globals: Identify Global Objects in R Expressions

agcounts

Version: 0.6.6
GitHub: NA
Source code: https://github.com/cran/agcounts
Date/Publication: 2024-02-29 20:12:36 UTC
Number of recursive dependencies: 166

Run revdep_details(, "agcounts") for more info

checking whether package ‘agcounts’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/agcounts/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/agcounts/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/agcounts/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/agcounts/new/agcounts.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: extdata 3.4Mb libs 3.0Mb

AIPW

Version: 0.6.3.2
GitHub: https://github.com/yqzhong7/AIPW
Source code: https://github.com/cran/AIPW
Date/Publication: 2021-06-11 09:30:02 UTC
Number of recursive dependencies: 100

Run revdep_details(, "AIPW") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’ ‘utils’ All declared Imports should be used.

AlpsNMR

Version: 4.4.0
GitHub: https://github.com/sipss/AlpsNMR
Source code: https://github.com/cran/AlpsNMR
Date/Publication: 2023-10-24
Number of recursive dependencies: 185

Run revdep_details(, "AlpsNMR") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b ad argument #1 to 'insert' (table expected, got nil) stack traceback: [C]: in function 'insert' .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk [C]: in function 'dofile' [string "\directlua "]:6: in main chunk. l.139 } ... LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’

SUMMARY: processing the following files failed: ‘Vig01-introduction-to-alpsnmr.Rmd’ ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ ‘Vig02-handling-metadata-and-annotations.Rmd’

Error: Vignette re-building failed. Execution halted ```

altdoc

Version: 0.3.0
GitHub: https://github.com/etiennebacher/altdoc
Source code: https://github.com/cran/altdoc
Date/Publication: 2024-02-21 16:00:06 UTC
Number of recursive dependencies: 85

Run revdep_details(, "altdoc") for more info

checking tests ... `` Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: v Setting active project to '<no active project>' v Setting active project to '/scratch/henrik/1701657/RtmpS2ZQsi/testpkg3b30f233c050d' v Setting active project to '<no active project>' v Setting active project to '/scratch/henrik/1701657/RtmpS2ZQsi/testpkg3b30f2ab089d5' v Setting active project to '<no active project>' ... Error inrender_docs(path = getwd())`: There were some failures when rendering vignettes. Backtrace: ▆
1. └─altdoc::render_docs(path = getwd()) at test-update.R:111:5
2. └─cli::cli_abort("There were some failures when rendering vignettes.")
3. └─rlang::abort(...)
[ FAIL 5 | WARN 0 | SKIP 7 | PASS 56 ] Error: Test failures Execution halted ```

amapGeocode

Version: 0.6.0
GitHub: https://github.com/womeimingzi11/amapGeocode
Source code: https://github.com/cran/amapGeocode
Date/Publication: 2021-04-19 07:20:02 UTC
Number of recursive dependencies: 79

Run revdep_details(, "amapGeocode") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘jsonlite’ All declared Imports should be used.

aroma.core

Version: 3.3.1
GitHub: https://github.com/HenrikBengtsson/aroma.core
Source code: https://github.com/cran/aroma.core
Date/Publication: 2024-02-19 08:40:02 UTC
Number of recursive dependencies: 68

Run revdep_details(, "aroma.core") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

BAMBI

Version: 2.3.5
GitHub: https://github.com/c7rishi/BAMBI
Source code: https://github.com/cran/BAMBI
Date/Publication: 2023-03-08 23:10:05 UTC
Number of recursive dependencies: 53

Run revdep_details(, "BAMBI") for more info

checking whether package ‘BAMBI’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/BAMBI/new/BAMBI.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: libs 6.8Mb

bamm

Version: 0.4.3
GitHub: https://github.com/luismurao/bamm
Source code: https://github.com/cran/bamm
Date/Publication: 2022-12-20 11:10:05 UTC
Number of recursive dependencies: 109

Run revdep_details(, "bamm") for more info

checking whether package ‘bamm’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/bamm/new/bamm.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

batchtools

Version: 0.9.17
GitHub: https://github.com/mllg/batchtools
Source code: https://github.com/cran/batchtools
Date/Publication: 2023-04-20 14:20:06 UTC
Number of recursive dependencies: 83

Run revdep_details(, "batchtools") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘doMPI’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Rmpi’

bayesmove

Version: 0.2.1
GitHub: https://github.com/joshcullen/bayesmove
Source code: https://github.com/cran/bayesmove
Date/Publication: 2021-10-22 08:50:09 UTC
Number of recursive dependencies: 168

Run revdep_details(, "bayesmove") for more info

checking whether package ‘bayesmove’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/bayesmove/new/bayesmove.Rcheck/00install.out’ for details.

BEKKs

Version: 1.4.4
GitHub: NA
Source code: https://github.com/cran/BEKKs
Date/Publication: 2024-01-14 15:50:09 UTC
Number of recursive dependencies: 86

Run revdep_details(, "BEKKs") for more info

checking whether package ‘BEKKs’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/BEKKs/new/BEKKs.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 18.5Mb sub-directories of 1Mb or more: libs 17.6Mb

bigDM

Version: 0.5.3
GitHub: https://github.com/spatialstatisticsupna/bigDM
Source code: https://github.com/cran/bigDM
Date/Publication: 2023-10-17 12:50:02 UTC
Number of recursive dependencies: 135

Run revdep_details(, "bigDM") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking data for non-ASCII characters ... NOTE Note: found 940 marked Latin-1 strings

bistablehistory

Version: 1.1.2
GitHub: https://github.com/alexander-pastukhov/bistablehistory
Source code: https://github.com/cran/bistablehistory
Date/Publication: 2023-09-13 13:20:09 UTC
Number of recursive dependencies: 97

Run revdep_details(, "bistablehistory") for more info

checking installed package size ... NOTE installed size is 75.5Mb sub-directories of 1Mb or more: libs 74.6Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

blavaan

Version: 0.5-3
GitHub: https://github.com/ecmerkle/blavaan
Source code: https://github.com/cran/blavaan
Date/Publication: 2024-01-19 22:50:02 UTC
Number of recursive dependencies: 98

Run revdep_details(, "blavaan") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 196.2Mb sub-directories of 1Mb or more: R 1.2Mb libs 193.4Mb testdata 1.4Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

BPrinStratTTE

Version: 0.0.2
GitHub: https://github.com/Boehringer-Ingelheim/BPrinStratTTE
Source code: https://github.com/cran/BPrinStratTTE
Date/Publication: 2023-12-20 16:40:07 UTC
Number of recursive dependencies: 74

Run revdep_details(, "BPrinStratTTE") for more info

checking whether package ‘BPrinStratTTE’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/globals/revdep/checks/BPrinStratTTE/new/BPrinStratTTE.Rcheck/00install.out’ for details.

* installing *source* package ‘BPrinStratTTE’ ...
** package ‘BPrinStratTTE’ successfully unpacked and MD5 sums checked
** using staged installation
Error in loadNamespace(x) : there is no package called ‘rstantools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: configuration failed for package ‘BPrinStratTTE’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/BPrinStratTTE/new/BPrinStratTTE.Rcheck/BPrinStratTTE’

* installing *source* package ‘BPrinStratTTE’ ...
** package ‘BPrinStratTTE’ successfully unpacked and MD5 sums checked
** using staged installation
Error in loadNamespace(x) : there is no package called ‘rstantools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: configuration failed for package ‘BPrinStratTTE’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/BPrinStratTTE/old/BPrinStratTTE.Rcheck/BPrinStratTTE’

brms

Version: 2.20.4
GitHub: https://github.com/paul-buerkner/brms
Source code: https://github.com/cran/brms
Date/Publication: 2023-09-25 19:00:09 UTC
Number of recursive dependencies: 200

Run revdep_details(, "brms") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: R 3.0Mb doc 3.5Mb

broom.mixed

Version: 0.2.9.4
GitHub: https://github.com/bbolker/broom.mixed
Source code: https://github.com/cran/broom.mixed
Date/Publication: 2022-04-17 17:42:29 UTC
Number of recursive dependencies: 166

Run revdep_details(, "broom.mixed") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘glmmADMB’

bsitar

Version: 0.1.1
GitHub: https://github.com/Sandhu-SS/bsitar
Source code: https://github.com/cran/bsitar
Date/Publication: 2024-01-25 13:50:09 UTC
Number of recursive dependencies: 167

Run revdep_details(, "bsitar") for more info

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 2.9Mb doc 1.3Mb

ceRNAnetsim

Version: 1.14.1
GitHub: https://github.com/selcenari/ceRNAnetsim
Source code: https://github.com/cran/ceRNAnetsim
Date/Publication: 2023-12-18
Number of recursive dependencies: 101

Run revdep_details(, "ceRNAnetsim") for more info

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

Name: find_node_perturbation

Title: Calculates average expression changes of all (or specified)

nodes except trigger and finds the perturbed node count for all (or

specified) nodes in system.

Aliases: find_node_perturbation

** Examples

... 23. │ └─dplyr (local) eval() 24. └─tidygraph::map_bfs(...) 25. └─tidygraph:::bfs_df(graph, root, mode, unreachable) 26. └─tibble::tibble(...) 27. └─tibble:::tibble_quos(xs, .rows, .name_repair) 28. └─tibble:::vectbl_recycle_rows(...) 29. └─tibble:::abort_incompatible_size(...) 30. └─tibble:::tibble_abort(...) 31. └─rlang::abort(x, class, ..., call = call, parent = parent, use_cli_format = TRUE) Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: > library(testthat) > library(ceRNAnetsim) Loading required package: dplyr

Attaching package: 'dplyr'

... ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-iter_perturb.R:33:3'): Could the functions work? ──────────── node_efficiencies not equal to c(NA, NA, NA, 3.18, 2.27, 3.18, NA, 32). 2/8 mismatches (average diff: 14.9) [5] 3.18 - 2.27 == 0.91 [8] 3.18 - 32.00 == -28.82

[ FAIL 1 | WARN 35 | SKIP 0 | PASS 36 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘auxiliary_commands.Rmd’ using rmarkdown --- finished re-building ‘auxiliary_commands.Rmd’

--- re-building ‘basic_usage.Rmd’ using rmarkdown --- finished re-building ‘basic_usage.Rmd’

--- re-building ‘convenient_iteration.Rmd’ using rmarkdown

Quitting from lines 226-233 [unnamed-chunk-15] (convenient_iteration.Rmd) ... • Size 5: Existing data. • Size 53: Column rank. ℹ Only values of size one are recycled. --- failed re-building ‘mirtarbase_example.Rmd’

SUMMARY: processing the following files failed: ‘convenient_iteration.Rmd’ ‘mirtarbase_example.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking R code for possible problems ... NOTE simulate: no visible binding for global variable ‘avg_count_current’ simulate: no visible binding for global variable ‘avg_count_pre’ Undefined global functions or variables: avg_count_current avg_count_pre

cft

Version: 1.0.0
GitHub: https://github.com/earthlab/cft-CRAN
Source code: https://github.com/cran/cft
Date/Publication: 2022-10-03 07:12:18 UTC
Number of recursive dependencies: 90

Run revdep_details(, "cft") for more info

checking whether package ‘cft’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/globals/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details.

