names’ instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package kirby21.t1

Current CRAN status: OK: 11, NOTE: 2

Package mapnhanespa

Current CRAN status: OK: 13

Package matlabr

Current CRAN status: OK: 13

Package mscstts

Current CRAN status: OK: 13

Package neurobase

Current CRAN status: OK: 8, NOTE: 5

Version: 1.34.0
Check: R code for possible problems
Result: NOTE Found calls to structure() using deprecated special names: neurobase/tests/testthat/test-cog.R (.Names: 1) '.Names' should be changed to 'names'. 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

Package neurohcp

Current CRAN status: OK: 13

Package rscopus

Current CRAN status: OK: 8, NOTE: 5

Version: 0.9.0
Check: R code for possible problems
Result: NOTE Found calls to structure() using deprecated special names: rscopus/R/replace_non_ascii.R (.Names: 1) '.Names' should be changed to 'names'. 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

Package sleeper

Current CRAN status: OK: 13

Package stapler

Current CRAN status: OK: 11, NOTE: 2

Version: 0.8.0
Flags: --no-vignettes
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘John Muschelli <muschellij2@gmail.com>’ Problems when reading CITATION file: Replacing special names ‘.Names’ is deprecated; use ‘names’ instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package stepcount

Current CRAN status: OK: 13

Package text2speech

Current CRAN status: OK: 13

Package walking

Current CRAN status: OK: 13

Package WhiteStripe

Current CRAN status: OK: 11, NOTE: 2

Version: 2.5.0
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘John Muschelli <muschellij2@gmail.com>’ Problems when reading CITATION file: Replacing special names ‘.Names’ is deprecated; use ‘names’ instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc