revdep/dplyr/problems.md

In lionel-/selectr: Select from a Set of Strings

AMARETTO

• Version: 1.0.0
• Source code: https://github.com/cran/AMARETTO
• Date/Publication: 2019-05-02
• Number of recursive dependencies: 141

Run revdep_details(,"AMARETTO") for more info

Newly broken

• checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Nr of reassignments is: 1 ── 1. Error: (unknown) (@test_AMARETTO.R#11) ────────────────────────────────── length of 'dimnames' [2] not equal to array extent Backtrace:

  1. AMARETTO::AMARETTO_Run(AMARETTOinit)
  2. AMARETTO:::AMARETTO_LarsenBased(...) revdep-all/dplyr/checks.noindex/AMARETTO/new/AMARETTO.Rcheck/00_pkg_src/AMARETTO/R/amaretto_functions.R:121:12
  3. AMARETTO:::AMARETTO_LearnRegulatoryProgramsLarsen(...) revdep-all/dplyr/checks.noindex/AMARETTO/new/AMARETTO.Rcheck/00_pkg_src/AMARETTO/R/amaretto_run.R:29:12
  4. base::colnames<-(*tmp*, value = RegulatorData_rownames) revdep-all/dplyr/checks.noindex/AMARETTO/new/AMARETTO.Rcheck/00_pkg_src/AMARETTO/R/amaretto_run.R:212:4

  ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] 1. Error: (unknown) (@test_AMARETTO.R#11)

  Error: testthat unit tests failed Execution halted ```

In both

• checking examples ... ERROR ``` Running examples in ‘AMARETTO-Ex.R’ failed The error most likely occurred in:

  Name: AMARETTO_Download

  Title: AMARETTO_Download

  Aliases: AMARETTO_Download

  ** Examples

  TargetDirectory <- file.path(getwd(),"Downloads/");dir.create(TargetDirectory) CancerSite <- 'CHOL' DataSetDirectories <- AMARETTO_Download(CancerSite,TargetDirectory = TargetDirectory) Downloading Gene Expression and Copy Number Variation data for: CHOL

  This TCGA cancer site/type was not tested, continue at your own risk.

  Error in .local(x, i, j, ...) : 'i' must be length 1 Calls: AMARETTO_Download ... .getResources -> lapply -> FUN -> [[ -> [[ -> .local Execution halted ```

• checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: Apache License (== 2.0) + file LICENSE 'LinkingTo' field is unused: package has no 'src' directory

assertr

• Version: 2.6
• Source code: https://github.com/cran/assertr
• URL: https://github.com/ropensci/assertr
• BugReports: https://github.com/ropensci/assertr/issues
• Date/Publication: 2019-01-22 20:50:06 UTC
• Number of recursive dependencies: 45

Run revdep_details(,"assertr") for more info

Newly broken

• checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1. testthat::expect_error(...) 6. assertr::insist(mtcars, within_n_sds(5), tree) 8. dplyr:::select.data.frame(data, !!!(keeper.vars)) 9. tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))

  1. tidyselect:::eval_select_impl(...)
  2. tidyselect:::subclass_index_errors(...)

  ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 388 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 3 ] 1. Failure: assert breaks appropriately (@test-assertions.R#224) 2. Failure: assert_rows breaks appropriately (@test-assertions.R#290) 3. Failure: insist breaks appropriately (@test-assertions.R#341)

  Error: testthat unit tests failed Execution halted ```

ddpcr

• Version: 1.11
• Source code: https://github.com/cran/ddpcr
• URL: https://github.com/daattali/ddpcr
• BugReports: https://github.com/daattali/ddpcr/issues
• Date/Publication: 2019-01-03 15:10:10 UTC
• Number of recursive dependencies: 88

Run revdep_details(,"ddpcr") for more info

Newly broken

• checking examples ... ERROR ``` ...