* installing *source* package ‘cft’ ...
** package ‘cft’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘cft’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/cft/new/cft.Rcheck/cft’

* installing *source* package ‘cft’ ...
** package ‘cft’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘cft’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/cft/old/cft.Rcheck/cft’

ChromSCape

Version: 1.12.0
GitHub: https://github.com/vallotlab/ChromSCape
Source code: https://github.com/cran/ChromSCape
Date/Publication: 2023-10-25
Number of recursive dependencies: 232

Run revdep_details(, "ChromSCape") for more info

checking dependencies in R code ... WARNING 'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' call to ‘dplyr’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'generate_analysis': generate_analysis Code: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", "DenseMatrix", "SparseMatrix", "scBAM")[1], feature_count_on = c("bins", "genebody", "peaks")[1], feature_count_parameter = 50000, rebin_sparse_matrix = FALSE, ref_genome = c("hg38", "mm10")[1], run = c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)], ... Mismatches in argument names: Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix Position: 6 Code: feature_count_parameter Docs: feature_count_on Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter Mismatches in argument default values: Name: 'run' Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)] Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)]
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'rebin_matrix' ‘rebin_function’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking examples ... WARNING ``` Found the following significant warnings:

Warning: 'as(, "dspMatrix")' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: data 1.4Mb doc 2.9Mb libs 1.0Mb www 2.0Mb
checking R code for possible problems ... NOTE bams_to_matrix_indexes: no visible binding for global variable ‘files_dir_list’ enrich_TF_ChEA3_genes: no visible binding for global variable ‘CheA3_TF_nTargets’ filter_correlated_cell_scExp: no visible binding for global variable ‘run_tsne’ generate_analysis: no visible global function definition for ‘head’ generate_analysis: no visible binding for global variable ‘k’ generate_analysis: no visible binding for global variable ‘clusterConsensus’ ... subset_bam_call_peaks: no visible binding for global variable ‘merged_bam’ Undefined global functions or variables: CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2 absolute_value cluster clusterConsensus cytoBand files_dir_list genes group head k merged_bam molecule ncells new_row orientation origin_value percent_active run_tsne sample_id total_counts Consider adding importFrom("utils", "head") to your NAMESPACE file.
checking Rd files ... NOTE prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source

clickR

Version: 0.9.39
GitHub: NA
Source code: https://github.com/cran/clickR
Date/Publication: 2023-08-07 17:40:06 UTC
Number of recursive dependencies: 9

Run revdep_details(, "clickR") for more info

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

clustermq

Version: 0.9.4
GitHub: https://github.com/mschubert/clustermq
Source code: https://github.com/cran/clustermq
Date/Publication: 2024-03-04 15:20:10 UTC
Number of recursive dependencies: 110

Run revdep_details(, "clustermq") for more info

checking installed package size ... NOTE installed size is 22.0Mb sub-directories of 1Mb or more: libs 21.4Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used.

codebook

Version: 0.9.2
GitHub: https://github.com/rubenarslan/codebook
Source code: https://github.com/cran/codebook
Date/Publication: 2020-06-06 23:40:03 UTC
Number of recursive dependencies: 156

Run revdep_details(, "codebook") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘userfriendlyscience’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 65 marked UTF-8 strings

collinear

Version: 1.1.1
GitHub: NA
Source code: https://github.com/cran/collinear
Date/Publication: 2023-12-08 08:50:02 UTC
Number of recursive dependencies: 55

Run revdep_details(, "collinear") for more info

checking data for non-ASCII characters ... NOTE Note: found 89 marked Latin-1 strings Note: found 1203 marked UTF-8 strings

colocr

Version: 0.1.1
GitHub: https://github.com/ropensci/colocr
Source code: https://github.com/cran/colocr
Date/Publication: 2020-05-08 13:20:06 UTC
Number of recursive dependencies: 126

Run revdep_details(, "colocr") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

corporaexplorer

Version: 0.8.6
GitHub: https://github.com/kgjerde/corporaexplorer
Source code: https://github.com/cran/corporaexplorer
Date/Publication: 2022-06-20 12:50:02 UTC
Number of recursive dependencies: 109

Run revdep_details(, "corporaexplorer") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’ All declared Imports should be used.

cSEM

Version: 0.5.0
GitHub: https://github.com/M-E-Rademaker/cSEM
Source code: https://github.com/cran/cSEM
Date/Publication: 2022-11-24 17:50:05 UTC
Number of recursive dependencies: 128

Run revdep_details(, "cSEM") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rdpack’ All declared Imports should be used.

CSGo

Version: 0.6.7
GitHub: https://github.com/adsoncostanzifilho/CSGo
Source code: https://github.com/cran/CSGo
Date/Publication: 2021-05-07 18:50:02 UTC
Number of recursive dependencies: 77

Run revdep_details(, "CSGo") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘extrafont’ ‘future’ All declared Imports should be used.

cuda.ml

Version: 0.3.2
GitHub: https://github.com/mlverse/cuda.ml
Source code: https://github.com/cran/cuda.ml
Date/Publication: 2022-01-08 01:42:47 UTC
Number of recursive dependencies: 75

Run revdep_details(, "cuda.ml") for more info

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 5.8Mb

cytomapper

Version: 1.14.0
GitHub: https://github.com/BodenmillerGroup/cytomapper
Source code: https://github.com/cran/cytomapper
Date/Publication: 2023-10-24
Number of recursive dependencies: 162

Run revdep_details(, "cytomapper") for more info

checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: R 1.3Mb doc 5.0Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘CATALYST’

deseats

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/deseats
Date/Publication: 2023-11-08 19:50:02 UTC
Number of recursive dependencies: 109

Run revdep_details(, "deseats") for more info

checking whether package ‘deseats’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/deseats/new/deseats.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: libs 7.6Mb

dipsaus

Version: 0.2.8
GitHub: https://github.com/dipterix/dipsaus
Source code: https://github.com/cran/dipsaus
Date/Publication: 2023-07-03 20:00:03 UTC
Number of recursive dependencies: 70

Run revdep_details(, "dipsaus") for more info

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: doc 1.1Mb libs 3.5Mb

dispositionEffect

Version: 1.0.1
GitHub: https://github.com/marcozanotti/dispositionEffect
Source code: https://github.com/cran/dispositionEffect
Date/Publication: 2022-05-30 07:50:02 UTC
Number of recursive dependencies: 136

Run revdep_details(, "dispositionEffect") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: ── Failure ('test-realized_duration.R:113:2'): realized_duration works (realized_only = TRUE) ── realized_duration(...) not equal to c(...). 1/4 mismatches [2] 34 - 28 == 6 ── Failure ('test-realized_duration.R:116:2'): realized_duration works (realized_only = TRUE) ── realized_duration(...) not equal to c(...). ... 1/4 mismatches [2] 34 - 28 == 6 ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ── realized_duration(...) not equal to c(...). 1/4 mismatches [1] 34 - 28 == 6

[ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ] Error: Test failures Execution halted ```

dragon

Version: 1.2.1
GitHub: https://github.com/sjspielman/dragon
Source code: https://github.com/cran/dragon
Date/Publication: 2022-04-08 08:42:33 UTC
Number of recursive dependencies: 131

Run revdep_details(, "dragon") for more info

checking tests ... `` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(dragon) > > test_check("dragon") Error inFUN()`: ! In path: "/c4/home/henrik/repositories/globals/revdep/checks/dragon/new/dragon.Rcheck/tests/testthat/setup_test-settings.R" ...
1. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
2. │ ├─base::withCallingHandlers(...)
3. │ └─base::eval(exprs, env)
4. │ └─base::eval(exprs, env)
5. │ └─igraph::read_graph("graph_by_redox.igraph", format = "ncol") at tests/testthat/setup_test-settings.R:8:1
6. │ └─igraph:::read.graph.ncol(file, ...)
7. └─base::.handleSimpleError(...)
8. └─testthat (local) h(simpleError(msg, call))
9. └─rlang::abort(...) Execution halted ```
checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: No news entries found.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘htmltools’ All declared Imports should be used.

drake

Version: 7.13.9
GitHub: https://github.com/ropensci/drake
Source code: https://github.com/cran/drake
Date/Publication: 2024-03-04 15:20:02 UTC
Number of recursive dependencies: 165

Run revdep_details(, "drake") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘clustermq’

DT

Version: 0.32
GitHub: https://github.com/rstudio/DT
Source code: https://github.com/cran/DT
Date/Publication: 2024-02-19 16:50:02 UTC
Number of recursive dependencies: 53

Run revdep_details(, "DT") for more info

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: htmlwidgets 4.8Mb

EFAtools

Version: 0.4.4
GitHub: https://github.com/mdsteiner/EFAtools
Source code: https://github.com/cran/EFAtools
Date/Publication: 2023-01-06 14:50:40 UTC
Number of recursive dependencies: 94

Run revdep_details(, "EFAtools") for more info

checking whether package ‘EFAtools’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/EFAtools/new/EFAtools.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: libs 6.0Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘progress’ All declared Imports should be used.

effectsize

Version: 0.8.6
GitHub: https://github.com/easystats/effectsize
Source code: https://github.com/cran/effectsize
Date/Publication: 2023-09-14 10:40:02 UTC
Number of recursive dependencies: 192

Run revdep_details(, "effectsize") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘see’

envi

Version: 0.1.19
GitHub: https://github.com/lance-waller-lab/envi
Source code: https://github.com/cran/envi
Date/Publication: 2024-01-23 14:40:03 UTC
Number of recursive dependencies: 153

Run revdep_details(, "envi") for more info

checking whether package ‘envi’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/globals/revdep/checks/envi/new/envi.Rcheck/00install.out’ for details.

EpiNow2

Version: 1.4.0
GitHub: https://github.com/epiforecasts/EpiNow2
Source code: https://github.com/cran/EpiNow2
Date/Publication: 2023-09-26 12:00:02 UTC
Number of recursive dependencies: 131

Run revdep_details(, "EpiNow2") for more info

checking installed package size ... NOTE installed size is 223.7Mb sub-directories of 1Mb or more: help 2.0Mb libs 220.8Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

epitweetr

Version: 2.2.16
GitHub: https://github.com/EU-ECDC/epitweetr
Source code: https://github.com/cran/epitweetr
Date/Publication: 2023-11-15 09:30:08 UTC
Number of recursive dependencies: 149

Run revdep_details(, "epitweetr") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘taskscheduleR’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘xml2’ All declared Imports should be used.

epoxy

Version: 1.0.0
GitHub: https://github.com/gadenbuie/epoxy
Source code: https://github.com/cran/epoxy
Date/Publication: 2023-09-20 00:00:02 UTC
Number of recursive dependencies: 94

Run revdep_details(, "epoxy") for more info

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

erah

Version: 2.0.1
GitHub: https://github.com/xdomingoal/erah-devel
Source code: https://github.com/cran/erah
Date/Publication: 2023-12-20 10:10:02 UTC
Number of recursive dependencies: 92

Run revdep_details(, "erah") for more info

checking whether package ‘erah’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/globals/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Package suggested but not available for checking: ‘ncdf4’

* installing *source* package ‘erah’ ...
** package ‘erah’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR
installing to /c4/home/henrik/repositories/globals/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs
** R
...
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘erah’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/erah/new/erah.Rcheck/erah’

* installing *source* package ‘erah’ ...
** package ‘erah’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR
installing to /c4/home/henrik/repositories/globals/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs
** R
...
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘erah’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/erah/old/erah.Rcheck/erah’

evalITR

Version: 1.0.0
GitHub: https://github.com/MichaelLLi/evalITR
Source code: https://github.com/cran/evalITR
Date/Publication: 2023-08-25 23:10:06 UTC
Number of recursive dependencies: 167

Run revdep_details(, "evalITR") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘forcats’ ‘rqPen’ ‘utils’ All declared Imports should be used.

fdacluster

Version: 0.3.0
GitHub: https://github.com/astamm/fdacluster
Source code: https://github.com/cran/fdacluster
Date/Publication: 2023-07-04 15:53:04 UTC
Number of recursive dependencies: 118

Run revdep_details(, "fdacluster") for more info

checking whether package ‘fdacluster’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/fdacluster/new/fdacluster.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 22.2Mb sub-directories of 1Mb or more: R 1.8Mb doc 1.4Mb help 2.1Mb libs 16.4Mb

fect

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/fect
Date/Publication: 2022-10-14 09:52:32 UTC
Number of recursive dependencies: 81

Run revdep_details(, "fect") for more info

checking whether package ‘fect’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/fect/new/fect.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 13.9Mb sub-directories of 1Mb or more: libs 12.6Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘panelView’ All declared Imports should be used.

FLAMES

Version: 1.8.0
GitHub: https://github.com/OliverVoogd/FLAMES
Source code: https://github.com/cran/FLAMES
Date/Publication: 2023-10-24
Number of recursive dependencies: 255

Run revdep_details(, "FLAMES") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking whether package ‘FLAMES’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/c4/home/henrik/repositories/globals/revdep/checks/FLAMES/new/FLAMES.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: data 2.7Mb doc 1.7Mb
checking R code for possible problems ... NOTE annotation_to_fasta: no visible global function definition for 'write.table' generate_sc_sce: no visible binding for global variable 'FSM_match' plot_coverage: no visible binding for global variable 'x' plot_coverage: no visible binding for global variable 'transcript' plot_coverage: no visible binding for global variable 'length_bin' plot_demultiplex: no visible binding for global variable 'Freq' plot_demultiplex: no visible binding for global variable '.' plot_demultiplex: no visible binding for global variable 'x' plot_demultiplex: no visible binding for global variable ... sc_umap_expression : plot_idx: no visible binding for global variable 'y' transcript_coverage: no visible binding for global variable 'mat' Undefined global functions or variables: . BarcodeEditDist FSM_match FlankEditDist Freq all_vars cell_id cnt everything gene_id heatmap_annotation_colors label length_bin mat n name tr_id transcript transcript_id value write.table x y Consider adding importFrom("utils", "write.table") to your NAMESPACE file.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

flowGraph

Version: 1.10.0
GitHub: https://github.com/aya49/flowGraph
Source code: https://github.com/cran/flowGraph
Date/Publication: 2023-10-24
Number of recursive dependencies: 94

Run revdep_details(, "flowGraph") for more info

checking R code for possible problems ... NOTE get_child: no visible binding for global variable ‘no_cores’ get_paren: no visible binding for global variable ‘no_cores’ ms_psig: no visible binding for global variable ‘meta’ Undefined global functions or variables: meta no_cores
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘doParallel’

forecastML

Version: 0.9.0
GitHub: https://github.com/nredell/forecastML
Source code: https://github.com/cran/forecastML
Date/Publication: 2020-05-07 15:10:17 UTC
Number of recursive dependencies: 105

Run revdep_details(, "forecastML") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘dtplyr’ All declared Imports should be used.

genBaRcode

Version: 1.2.7
GitHub: NA
Source code: https://github.com/cran/genBaRcode
Date/Publication: 2023-12-11 13:10:05 UTC
Number of recursive dependencies: 160

Run revdep_details(, "genBaRcode") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: --- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'genBaRcode_GUI_Vignette.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_GUI_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_GUI_Vignette.log for more info. --- failed re-building ‘genBaRcode_GUI_Vignette.Rmd’ ...

Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_Vignette.log for more info. --- failed re-building ‘genBaRcode_Vignette.Rmd’

SUMMARY: processing the following files failed: ‘genBaRcode_GUI_Vignette.Rmd’ ‘genBaRcode_Vignette.Rmd’

Error: Vignette re-building failed. Execution halted ```

geocmeans

Version: 0.3.4
GitHub: https://github.com/JeremyGelb/geocmeans
Source code: https://github.com/cran/geocmeans
Date/Publication: 2023-09-12 03:10:02 UTC
Number of recursive dependencies: 197

Run revdep_details(, "geocmeans") for more info

checking whether package ‘geocmeans’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/geocmeans/new/geocmeans.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 13.5Mb sub-directories of 1Mb or more: extdata 3.0Mb libs 8.2Mb

geospark

Version: 0.3.1
GitHub: https://github.com/harryprince/geospark
Source code: https://github.com/cran/geospark
Date/Publication: 2020-03-02 05:40:02 UTC
Number of recursive dependencies: 60

Run revdep_details(, "geospark") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘dbplyr’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

googleComputeEngineR

Version: 0.3.0
GitHub: https://github.com/cloudyr/googleComputeEngineR
Source code: https://github.com/cran/googleComputeEngineR
Date/Publication: 2019-05-04 22:40:02 UTC
Number of recursive dependencies: 67

Run revdep_details(, "googleComputeEngineR") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

googleTagManageR

Version: 0.2.0
GitHub: NA
Source code: https://github.com/cran/googleTagManageR
Date/Publication: 2022-04-16 18:12:29 UTC
Number of recursive dependencies: 69

Run revdep_details(, "googleTagManageR") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘assertthat’ ‘future’ ‘httr’ All declared Imports should be used.

grapesAgri1

Version: 1.1.0
GitHub: https://github.com/pratheesh3780/grapesAgri1
Source code: https://github.com/cran/grapesAgri1
Date/Publication: 2021-08-14 12:50:02 UTC
Number of recursive dependencies: 166

Run revdep_details(, "grapesAgri1") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’ ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’ ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’ ‘summarytools’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \& checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \& checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \& checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \& checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \& checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&

graphframes

Version: 0.1.2
GitHub: https://github.com/rstudio/graphframes
Source code: https://github.com/cran/graphframes
Date/Publication: 2018-10-30 19:20:03 UTC
Number of recursive dependencies: 61

Run revdep_details(, "graphframes") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

greed

Version: 0.6.1
GitHub: https://github.com/comeetie/greed
Source code: https://github.com/cran/greed
Date/Publication: 2022-10-03 22:00:05 UTC
Number of recursive dependencies: 98

Run revdep_details(, "greed") for more info

checking whether package ‘greed’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/greed/new/greed.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 36.5Mb sub-directories of 1Mb or more: libs 34.3Mb
checking data for non-ASCII characters ... NOTE Note: found 989 marked UTF-8 strings

gsynth

Version: 1.2.1
GitHub: NA
Source code: https://github.com/cran/gsynth
Date/Publication: 2021-08-06 07:50:05 UTC
Number of recursive dependencies: 77

Run revdep_details(, "gsynth") for more info

checking whether package ‘gsynth’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/gsynth/new/gsynth.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 4.9Mb

hackeRnews

Version: 0.1.0
GitHub: https://github.com/szymanskir/hackeRnews
Source code: https://github.com/cran/hackeRnews
Date/Publication: 2019-12-13 13:20:05 UTC
Number of recursive dependencies: 69

Run revdep_details(, "hackeRnews") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

hal9001

Version: 0.4.6
GitHub: https://github.com/tlverse/hal9001
Source code: https://github.com/cran/hal9001
Date/Publication: 2023-11-14 15:00:02 UTC
Number of recursive dependencies: 100

Run revdep_details(, "hal9001") for more info

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: libs 4.9Mb

hbamr

Version: 2.2.1
GitHub: https://github.com/jbolstad/hbamr
Source code: https://github.com/cran/hbamr
Date/Publication: 2024-02-23 12:30:02 UTC
Number of recursive dependencies: 91

Run revdep_details(, "hbamr") for more info

checking installed package size ... NOTE installed size is 353.1Mb sub-directories of 1Mb or more: libs 351.6Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

healthyR.ts

Version: 0.3.0
GitHub: https://github.com/spsanderson/healthyR.ts
Source code: https://github.com/cran/healthyR.ts
Date/Publication: 2023-11-15 06:00:05 UTC
Number of recursive dependencies: 221

Run revdep_details(, "healthyR.ts") for more info

checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 5.2Mb

hero

Version: 0.6
GitHub: NA
Source code: https://github.com/cran/hero
Date/Publication: 2023-07-15 21:10:09 UTC
Number of recursive dependencies: 160

Run revdep_details(, "hero") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘Rmpi’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Rmpi’

heterogen

Version: 1.2.33
GitHub: https://github.com/patauchi/heterogen
Source code: https://github.com/cran/heterogen
Date/Publication: 2023-08-17 07:42:33 UTC
Number of recursive dependencies: 56

Run revdep_details(, "heterogen") for more info

checking whether package ‘heterogen’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/heterogen/new/heterogen.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: extdata 2.5Mb libs 6.0Mb

historicalborrowlong

Version: 0.0.8
GitHub: https://github.com/wlandau/historicalborrowlong
Source code: https://github.com/cran/historicalborrowlong
Date/Publication: 2023-11-30 08:00:07 UTC
Number of recursive dependencies: 110

Run revdep_details(, "historicalborrowlong") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘clustermq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

hwep

Version: 2.0.2
GitHub: https://github.com/dcgerard/hwep
Source code: https://github.com/cran/hwep
Date/Publication: 2023-05-16 17:40:02 UTC
Number of recursive dependencies: 116

Run revdep_details(, "hwep") for more info

checking installed package size ... NOTE installed size is 84.5Mb sub-directories of 1Mb or more: libs 83.9Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

infercnv

Version: 1.18.1
GitHub: https://github.com/broadinstitute/inferCNV
Source code: https://github.com/cran/infercnv
Date/Publication: 2023-12-01
Number of recursive dependencies: 204

Run revdep_details(, "infercnv") for more info

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: extdata 3.1Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’ See the note in ?`:::` about the use of this operator.