  • well_info(wells_success(plate), "negative_freq") Error: Can't use arithmetic operator * in selection context. Can't use arithmetic operator * in selection context. Backtrace: █
  • └─%>%(...)
  • ├─base::withVisible(eval(quote(_fseq(_lhs)), env, env))
  • └─base::eval(quote(_fseq(_lhs)), env, env)
  • └─base::eval(quote(_fseq(_lhs)), env, env)
  • └─_fseq(_lhs)
  • └─magrittr::freduce(value, _function_list)
  • └─function_list[i]
  • └─ddpcr::calculate_negative_freqs(.)
  • └─%>%(...) 00_pkg_src/ddpcr/R/pnpp_experiment-calculate_neg_freq.R:57:2
  • ├─base::withVisible(eval(quote(_fseq(_lhs)), env, env))
  • └─base::eval(quote(_fseq(_lhs)), env, env)
  • └─base::eval(quote(_fseq(_lhs)), env, env)
  • └─ddpcr:::_fseq(_lhs)
  • └─magrittr::fre Execution halted ```

• checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 136 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 23 ]

  1. Error: (unknown) (@test-custom_thresholds.R#4)
  2. Error: get_empty_cutoff works (@test-empty.R#4)
  3. Error: get_empty_cutoff for pnpp works (@test-empty.R#18)
  4. Error: is_well_success works (@test-failures.R#4)
  5. Error: get_outlier_cutoff works (@test-outliers.R#4)
  6. Error: test basic plate attribute getters/setters (@test-plate-attribs.R#4)
  7. Error: (unknown) (@test-plate.R#3)
  8. Error: calculate_negative_freqs works (@test-pnpp_experiment-calculate_neg_freq.R#21)
  9. Error: (unknown) (@test-pnpp_experiment.R#4)
  10. ...

  Error: testthat unit tests failed Execution halted ```

disk.frame

• Version: 0.3.1
• Source code: https://github.com/cran/disk.frame
• URL: https://diskframe.com
• BugReports: https://github.com/xiaodaigh/disk.frame/issues
• Date/Publication: 2019-12-20 09:00:02 UTC
• Number of recursive dependencies: 115

Run revdep_details(,"disk.frame") for more info

Newly broken

• checking examples ... ERROR ``` ...

  • only run in interactive()

  • setup_disk.frame(gui = TRUE)
  • }

    set the number workers to 2

    setup_disk.frame(2) Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : port 37400 cannot be opened Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : Failed to launch and connect to R worker on local machine ‘localhost’ from local machine ‘Eustache’.

  • The error produced by socketConnection() was: ‘cannot open the connection’
  • In addition, socketConnection() produced 1 warning(s):
  • Warning #1: ‘port 37400 cannot be opened’ (which suggests that this port is either already occupied by another process or blocked by the firewall on your local machine)
  • The localhost socket connection that failed to connect to the R worker used port 37400 using a communication timeout of 120 seconds and a connection timeout of 120 seconds.
  • Worker launch call: '/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,stats,methods -e '#label=UNKNOWN:97989:Eustache:lionel' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/b9/1vbq6rn93_1fk71sn95dqb8r0000gn/T//RtmpZZAqd7/future.parent=97989.17ec528e44deb.pid")), silent = TRUE)' -e 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=37400 OUT=/dev/null TIMEOUT=120 XDR=TRUE.
  • Worker (PID 98289) was successfully killed: TRUE
  • Troubleshooting suggestions:
  • Suggestion #1: Set 'verbose=TRUE' to see more details.
  • Suggestion #2: Set 'outfile=NULL' to see output from worker. Calls: setup_disk.frame ... tryCatchList -> tryCatchOne -> -> Execution halted ```

levi

• Version: 1.2.0
• Source code: https://github.com/cran/levi
• Date/Publication: 2019-05-02
• Number of recursive dependencies: 83

Run revdep_details(,"levi") for more info

Newly broken

• checking examples ... ERROR ``` ... ℹ There are only 2 elements. Backtrace: █
  1. └─levi::levi(...)
  2. └─levi:::levi_function(...) 00_pkg_src/levi/R/levi.R:83:8
  3. ├─dplyr::select(edges, -3) 00_pkg_src/levi/R/levi_function.R:295:12
  4. └─dplyr:::select.data.frame(edges, -3)
  5. └─tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
  6. └─tidyselect:::eval_select_impl(...)
  7. └─tidyselect:::subclass_index_errors(...) Must index existing elements. ✖ Can't subset position 3. ℹ There are only 2 elements. Backtrace: █
  8. ├─tidyselect:::sanitise_base_errors(expr)
  9. │ └─base::withCallingHandlers(...)
  10. ├─tidyselect:::vars_select_eval(...)
  11. │ └─tidyselect:::wa Execution halted ```