InPAS

Version: 2.10.0
GitHub: NA
Source code: https://github.com/cran/InPAS
Date/Publication: 2023-10-24
Number of recursive dependencies: 172

Run revdep_details(, "InPAS") for more info

checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’ ‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’ ‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’ ‘search_distalCPs’ ‘search_proximalCPs’

interflex

Version: 1.2.6
GitHub: NA
Source code: https://github.com/cran/interflex
Date/Publication: 2021-05-18 11:40:02 UTC
Number of recursive dependencies: 103

Run revdep_details(, "interflex") for more info

checking whether package ‘interflex’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/interflex/new/interflex.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: libs 5.1Mb

ISAnalytics

Version: 1.12.0
GitHub: https://github.com/calabrialab/ISAnalytics
Source code: https://github.com/cran/ISAnalytics
Date/Publication: 2023-10-24
Number of recursive dependencies: 173

Run revdep_details(, "ISAnalytics") for more info

checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: data 1.4Mb doc 3.5Mb

ivmte

Version: 1.4.0
GitHub: NA
Source code: https://github.com/cran/ivmte
Date/Publication: 2021-09-17 12:20:07 UTC
Number of recursive dependencies: 112

Run revdep_details(, "ivmte") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'gurobi', 'cplexAPI'

keyATM

Version: 0.5.1
GitHub: https://github.com/keyATM/keyATM
Source code: https://github.com/cran/keyATM
Date/Publication: 2024-02-04 23:30:02 UTC
Number of recursive dependencies: 107

Run revdep_details(, "keyATM") for more info

checking installed package size ... NOTE installed size is 24.7Mb sub-directories of 1Mb or more: libs 24.3Mb

ldsr

Version: 0.0.2
GitHub: https://github.com/ntthung/ldsr
Source code: https://github.com/cran/ldsr
Date/Publication: 2020-05-04 14:40:09 UTC
Number of recursive dependencies: 78

Run revdep_details(, "ldsr") for more info

checking whether package ‘ldsr’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/ldsr/new/ldsr.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

leafdown

Version: 1.2.0
GitHub: NA
Source code: https://github.com/cran/leafdown
Date/Publication: 2022-09-19 06:06:11 UTC
Number of recursive dependencies: 133

Run revdep_details(, "leafdown") for more info

checking data for non-ASCII characters ... NOTE Note: found 75 marked UTF-8 strings

lidR

Version: 4.1.1
GitHub: https://github.com/r-lidar/lidR
Source code: https://github.com/cran/lidR
Date/Publication: 2024-03-05 17:00:11 UTC
Number of recursive dependencies: 156

Run revdep_details(, "lidR") for more info

checking tests ... ``` Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/BATCH: line 60: 39355 Aborted (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output:

Sys.setenv("R_TESTS" = "")

library(testthat) library(lidR) test_check("lidR") Tests using raster: terra Tests using future: TRUE Tests using OpenMP thread: 32 OGR: Unsupported geometry type OGR: Unsupported geometry type Chunk 1 of 1 (100%): state ✓ terminate called after throwing an instance of 'std::length_error' what(): basic_string::_S_create ```
checking whether package ‘lidR’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/lidR/new/lidR.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 20.0Mb sub-directories of 1Mb or more: R 1.0Mb extdata 1.1Mb libs 16.3Mb

MAI

Version: 1.8.0
GitHub: https://github.com/KechrisLab/MAI
Source code: https://github.com/cran/MAI
Date/Publication: 2023-10-24
Number of recursive dependencies: 176

Run revdep_details(, "MAI") for more info

checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.

manynet

Version: 0.4.1
GitHub: https://github.com/stocnet/manynet
Source code: https://github.com/cran/manynet
Date/Publication: 2024-01-24 23:10:06 UTC
Number of recursive dependencies: 142

Run revdep_details(, "manynet") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘Rgraphviz’
checking data for non-ASCII characters ... NOTE Note: found 7 marked UTF-8 strings

metabolomicsR

Version: 1.0.0
GitHub: https://github.com/XikunHan/metabolomicsR
Source code: https://github.com/cran/metabolomicsR
Date/Publication: 2022-04-29 07:40:02 UTC
Number of recursive dependencies: 182

Run revdep_details(, "metabolomicsR") for more info

checking dependencies in R code ... WARNING Missing or unexported object: ‘future::multiprocess’
checking package dependencies ... NOTE Package suggested but not available for checking: ‘genuMet’

metaGE

Version: 1.0.3
GitHub: NA
Source code: https://github.com/cran/metaGE
Date/Publication: 2023-09-28 08:50:02 UTC
Number of recursive dependencies: 149

Run revdep_details(, "metaGE") for more info

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: data 4.2Mb

microservices

Version: 0.2.0
GitHub: https://github.com/tidylab/microservices
Source code: https://github.com/cran/microservices
Date/Publication: 2022-10-01 09:50:02 UTC
Number of recursive dependencies: 72

Run revdep_details(, "microservices") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(microservices) > test_check("microservices") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]

══ Failed tests ════════════════════════════════════════════════════════════════ ... Backtrace: ▆ 1. ├─config::get(...) at test-endpoint-plumber-{route_name}.R:2:1 2. │ └─base::normalizePath(file, mustWork = FALSE) 3. │ └─base::path.expand(path) 4. └─base::system.file(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] Error: Test failures Execution halted ```

MineICA

Version: 1.42.0
GitHub: NA
Source code: https://github.com/cran/MineICA
Date/Publication: 2023-10-24
Number of recursive dependencies: 216

Run revdep_details(, "MineICA") for more info

checking dependencies in R code ... WARNING Namespace in Imports field not imported from: ‘lumiHumanAll.db’ All declared Imports should be used. Packages in Depends field not imported from: ‘GOstats’ ‘Hmisc’ ‘JADE’ ‘RColorBrewer’ ‘Rgraphviz’ ‘annotate’ ‘biomaRt’ ‘cluster’ ‘colorspace’ ‘fastICA’ ‘foreach’ ‘ggplot2’ ‘graph’ ‘gtools’ ‘igraph’ ‘marray’ ‘mclust’ ‘methods’ ‘plyr’ ‘scales’ ‘xtable’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Missing or unexported object: ‘GOstats::geneIdsByCategory’ ':::' calls which should be '::': ‘Biobase:::annotation<-’ ‘Biobase:::validMsg’ ‘fpc:::pamk’ ‘lumi:::getChipInfo’ ‘mclust:::adjustedRandIndex’ See the note in ?`:::` about the use of this operator. Unexported object imported by a ':::' call: ‘Biobase:::isValidVersion’ See the note in ?`:::` about the use of this operator.
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'Alist.Rd': ‘class-IcaSet’

Missing link or links in documentation object 'Slist.Rd': ‘class-IcaSet’

Missing link or links in documentation object 'class-IcaSet.Rd': ‘class-IcaSet’

Missing link or links in documentation object 'getComp.Rd': ‘class-IcaSet’

Missing link or links in documentation object 'runAn.Rd': ‘[Category:class-GOHyperGParams]{GOHyperGParams}’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking for missing documentation entries ... WARNING Undocumented S4 classes: ‘MineICAParams’ All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘doMC’

Depends: includes the non-default packages: 'BiocGenerics', 'Biobase', 'plyr', 'ggplot2', 'scales', 'foreach', 'xtable', 'biomaRt', 'gtools', 'GOstats', 'cluster', 'marray', 'mclust', 'RColorBrewer', 'colorspace', 'igraph', 'Rgraphviz', 'graph', 'annotate', 'Hmisc', 'fastICA', 'JADE' Adding so many packages to the search path is excessive and importing selectively is preferable. ```
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘biomaRt’ ‘GOstats’ ‘cluster’ ‘mclust’ ‘igraph’ A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE addGenesToGoReport: no visible global function definition for ‘conditional’ addGenesToGoReport: no visible global function definition for ‘sigCategories’ annot2Color: no visible global function definition for ‘brewer.pal’ annot2Color: no visible global function definition for ‘heat_hcl’ annot2Color: no visible global function definition for ‘terrain_hcl’ annot2Color: no visible global function definition for ‘cm.colors’ annot2Color: no visible global function definition for ‘rainbow_hcl’ annotFeatures: no visible global function definition for ‘na.omit’ ... importFrom("methods", "callNextMethod", "new", "validObject") importFrom("stats", "aggregate", "as.dendrogram", "as.dist", "as.hclust", "chisq.test", "cor", "cor.test", "cutree", "dist", "hclust", "kmeans", "kruskal.test", "lm", "median", "na.omit", "order.dendrogram", "p.adjust", "quantile", "reorder", "shapiro.test", "wilcox.test") importFrom("utils", "capture.output", "combn", "read.table", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘MineICA.Rnw’ using Sweave Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:
```
IQR, mad, sd, var, xtabs
```
... l.23 \usepackage {subfig}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MineICA.Rnw’

SUMMARY: processing the following file failed: ‘MineICA.Rnw’

Error: Vignette re-building failed. Execution halted ```

missSBM

Version: 1.0.4
GitHub: https://github.com/grossSBM/missSBM
Source code: https://github.com/cran/missSBM
Date/Publication: 2023-10-24 16:00:05 UTC
Number of recursive dependencies: 114

Run revdep_details(, "missSBM") for more info

checking whether package ‘missSBM’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/missSBM/new/missSBM.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 9.8Mb sub-directories of 1Mb or more: libs 7.8Mb

mistyR

Version: 1.10.0
GitHub: https://github.com/saezlab/mistyR
Source code: https://github.com/cran/mistyR
Date/Publication: 2023-10-24
Number of recursive dependencies: 155

Run revdep_details(, "mistyR") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:

Collecting contributions

Collecting importances

Aggregating ... ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-misty.R:212:3'): k for cv , n.bags for bagging can be changed and approx works ── first.run < second.run is not TRUE

actual: FALSE expected: TRUE

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ] Error: Test failures Execution halted ```

checking R code for possible problems ... NOTE aggregate_results: no visible binding for global variable ‘measure’ aggregate_results: no visible binding for global variable ‘target’ aggregate_results: no visible binding for global variable ‘value’ aggregate_results: no visible binding for global variable ‘sd’ aggregate_results: no visible binding for global variable ‘view’ aggregate_results: no visible binding for global variable ‘.PT’ aggregate_results: no visible binding for global variable ‘Importance’ aggregate_results_subset: no visible binding for global variable ‘view’ aggregate_results_subset: no visible binding for global variable ‘.PT’ aggregate_results_subset: no visible binding for global variable ... run_misty : <anonymous>: no visible binding for global variable ‘multi.R2’ svm_model: no visible binding for global variable ‘index’ Undefined global functions or variables: .PT Importance Predictor Target fraction index intra.R2 intra.RMSE measure multi.R2 multi.RMSE nsamples p prediction sd target total ts value view Consider adding importFrom("stats", "sd", "ts") to your NAMESPACE file.

MLDataR

Version: 1.0.1
GitHub: https://github.com/StatsGary/MLDataR
Source code: https://github.com/cran/MLDataR
Date/Publication: 2022-10-03 15:10:02 UTC
Number of recursive dependencies: 126

Run revdep_details(, "MLDataR") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’ ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’ All declared Imports should be used.

mlr3shiny

Version: 0.3.0
GitHub: NA
Source code: https://github.com/cran/mlr3shiny
Date/Publication: 2023-09-30 20:30:05 UTC
Number of recursive dependencies: 179

Run revdep_details(, "mlr3shiny") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DT’ ‘Metrics’ ‘data.table’ ‘dplyr’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘mlr3pipelines’ ‘patchwork’ ‘plyr’ ‘purrr’ ‘shinyWidgets’ ‘shinyalert’ ‘shinydashboard’ ‘shinyjs’ ‘stats’ ‘stringr’ All declared Imports should be used.

mmaqshiny

Version: 1.0.0
GitHub: https://github.com/meenakshi-kushwaha/mmaqshiny
Source code: https://github.com/cran/mmaqshiny
Date/Publication: 2020-06-26 16:00:23 UTC
Number of recursive dependencies: 145

Run revdep_details(, "mmaqshiny") for more info

checking installed package size ... NOTE installed size is 15.5Mb sub-directories of 1Mb or more: images 1.0Mb shiny 14.4Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’ ‘zoo’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

mmrm

Version: 0.3.11
GitHub: https://github.com/openpharma/mmrm
Source code: https://github.com/cran/mmrm
Date/Publication: 2024-03-05 08:10:02 UTC
Number of recursive dependencies: 158

Run revdep_details(, "mmrm") for more info

checking installed package size ... NOTE installed size is 198.1Mb sub-directories of 1Mb or more: libs 196.4Mb

modeltime

Version: 1.2.8
GitHub: https://github.com/business-science/modeltime
Source code: https://github.com/cran/modeltime
Date/Publication: 2023-09-02 15:10:02 UTC
Number of recursive dependencies: 252

Run revdep_details(, "modeltime") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘tidymodels’ ‘tidyverse’ All declared Imports should be used.

modeltime.ensemble

Version: 1.0.3
GitHub: https://github.com/business-science/modeltime.ensemble
Source code: https://github.com/cran/modeltime.ensemble
Date/Publication: 2023-04-18 11:50:02 UTC
Number of recursive dependencies: 229

Run revdep_details(, "modeltime.ensemble") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘parsnip’ All declared Imports should be used.

modeltime.resample

Version: 0.2.3
GitHub: https://github.com/business-science/modeltime.resample
Source code: https://github.com/cran/modeltime.resample
Date/Publication: 2023-04-12 15:50:02 UTC
Number of recursive dependencies: 228

Run revdep_details(, "modeltime.resample") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’ All declared Imports should be used.

momentuHMM

Version: 1.5.5
GitHub: https://github.com/bmcclintock/momentuHMM
Source code: https://github.com/cran/momentuHMM
Date/Publication: 2022-10-18 20:52:35 UTC
Number of recursive dependencies: 145

Run revdep_details(, "momentuHMM") for more info

checking whether package ‘momentuHMM’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/momentuHMM/new/momentuHMM.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 10.2Mb sub-directories of 1Mb or more: R 1.2Mb doc 1.7Mb libs 6.7Mb

MOSS

Version: 0.2.2
GitHub: https://github.com/agugonrey/MOSS
Source code: https://github.com/cran/MOSS
Date/Publication: 2022-03-25 15:50:05 UTC
Number of recursive dependencies: 182

Run revdep_details(, "MOSS") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘MOSS_working_example.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'MOSS_working_example.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/MOSS/new/MOSS.Rcheck/vign_test/MOSS/vignettes/MOSS_working_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MOSS_working_example.log for more info. --- failed re-building ‘MOSS_working_example.Rmd’

SUMMARY: processing the following file failed: ‘MOSS_working_example.Rmd’

Error: Vignette re-building failed. Execution halted ```

MSstatsBig

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/MSstatsBig
Date/Publication: 2023-10-24
Number of recursive dependencies: 128

Run revdep_details(, "MSstatsBig") for more info

checking R code for possible problems ... NOTE MSstatsPreprocessBig: no visible binding for global variable ‘input’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘PeptideSequence’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘PrecursorCharge’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘FragmentIon’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘ProductCharge’ MSstatsPreprocessBigArrow: no visible binding for global variable ... cleanSpectronautChunk: no visible binding for global variable ‘BioReplicate’ cleanSpectronautChunk: no visible binding for global variable ‘Condition’ Undefined global functions or variables: %>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature FragmentIon Identified Intensity IsLabeled IsotopeLabelType LabeledSequence MeanAbundance NumObs NumProteins PGQvalue PeptideSequence PrecursorCharge ProductCharge ProteinName Rank Run all_of feature_rank if_else input min_rank n_distinct tbl

MSstatsShiny

Version: 1.4.3
GitHub: https://github.com/Vitek-Lab/MSstatsShiny
Source code: https://github.com/cran/MSstatsShiny
Date/Publication: 2024-03-04
Number of recursive dependencies: 155

Run revdep_details(, "MSstatsShiny") for more info

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘MSstatsTMT:::.logSum’ ‘MSstatsTMT:::.summarizeSimpleStat’ ‘MSstatsTMT:::.summarizeTMP’ ‘MSstatsTMT:::MSstatsFitComparisonModelsTMT’ ‘MSstatsTMT:::MSstatsGroupComparisonOutputTMT’ ‘MSstatsTMT:::MSstatsModerateTTest’ ‘MSstatsTMT:::MSstatsNormalizeTMT’ ‘MSstatsTMT:::MSstatsPrepareForGroupComparisonTMT’ ‘MSstatsTMT:::MSstatsPrepareForSummarizationTMT’ ‘MSstatsTMT:::MSstatsSummarizationOutputTMT’ ‘MSstatsTMT:::MSstatsTestSingleProteinTMT’ ‘MSstatsTMT:::getProcessedTMT’ ‘MSstatsTMT:::getSummarizedTMT’ ‘shinyBS:::buildTooltipOrPopoverOptionsList’ ‘shinyBS:::shinyBSDep’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE getAnnot: no visible binding for global variable ‘annotation.pd’ getSummary1: no visible binding for global variable ‘Condition’ getSummary1: no visible binding for global variable ‘BioReplicate’ getSummary1: no visible binding for global variable ‘Mixture’ getSummary1: no visible binding for global variable ‘Run’ getSummary1: no visible binding for global variable ‘TechRepMixture’ getSummary1: no visible binding for global variable ‘Fraction’ getSummary1: no visible binding for global variable ‘Condition_Run’ getSummary1: no visible binding for global variable ‘BioReplicate_Run’ getSummary1: no visible binding for global variable ‘Number of ... server: no visible global function definition for ‘callModule’ statmodelServer: no visible global function definition for ‘updateNumericInput’ Undefined global functions or variables: BioReplicate BioReplicate_Run Charge Condition Condition_Run FEATURES Features_Peptides_max Features_Peptides_min Fraction FragmentIon Intensity Max_Intensity Min_Intensity Mixture Number of Fractions PeptideSequence Peptides_Proteins_max Peptides_Proteins_min PrecursorCharge ProductCharge ProteinName Run TechRepMixture annotation.pd callModule moduleServer nfea npep updateNumericInput

MtreeRing

Version: 1.4.5
GitHub: https://github.com/ropensci/MtreeRing
Source code: https://github.com/cran/MtreeRing
Date/Publication: 2021-04-19 22:10:06 UTC
Number of recursive dependencies: 115

Run revdep_details(, "MtreeRing") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

mvrsquared

Version: 0.1.5
GitHub: https://github.com/TommyJones/mvrsquared
Source code: https://github.com/cran/mvrsquared
Date/Publication: 2023-07-15 00:10:02 UTC
Number of recursive dependencies: 91

Run revdep_details(, "mvrsquared") for more info

checking whether package ‘mvrsquared’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/mvrsquared/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/mvrsquared/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/mvrsquared/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/mvrsquared/new/mvrsquared.Rcheck/00install.out’ for details.

nebula

Version: 1.5.3
GitHub: https://github.com/lhe17/nebula
Source code: https://github.com/cran/nebula
Date/Publication: 2024-02-15 23:00:02 UTC
Number of recursive dependencies: 184

Run revdep_details(, "nebula") for more info

checking installed package size ... NOTE installed size is 37.4Mb sub-directories of 1Mb or more: libs 35.9Mb

nevada

Version: 0.2.0
GitHub: https://github.com/astamm/nevada
Source code: https://github.com/cran/nevada
Date/Publication: 2023-09-03 21:00:02 UTC
Number of recursive dependencies: 108

Run revdep_details(, "nevada") for more info

checking whether package ‘nevada’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/nevada/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/nevada/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/nevada/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/nevada/new/nevada.Rcheck/00install.out’ for details.

nfl4th

Version: 1.0.4
GitHub: https://github.com/nflverse/nfl4th
Source code: https://github.com/cran/nfl4th
Date/Publication: 2023-08-21 09:32:33 UTC
Number of recursive dependencies: 111

Run revdep_details(, "nfl4th") for more info

checking whether package ‘nfl4th’ can be installed ... WARNING Found the following significant warnings: Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection. See ‘/c4/home/henrik/repositories/globals/revdep/checks/nfl4th/new/nfl4th.Rcheck/00install.out’ for details.
checking whether the namespace can be loaded with stated dependencies ... NOTE `` Warning: GitHub.com seems offline, andoptions(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection.

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```

occupationMeasurement

Version: 0.3.2
GitHub: https://github.com/occupationMeasurement/occupationMeasurement
Source code: https://github.com/cran/occupationMeasurement
Date/Publication: 2023-09-27 13:40:02 UTC
Number of recursive dependencies: 126

Run revdep_details(, "occupationMeasurement") for more info

checking data for non-ASCII characters ... NOTE Note: found 6986 marked UTF-8 strings

oncomsm

Version: 0.1.4
GitHub: https://github.com/Boehringer-Ingelheim/oncomsm
Source code: https://github.com/cran/oncomsm
Date/Publication: 2023-04-17 07:00:02 UTC
Number of recursive dependencies: 127

Run revdep_details(, "oncomsm") for more info

checking installed package size ... NOTE installed size is 67.6Mb sub-directories of 1Mb or more: doc 1.0Mb libs 65.5Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

onemapsgapi

Version: 1.1.0
GitHub: NA
Source code: https://github.com/cran/onemapsgapi
Date/Publication: 2022-11-29 08:00:03 UTC
Number of recursive dependencies: 71

Run revdep_details(, "onemapsgapi") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘onemapsgapi_vignette.Rmd’ using rmarkdown

Quitting from lines 36-37 [unnamed-chunk-4] (onemapsgapi_vignette.Rmd) Error: processing vignette 'onemapsgapi_vignette.Rmd' failed with diagnostics: Peer certificate cannot be authenticated with given CA certificates: [developers.onemap.sg] Peer's Certificate has expired. --- failed re-building ‘onemapsgapi_vignette.Rmd’

SUMMARY: processing the following file failed: ‘onemapsgapi_vignette.Rmd’

Error: Vignette re-building failed. Execution halted ```

OOS

Version: 1.0.0
GitHub: https://github.com/tylerJPike/OOS
Source code: https://github.com/cran/OOS
Date/Publication: 2021-03-17 13:20:20 UTC
Number of recursive dependencies: 137

Run revdep_details(, "OOS") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

pareg

Version: 1.6.0
GitHub: https://github.com/cbg-ethz/pareg
Source code: https://github.com/cran/pareg
Date/Publication: 2023-10-24
Number of recursive dependencies: 320

Run revdep_details(, "pareg") for more info

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

Name: as.data.frame.pareg

Title: as.data.frame for an object of class 'pareg'.

Aliases: as.data.frame.pareg

** Examples

df_genes <- data.frame( ... + ) fit <- pareg(df_genes, df_terms, max_iterations = 10) Error in py_module_import(module, convert = convert) : ImportError: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) Runreticulate::py_last_error()for details. Error in .activate_fallback(proc, testload, env = env, envpath = envpath, : ImportError: /lib64/libstdc++.so.6: versionCXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) Run reticulate::py_last_error() for details. Calls: pareg -> basiliskStart -> .activate_fallback Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(pareg) Loading required package: tensorflow Loading required package: tfprobability

... + testload = c("tensorflow", "tensorflow_probability") + ) Error in py_module_import(module, convert = convert) : ImportError: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) Runreticulate::py_last_error()for details. Error in .activate_fallback(proc, testload, env = env, envpath = envpath, : ImportError: /lib64/libstdc++.so.6: versionCXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) Run reticulate::py_last_error() for details. Calls: -> .activate_fallback Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘pareg.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/globals/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/globals/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-5-1.png" but not available.