In both

• checking R code for possible problems ... NOTE levi_function: no visible binding for global variable ‘x’ (/Users/lionel/Desktop/tidyselect/revdep-all/dplyr/checks.noindex/levi/new/levi.Rcheck/00_pkg_src/levi/R/levi_function.R:34) levi_function: no visible binding for global variable ‘x’ (/Users/lionel/Desktop/tidyselect/revdep-all/dplyr/checks.noindex/levi/new/levi.Rcheck/00_pkg_src/levi/R/levi_function.R:503-532) levi_function: no visible binding for global variable ‘x’ (/Users/lionel/Desktop/tidyselect/revdep-all/dplyr/checks.noindex/levi/new/levi.Rcheck/00_pkg_src/levi/R/levi_function.R:534-562) LEVIui: no visible global function definition for ‘is’ (/Users/lionel/Desktop/tidyselect/revdep-all/dplyr/checks.noindex/levi/new/levi.Rcheck/00_pkg_src/levi/R/LEVIui.R:23-24) Undefined global functions or variables: is x Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

Mapinguari

• Version: 1.0.0
• Source code: https://github.com/cran/Mapinguari
• URL: http://github.com/gabrielhoc/Mapinguari
• BugReports: http://github.com/gabrielhoc/Mapinguari/issues
• Date/Publication: 2019-09-30 16:40:02 UTC
• Number of recursive dependencies: 51

Run revdep_details(,"Mapinguari") for more info

Newly broken

• checking examples ... ERROR ``` ... The error most likely occurred in:

  Name: transform_rasters

  Title: Transform raster values using custom calls.

  Aliases: transform_rasters

  ** Examples

  You can apply any function to subsets of rasters in the stack,

  by selecting the layers with double brackets.

  transform_rasters(raster_stack = df_tmax, + total_1sem = sum(tmax[1:6]), + mean_1sem = mean(tmax[1:6]), + sd_1sem = sd(tmax[1:6])) Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : port 11831 cannot be opened Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : cannot open the connection Calls: transform_rasters ... makePSOCKcluster -> newPSOCKnode -> socketConnection Execution halted ```

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’ All declared Imports should be used.

SemNeT

• Version: 1.1.2
• Source code: https://github.com/cran/SemNeT
• URL: https://github.com/AlexChristensen/SemNeT
• BugReports: https://github.com/AlexChristensen/SemNeT/issues
• Date/Publication: 2019-10-28 23:40:16 UTC
• Number of recursive dependencies: 187

Run revdep_details(,"SemNeT") for more info

Newly broken

• checking examples ... ERROR ... > > ### ** Examples > > # Simulate Datasets > one <- sim.fluency(10) > > # Compute similarity matrix > cos <- similarity(one, method = "cosine") > > # Compute networks using NetworkToolbox > net <- NetworkToolbox::TMFG(cos)$A > ## Don't show: > randnet.test(net, iter = 1, cores = 2) Generating random networks...done Computing network measures... Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : port 11067 cannot be opened Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : cannot open the connection Calls: randnet.test ... makePSOCKcluster -> newPSOCKnode -> socketConnection Execution halted

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘grid’ ‘purrr’ ‘RColorBrewer’ ‘SemNetCleaner’ All declared Imports should be used.

teamcolors

• Version: 0.0.3
• Source code: https://github.com/cran/teamcolors
• URL: http://github.com/beanumber/teamcolors
• BugReports: https://github.com/beanumber/teamcolors/issues
• Date/Publication: 2019-11-27 07:20:02 UTC
• Number of recursive dependencies: 57

Run revdep_details(,"teamcolors") for more info

Newly broken

• checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Expected match: "between" Actual message: "Must select existing columns.\n✖ Can't subset position 15.\nℹ There are only 11 elements." Backtrace: 1. testthat::expect_error(team_pal(13), "between") 6. teamcolors::team_pal(13) 8. dplyr:::pull.data.frame(teams, which + 2) 9. tidyselect::vars_pull(names(.data), !!enquo(var))

  1. tidyselect:::subclass_index_errors(...)

  ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 6 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] 1. Failure: colors work (@test-colors.R#7)

  Error: testthat unit tests failed Execution halted ```

lionel-/selectr documentation built on March 14, 2024, 10:04 p.m.