Quitting from lines 145-150 [unnamed-chunk-9] (pareg.Rmd) Error: processing vignette 'pareg.Rmd' failed with diagnostics: ImportError: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) Runreticulate::py_last_error()` for details. ... --- re-building ‘pathway_similarities.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/globals/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/globals/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-3-1.png" but not available. --- finished re-building ‘pathway_similarities.Rmd’

SUMMARY: processing the following file failed: ‘pareg.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking for portable file names ... NOTE ``` Found the following non-portable file paths: pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml ... pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter

Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```
checking whether package ‘pareg’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/c4/home/henrik/repositories/globals/revdep/checks/pareg/new/pareg.Rcheck/00install.out’ for details.

parseRPDR

Version: 1.1.0
GitHub: https://github.com/martonkolossvary/parseRPDR
Source code: https://github.com/cran/parseRPDR
Date/Publication: 2024-01-09 12:10:02 UTC
Number of recursive dependencies: 89

Run revdep_details(, "parseRPDR") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘doParallel’ All declared Imports should be used.

partR2

Version: 0.9.2
GitHub: https://github.com/mastoffel/partR2
Source code: https://github.com/cran/partR2
Date/Publication: 2024-03-04 13:20:02 UTC
Number of recursive dependencies: 94

Run revdep_details(, "partR2") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used.

pavo

Version: 2.9.0
GitHub: https://github.com/rmaia/pavo
Source code: https://github.com/cran/pavo
Date/Publication: 2023-09-24 10:10:02 UTC
Number of recursive dependencies: 104

Run revdep_details(, "pavo") for more info

checking whether package ‘pavo’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/globals/revdep/checks/pavo/new/pavo.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Package suggested but not available for checking: ‘imager’

PCRedux

Version: 1.1-2
GitHub: https://github.com/PCRuniversum/PCRedux
Source code: https://github.com/cran/PCRedux
Date/Publication: 2022-05-11 11:40:02 UTC
Number of recursive dependencies: 153

Run revdep_details(, "PCRedux") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘PCRedux.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'PCRedux.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/PCRedux/new/PCRedux.Rcheck/vign_test/PCRedux/vignettes/PCRedux.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See PCRedux.log for more info. --- failed re-building ‘PCRedux.Rmd’

SUMMARY: processing the following file failed: ‘PCRedux.Rmd’

Error: Vignette re-building failed. Execution halted ```

phecodemap

Version: 0.1.0
GitHub: https://github.com/celehs/phecodemap
Source code: https://github.com/cran/phecodemap
Date/Publication: 2022-01-15 09:02:44 UTC
Number of recursive dependencies: 123

Run revdep_details(, "phecodemap") for more info

checking data for non-ASCII characters ... NOTE Note: found 114 marked UTF-8 strings

photosynthesis

Version: 2.1.4
GitHub: https://github.com/cdmuir/photosynthesis
Source code: https://github.com/cran/photosynthesis
Date/Publication: 2023-08-15 07:20:05 UTC
Number of recursive dependencies: 144

Run revdep_details(, "photosynthesis") for more info

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: doc 6.0Mb
checking data for non-ASCII characters ... NOTE Note: found 13 marked UTF-8 strings

phylolm

Version: 2.6.2
GitHub: https://github.com/lamho86/phylolm
Source code: https://github.com/cran/phylolm
Date/Publication: 2020-06-22 05:10:08 UTC
Number of recursive dependencies: 41

Run revdep_details(, "phylolm") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘geiger’, ‘caper’

PLNmodels

Version: 1.2.0
GitHub: https://github.com/pln-team/PLNmodels
Source code: https://github.com/cran/PLNmodels
Date/Publication: 2024-03-05 15:50:03 UTC
Number of recursive dependencies: 151

Run revdep_details(, "PLNmodels") for more info

checking whether package ‘PLNmodels’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/PLNmodels/new/PLNmodels.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 27.5Mb sub-directories of 1Mb or more: data 1.4Mb doc 2.0Mb libs 22.4Mb

plotly

Version: 4.10.4
GitHub: https://github.com/plotly/plotly.R
Source code: https://github.com/cran/plotly
Date/Publication: 2024-01-13 22:40:02 UTC
Number of recursive dependencies: 148

Run revdep_details(, "plotly") for more info

checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: htmlwidgets 3.8Mb

pointblank

Version: 0.12.0
GitHub: https://github.com/rstudio/pointblank
Source code: https://github.com/cran/pointblank
Date/Publication: 2024-03-01 08:30:02 UTC
Number of recursive dependencies: 135

Run revdep_details(, "pointblank") for more info

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

portvine

Version: 1.0.3
GitHub: https://github.com/EmanuelSommer/portvine
Source code: https://github.com/cran/portvine
Date/Publication: 2024-01-18 16:30:02 UTC
Number of recursive dependencies: 130

Run revdep_details(, "portvine") for more info

checking installed package size ... NOTE installed size is 52.9Mb sub-directories of 1Mb or more: libs 51.9Mb

ppseq

Version: 0.2.3
GitHub: https://github.com/zabore/ppseq
Source code: https://github.com/cran/ppseq
Date/Publication: 2024-01-23 15:00:06 UTC
Number of recursive dependencies: 107

Run revdep_details(, "ppseq") for more info

checking installed package size ... NOTE installed size is 10.9Mb sub-directories of 1Mb or more: doc 10.4Mb

ppsr

Version: 0.0.5
GitHub: NA
Source code: https://github.com/cran/ppsr
Date/Publication: 2024-02-18 12:30:02 UTC
Number of recursive dependencies: 61

Run revdep_details(, "ppsr") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘rpart’ ‘withr’ All declared Imports should be used.

projpred

Version: 2.8.0
GitHub: https://github.com/stan-dev/projpred
Source code: https://github.com/cran/projpred
Date/Publication: 2023-12-15 00:00:02 UTC
Number of recursive dependencies: 158

Run revdep_details(, "projpred") for more info

checking whether package ‘projpred’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/projpred/new/projpred.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: doc 1.4Mb libs 3.6Mb

Prostar

Version: 1.34.6
GitHub: https://github.com/prostarproteomics/Prostar
Source code: https://github.com/cran/Prostar
Date/Publication: 2024-02-15
Number of recursive dependencies: 331

Run revdep_details(, "Prostar") for more info

checking whether package ‘Prostar’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/globals/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details.

* installing *source* package ‘Prostar’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘Prostar’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’

* installing *source* package ‘Prostar’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘Prostar’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’

pseudohouseholds

Version: 0.1.1
GitHub: https://github.com/chris31415926535/pseudohouseholds
Source code: https://github.com/cran/pseudohouseholds
Date/Publication: 2023-07-19 09:30:02 UTC
Number of recursive dependencies: 105

Run revdep_details(, "pseudohouseholds") for more info

checking data for non-ASCII characters ... NOTE Note: found 596 marked UTF-8 strings

QDNAseq

Version: 1.38.0
GitHub: https://github.com/ccagc/QDNAseq
Source code: https://github.com/cran/QDNAseq
Date/Publication: 2023-10-24
Number of recursive dependencies: 89

Run revdep_details(, "QDNAseq") for more info

checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘QDNAseq.Rnw’ using Sweave EM algorithm started ...

Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead.

Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘QDNAseq.Rnw’

SUMMARY: processing the following file failed: ‘QDNAseq.Rnw’

Error: Vignette re-building failed. Execution halted ```

RAINBOWR

Version: 0.1.35
GitHub: NA
Source code: https://github.com/cran/RAINBOWR
Date/Publication: 2024-03-03 09:12:36 UTC
Number of recursive dependencies: 167

Run revdep_details(, "RAINBOWR") for more info

checking installed package size ... NOTE installed size is 45.2Mb sub-directories of 1Mb or more: libs 43.9Mb

raveio

Version: 0.9.0
GitHub: https://github.com/beauchamplab/raveio
Source code: https://github.com/cran/raveio
Date/Publication: 2023-07-16 19:10:02 UTC
Number of recursive dependencies: 134

Run revdep_details(, "raveio") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘clustermq’

receptiviti

Version: 0.1.7
GitHub: https://github.com/Receptiviti/receptiviti-r
Source code: https://github.com/cran/receptiviti
Date/Publication: 2024-02-23 23:50:05 UTC
Number of recursive dependencies: 67

Run revdep_details(, "receptiviti") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(receptiviti) > > test_check("receptiviti") Status: ERROR Message: 400 ...
1. └─receptiviti::receptiviti(...) ── Failure ('test-receptiviti_status.R:5:3'): failures works ─────────────────── receptiviti_status(...) is not NULL
actual is a list expected is NULL

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 6 ] Error: Test failures Execution halted ```

recipes

Version: 1.0.10
GitHub: https://github.com/tidymodels/recipes
Source code: https://github.com/cran/recipes
Date/Publication: 2024-02-18 18:00:02 UTC
Number of recursive dependencies: 139

Run revdep_details(, "recipes") for more info

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘fastICA’, ‘dimRed’

regmedint

Version: 1.0.1
GitHub: https://github.com/kaz-yos/regmedint
Source code: https://github.com/cran/regmedint
Date/Publication: 2024-01-13 00:50:02 UTC
Number of recursive dependencies: 154

Run revdep_details(, "regmedint") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Deriv’ All declared Imports should be used.

reservr

Version: 0.0.2
GitHub: https://github.com/AshesITR/reservr
Source code: https://github.com/cran/reservr
Date/Publication: 2023-10-18 20:50:05 UTC
Number of recursive dependencies: 143

Run revdep_details(, "reservr") for more info

checking whether package ‘reservr’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/reservr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/reservr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/reservr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/reservr/new/reservr.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 16.8Mb sub-directories of 1Mb or more: R 1.5Mb libs 14.7Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

rgee

Version: 1.1.7
GitHub: https://github.com/r-spatial/rgee
Source code: https://github.com/cran/rgee
Date/Publication: 2023-09-27 08:30:02 UTC
Number of recursive dependencies: 144

Run revdep_details(, "rgee") for more info

checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: doc 6.9Mb

robotstxt

Version: 0.7.13
GitHub: https://github.com/ropensci/robotstxt
Source code: https://github.com/cran/robotstxt
Date/Publication: 2020-09-03 19:30:02 UTC
Number of recursive dependencies: 70

Run revdep_details(, "robotstxt") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘future’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

rpm

Version: 0.7-1
GitHub: https://github.com/handcock/rpm
Source code: https://github.com/cran/rpm
Date/Publication: 2023-04-21 23:30:02 UTC
Number of recursive dependencies: 66

Run revdep_details(, "rpm") for more info

checking whether package ‘rpm’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/rpm/new/rpm.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 11.6Mb sub-directories of 1Mb or more: libs 11.1Mb

rsparkling

Version: 0.2.19
GitHub: https://github.com/h2oai/sparkling-water
Source code: https://github.com/cran/rsparkling
Date/Publication: 2020-01-28 23:10:02 UTC
Number of recursive dependencies: 60

Run revdep_details(, "rsparkling") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘h2o’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sapfluxnetr

Version: 0.1.4
GitHub: https://github.com/sapfluxnet/sapfluxnetr
Source code: https://github.com/cran/sapfluxnetr
Date/Publication: 2023-01-25 15:30:02 UTC
Number of recursive dependencies: 83

Run revdep_details(, "sapfluxnetr") for more info

checking data for non-ASCII characters ... NOTE Note: found 4 marked UTF-8 strings

scanMiRApp

Version: 1.8.0
GitHub: NA
Source code: https://github.com/cran/scanMiRApp
Date/Publication: 2023-10-24
Number of recursive dependencies: 177

Run revdep_details(, "scanMiRApp") for more info

checking dependencies in R code ... WARNING '::' or ':::' import not declared from: 'BSgenome.Mmusculus.UCSC.mm39' ':::' calls which should be '::': 'BSgenome.Hsapiens.UCSC.hg38:::BSgenome.Hsapiens.UCSC.hg38' 'BSgenome.Mmusculus.UCSC.mm10:::BSgenome.Mmusculus.UCSC.mm10' 'BSgenome.Rnorvegicus.UCSC.rn6:::BSgenome.Rnorvegicus.UCSC.rn6' See the note in ?`:::` about the use of this operator. Unavailable namespace imported from by a ':::' call: 'BSgenome.Mmusculus.UCSC.mm39' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .fakeAnno: no visible binding for global variable 'SampleTranscript' .fakeAnno: no visible binding for global variable 'SampleKdModel' plotSitesOnUTR: no visible binding for global variable 'logKd' plotSitesOnUTR: no visible binding for global variable 'note' Undefined global functions or variables: SampleKdModel SampleTranscript logKd note

SCArray.sat

Version: 1.2.1
GitHub: https://github.com/AbbVie-ComputationalGenomics/SCArray
Source code: https://github.com/cran/SCArray.sat
Date/Publication: 2024-01-16
Number of recursive dependencies: 180

Run revdep_details(, "SCArray.sat") for more info

checking S3 generic/method consistency ... WARNING ``` SetAssayData: function(object, layer, new.data, slot, ...) SetAssayData.SCArrayAssay: function(object, slot, new.data, ...)

CreateSeuratObject: function(counts, assay, names.field, names.delim, meta.data, project, ...) CreateSeuratObject.DelayedMatrix: function(counts, project, assay, names.field, names.delim, meta.data, min.cells, min.features, row.names, ...) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ```
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘Seurat:::DEmethods_counts’ ‘Seurat:::DEmethods_nocorrect’ ‘Seurat:::FastExpMean’ ‘Seurat:::FastLogVMR’ ‘Seurat:::NBResiduals’ ‘Seurat:::UpdateKey’ ‘Seurat:::ValidateDataForMerge’ See the note in ?`:::` about the use of this operator.

scRNAseqApp

Version: 1.2.2
GitHub: https://github.com/jianhong/scRNAseqApp
Source code: https://github.com/cran/scRNAseqApp
Date/Publication: 2023-11-02
Number of recursive dependencies: 235

Run revdep_details(, "scRNAseqApp") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'celldex', 'SingleR', 'tricycle'

sctransform

Version: 0.4.1
GitHub: https://github.com/satijalab/sctransform
Source code: https://github.com/cran/sctransform
Date/Publication: 2023-10-19 04:40:02 UTC
Number of recursive dependencies: 68

Run revdep_details(, "sctransform") for more info

checking whether package ‘sctransform’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/sctransform/new/sctransform.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘glmGamPoi’

sdmApp

Version: 0.0.2
GitHub: https://github.com/Abson-dev/sdmApp
Source code: https://github.com/cran/sdmApp
Date/Publication: 2021-07-07 08:30:02 UTC
Number of recursive dependencies: 176

Run revdep_details(, "sdmApp") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘sp’ All declared Imports should be used.

sdmTMB

Version: 0.4.3
GitHub: https://github.com/pbs-assess/sdmTMB
Source code: https://github.com/cran/sdmTMB
Date/Publication: 2024-02-29 01:40:02 UTC
Number of recursive dependencies: 115

Run revdep_details(, "sdmTMB") for more info

checking installed package size ... NOTE installed size is 105.4Mb sub-directories of 1Mb or more: libs 103.7Mb

semidist

Version: 0.1.0
GitHub: https://github.com/wzhong41/semidist
Source code: https://github.com/cran/semidist
Date/Publication: 2023-11-21 06:50:02 UTC
Number of recursive dependencies: 44

Run revdep_details(, "semidist") for more info

checking whether package ‘semidist’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/semidist/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/semidist/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/semidist/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/semidist/new/semidist.Rcheck/00install.out’ for details.

sentopics

Version: 0.7.2
GitHub: https://github.com/odelmarcelle/sentopics
Source code: https://github.com/cran/sentopics
Date/Publication: 2023-05-28 09:50:02 UTC
Number of recursive dependencies: 173

Run revdep_details(, "sentopics") for more info

checking whether package ‘sentopics’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/sentopics/new/sentopics.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: data 1.2Mb libs 6.2Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘lexicon’
checking data for non-ASCII characters ... NOTE Note: found 3128 marked UTF-8 strings

Seurat

Version: 5.0.2
GitHub: https://github.com/satijalab/seurat
Source code: https://github.com/cran/Seurat
Date/Publication: 2024-02-29 00:20:08 UTC
Number of recursive dependencies: 266

Run revdep_details(, "Seurat") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'BPCells', 'presto'
checking installed package size ... NOTE installed size is 16.0Mb sub-directories of 1Mb or more: R 1.7Mb libs 13.5Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Signac’

SeuratObject

Version: 5.0.1
GitHub: https://github.com/mojaveazure/seurat-object
Source code: https://github.com/cran/SeuratObject
Date/Publication: 2023-11-17 22:40:16 UTC
Number of recursive dependencies: 103

Run revdep_details(, "SeuratObject") for more info

checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘BPCells’

Package which this enhances but not available for checking: ‘Seurat’ ```
checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: R 1.5Mb libs 3.2Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘plotly’

sharp

Version: 1.4.6
GitHub: https://github.com/barbarabodinier/sharp
Source code: https://github.com/cran/sharp
Date/Publication: 2024-02-03 17:30:02 UTC
Number of recursive dependencies: 157

Run revdep_details(, "sharp") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rCOSA’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘rCOSA’

shiny

Version: 1.8.0
GitHub: https://github.com/rstudio/shiny
Source code: https://github.com/cran/shiny
Date/Publication: 2023-11-17 23:40:02 UTC
Number of recursive dependencies: 90

Run revdep_details(, "shiny") for more info

checking installed package size ... NOTE installed size is 11.4Mb sub-directories of 1Mb or more: R 1.4Mb www 8.9Mb

shiny.worker

Version: 0.0.1
GitHub: NA
Source code: https://github.com/cran/shiny.worker
Date/Publication: 2021-01-21 11:00:02 UTC
Number of recursive dependencies: 65

Run revdep_details(, "shiny.worker") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R6’ ‘shiny’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

shinybrms

Version: 1.8.0
GitHub: https://github.com/fweber144/shinybrms
Source code: https://github.com/cran/shinybrms
Date/Publication: 2022-08-05 22:50:07 UTC
Number of recursive dependencies: 149

Run revdep_details(, "shinybrms") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’

shinyML

Version: 1.0.1
GitHub: https://github.com/JeanBertinR/shinyML
Source code: https://github.com/cran/shinyML
Date/Publication: 2021-02-24 17:00:02 UTC
Number of recursive dependencies: 118

Run revdep_details(, "shinyML") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sigminer

Version: 2.3.0
GitHub: https://github.com/ShixiangWang/sigminer
Source code: https://github.com/cran/sigminer
Date/Publication: 2023-12-12 11:50:03 UTC
Number of recursive dependencies: 205

Run revdep_details(, "sigminer") for more info

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: help 1.7Mb libs 1.4Mb

Signac

Version: 1.12.0
GitHub: https://github.com/stuart-lab/signac
Source code: https://github.com/cran/Signac
Date/Publication: 2023-11-08 09:30:02 UTC
Number of recursive dependencies: 254

Run revdep_details(, "Signac") for more info

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: R 1.1Mb libs 2.9Mb

signeR

Version: 2.4.0
GitHub: https://github.com/TojalLab/signeR
Source code: https://github.com/cran/signeR
Date/Publication: 2023-10-24
Number of recursive dependencies: 244

Run revdep_details(, "signeR") for more info

checking whether package ‘signeR’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/signeR/new/signeR.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: R 1.2Mb doc 4.5Mb
checking R code for possible problems ... NOTE covariate: no visible binding for global variable ‘.’ explorepage: no visible binding for global variable ‘.’ genCountMatrixFromMAF: no visible binding for global variable ‘Variant_Type’ genCountMatrixFromMAF: no visible binding for global variable ‘Reference_Allele’ genCountMatrixFromMAF: no visible binding for global variable ‘Tumor_Seq_Allele2’ genCountMatrixFromMAF: no visible binding for global variable ‘Tumor_Seq_Allele1’ ... ExposureCorrelation,SignExp-numeric: no visible binding for global variable ‘exposure’ ExposureCorrelation,matrix-numeric: no visible binding for global variable ‘Feature’ ExposureCorrelation,matrix-numeric: no visible binding for global variable ‘exposure’ Undefined global functions or variables: . Col Feature Frequency Reference_Allele Row Samples Signatures Tumor_Seq_Allele1 Tumor_Seq_Allele2 Variant_Type alt<- exposure fc project sig sig_test
checking Rd files ... NOTE prepare_Rd: cosmic_data.Rd:91-93: Dropping empty section \details prepare_Rd: cosmic_data.Rd:98-100: Dropping empty section \references prepare_Rd: cosmic_data.Rd:101-102: Dropping empty section \examples prepare_Rd: tcga_similarities.Rd:96-98: Dropping empty section \details prepare_Rd: tcga_similarities.Rd:99-101: Dropping empty section \source prepare_Rd: tcga_similarities.Rd:102-104: Dropping empty section \references prepare_Rd: tcga_similarities.Rd:105-106: Dropping empty section \examples prepare_Rd: tcga_tumors.Rd:18-20: Dropping empty section \details prepare_Rd: tcga_tumors.Rd:21-23: Dropping empty section \source prepare_Rd: tcga_tumors.Rd:24-26: Dropping empty section \references prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples

SimDesign

Version: 2.14
GitHub: https://github.com/philchalmers/SimDesign
Source code: https://github.com/cran/SimDesign
Date/Publication: 2024-01-09 09:10:11 UTC
Number of recursive dependencies: 124

Run revdep_details(, "SimDesign") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘doMPI’
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: doc 5.2Mb

sits

Version: 1.4.2-1
GitHub: https://github.com/e-sensing/sits
Source code: https://github.com/cran/sits
Date/Publication: 2023-11-02 15:10:02 UTC
Number of recursive dependencies: 221

Run revdep_details(, "sits") for more info

checking whether package ‘sits’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/sits/new/sits.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 13.2Mb sub-directories of 1Mb or more: R 1.1Mb extdata 1.5Mb libs 9.9Mb

skpr

Version: 1.6.2
GitHub: https://github.com/tylermorganwall/skpr
Source code: https://github.com/cran/skpr
Date/Publication: 2024-02-06 19:50:02 UTC
Number of recursive dependencies: 149

Run revdep_details(, "skpr") for more info

checking installed package size ... NOTE installed size is 63.3Mb sub-directories of 1Mb or more: libs 62.8Mb

SmCCNet

Version: 2.0.2
GitHub: https://github.com/KechrisLab/SmCCNet
Source code: https://github.com/cran/SmCCNet
Date/Publication: 2024-01-13 21:50:17 UTC
Number of recursive dependencies: 162

Run revdep_details(, "SmCCNet") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ using rmarkdown ! kpathsea: Running mktexfmt xelatex.fmt

Error: processing vignette 'SmCCNet_Vignette_AutoSmCCNet.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_AutoSmCCNet.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_AutoSmCCNet.log for more info. --- failed re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’

--- re-building ‘SmCCNet_Vignette_MultiOmics.Rmd’ using rmarkdown ! kpathsea: Running mktexfmt xelatex.fmt ... Error: processing vignette 'SmCCNet_Vignette_SingleOmics.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/globals/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_SingleOmics.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_SingleOmics.log for more info. --- failed re-building ‘SmCCNet_Vignette_SingleOmics.Rmd’

SUMMARY: processing the following files failed: ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ ‘SmCCNet_Vignette_MultiOmics.Rmd’ ‘SmCCNet_Vignette_SingleOmics.Rmd’

Error: Vignette re-building failed. Execution halted ```

smoots

Version: 1.1.4
GitHub: NA
Source code: https://github.com/cran/smoots
Date/Publication: 2023-09-11 08:50:02 UTC
Number of recursive dependencies: 76

Run revdep_details(, "smoots") for more info

checking whether package ‘smoots’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/smoots/new/smoots.Rcheck/00install.out’ for details.

solitude

Version: 1.1.3
GitHub: https://github.com/talegari/solitude
Source code: https://github.com/cran/solitude
Date/Publication: 2021-07-29 20:00:02 UTC
Number of recursive dependencies: 131

Run revdep_details(, "solitude") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R6’ ‘lgr’ All declared Imports should be used.

SpaDES.core

Version: 2.0.3
GitHub: https://github.com/PredictiveEcology/SpaDES.core
Source code: https://github.com/cran/SpaDES.core
Date/Publication: 2023-11-10 10:20:02 UTC
Number of recursive dependencies: 136

Run revdep_details(, "SpaDES.core") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘NLMR’
checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: R 4.7Mb

spaMM

Version: 4.4.16
GitHub: NA
Source code: https://github.com/cran/spaMM
Date/Publication: 2023-12-20 13:50:02 UTC
Number of recursive dependencies: 102

Run revdep_details(, "spaMM") for more info

checking package dependencies ... NOTE ``` Packages suggested but not available for checking: 'Infusion', 'blackbox'

Packages which this enhances but not available for checking: 'multcomp', 'RLRsim', 'lmerTest' ```
checking installed package size ... NOTE installed size is 56.9Mb sub-directories of 1Mb or more: R 2.7Mb libs 52.9Mb

sparkavro

Version: 0.3.0
GitHub: https://github.com/chezou/sparkavro
Source code: https://github.com/cran/sparkavro
Date/Publication: 2020-01-10 04:40:02 UTC
Number of recursive dependencies: 57

Run revdep_details(, "sparkavro") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sparkbq

Version: 0.1.1
GitHub: https://github.com/miraisolutions/sparkbq
Source code: https://github.com/cran/sparkbq
Date/Publication: 2019-12-18 18:00:02 UTC
Number of recursive dependencies: 40

Run revdep_details(, "sparkbq") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sparkhail

Version: 0.1.1
GitHub: NA
Source code: https://github.com/cran/sparkhail
Date/Publication: 2019-12-23 17:50:02 UTC
Number of recursive dependencies: 83

Run revdep_details(, "sparkhail") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sparklyr

Version: 1.8.4
GitHub: https://github.com/sparklyr/sparklyr
Source code: https://github.com/cran/sparklyr
Date/Publication: 2023-10-30 08:20:05 UTC
Number of recursive dependencies: 116

Run revdep_details(, "sparklyr") for more info

checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: R 1.6Mb java 3.8Mb

sparktf

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/sparktf
Date/Publication: 2019-03-05 14:30:03 UTC
Number of recursive dependencies: 57

Run revdep_details(, "sparktf") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sparkwarc

Version: 0.1.6
GitHub: https://github.com/r-spark/sparkwarc
Source code: https://github.com/cran/sparkwarc
Date/Publication: 2022-01-11 08:50:02 UTC
Number of recursive dependencies: 41

Run revdep_details(, "sparkwarc") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

sparkxgb

Version: 0.1.1
GitHub: NA
Source code: https://github.com/cran/sparkxgb
Date/Publication: 2021-02-23 10:20:02 UTC
Number of recursive dependencies: 58

Run revdep_details(, "sparkxgb") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

sparrpowR

Version: 0.2.8
GitHub: https://github.com/machiela-lab/sparrpowR
Source code: https://github.com/cran/sparrpowR
Date/Publication: 2024-01-23 15:20:02 UTC
Number of recursive dependencies: 130

Run revdep_details(, "sparrpowR") for more info

checking whether package ‘sparrpowR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/globals/revdep/checks/sparrpowR/new/sparrpowR.Rcheck/00install.out’ for details.

SPARSEMODr

Version: 1.2.0
GitHub: https://github.com/NAU-CCL/SPARSEMODr
Source code: https://github.com/cran/SPARSEMODr
Date/Publication: 2022-07-19 20:50:02 UTC
Number of recursive dependencies: 127

Run revdep_details(, "SPARSEMODr") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’ All declared Imports should be used.

spatialwarnings

Version: 3.0.3
GitHub: https://github.com/spatial-ews/spatialwarnings
Source code: https://github.com/cran/spatialwarnings
Date/Publication: 2022-03-21 13:00:02 UTC
Number of recursive dependencies: 97

Run revdep_details(, "spatialwarnings") for more info

checking whether package ‘spatialwarnings’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/spatialwarnings/new/spatialwarnings.Rcheck/00install.out’ for details.
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'indictest.Rd': ‘mgcv’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: libs 6.0Mb

sphunif

Version: 1.3.0
GitHub: https://github.com/egarpor/sphunif
Source code: https://github.com/cran/sphunif
Date/Publication: 2023-12-04 19:50:02 UTC
Number of recursive dependencies: 77

Run revdep_details(, "sphunif") for more info

checking whether package ‘sphunif’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/sphunif/new/sphunif.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 24.7Mb sub-directories of 1Mb or more: libs 23.7Mb
checking data for non-ASCII characters ... NOTE Note: found 189 marked UTF-8 strings

spNetwork

Version: 0.4.3.8
GitHub: https://github.com/JeremyGelb/spNetwork
Source code: https://github.com/cran/spNetwork
Date/Publication: 2023-08-24 11:20:05 UTC
Number of recursive dependencies: 146

Run revdep_details(, "spNetwork") for more info

checking whether package ‘spNetwork’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/spNetwork/new/spNetwork.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 25.5Mb sub-directories of 1Mb or more: doc 1.0Mb extdata 2.6Mb libs 20.5Mb

squat

Version: 0.3.0
GitHub: https://github.com/LMJL-Alea/squat
Source code: https://github.com/cran/squat
Date/Publication: 2024-01-10 15:40:02 UTC
Number of recursive dependencies: 143

Run revdep_details(, "squat") for more info

checking whether package ‘squat’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/squat/new/squat.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 20.4Mb sub-directories of 1Mb or more: data 1.1Mb help 1.1Mb libs 18.0Mb

sRACIPE

Version: 1.18.0
GitHub: https://github.com/vivekkohar/sRACIPE
Source code: https://github.com/cran/sRACIPE
Date/Publication: 2023-10-24
Number of recursive dependencies: 104

Run revdep_details(, "sRACIPE") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking R code for possible problems ... NOTE sracipeSimulate: no visible global function definition for ‘registerDoFuture’ sracipeSimulate: no visible global function definition for ‘plan’ sracipeSimulate: no visible global function definition for ‘%dopar%’ sracipeSimulate: no visible global function definition for ‘foreach’ sracipeSimulate: no visible binding for global variable ‘configurationTmp’ sracipeSimulate: no visible binding for global variable ‘outFileGETmp’ sracipeSimulate: no visible binding for global variable ‘outFileParamsTmp’ sracipeSimulate: no visible binding for global variable ‘outFileICTmp’ Undefined global functions or variables: %dopar% configurationTmp foreach outFileGETmp outFileICTmp outFileParamsTmp plan registerDoFuture

ssdtools

Version: 1.0.6
GitHub: https://github.com/bcgov/ssdtools
Source code: https://github.com/cran/ssdtools
Date/Publication: 2023-09-07 14:10:02 UTC
Number of recursive dependencies: 120

Run revdep_details(, "ssdtools") for more info

checking installed package size ... NOTE installed size is 42.1Mb sub-directories of 1Mb or more: doc 1.2Mb libs 39.6Mb

SSLR

Version: 0.9.3.3
GitHub: NA
Source code: https://github.com/cran/SSLR
Date/Publication: 2021-07-22 08:10:07 UTC
Number of recursive dependencies: 228

Run revdep_details(, "SSLR") for more info

checking whether package ‘SSLR’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/SSLR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/SSLR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/SSLR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/SSLR/new/SSLR.Rcheck/00install.out’ for details.

stars

Version: 0.6-4
GitHub: https://github.com/r-spatial/stars
Source code: https://github.com/cran/stars
Date/Publication: 2023-09-11 11:50:02 UTC
Number of recursive dependencies: 164

Run revdep_details(, "stars") for more info

checking examples ...sh: line 1: 39344 Aborted (core dumped) LANGUAGE=en R_CHECK_INTERNALS2=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' ``` ERROR Running examples in ‘stars-Ex.R’ failed The error most likely occurred in:

Name: mdim

Title: Read or write data using GDAL's multidimensional array API

Aliases: mdim read_mdim write_mdim

** Examples

... dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no Bye... ```

checking examples ...sh: line 1: 39401 Aborted (core dumped) LANGUAGE=en R_CHECK_INTERNALS2=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' ``` ERROR Running examples in ‘stars-Ex.R’ failed The error most likely occurred in:

Name: mdim

Title: Read or write data using GDAL's multidimensional array API

Aliases: mdim read_mdim write_mdim

** Examples

... dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no Bye... ```

checking tests ... Running ‘aggregate.R’ Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4 < Linking to GEOS 3.11.2, GDAL 3.6.4, PROJ 8.2.1; sf_use_s2() is TRUE --- > Linking to GEOS 3.11.2, GDAL 3.6.2, PROJ 9.2.0; sf_use_s2() is TRUE Running ‘align.R’ Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK Running ‘area.R’ Comparing ‘area.Rout’ to ‘area.Rout.save’ ... OK Running ‘crop.R’ ... dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no Bye...
checking package dependencies ... NOTE Package suggested but not available for checking: ‘starsdata’
checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 2.4Mb nc 1.7Mb

startR

Version: 2.3.1
GitHub: NA
Source code: https://github.com/cran/startR
Date/Publication: 2023-12-21 16:20:02 UTC
Number of recursive dependencies: 60

Run revdep_details(, "startR") for more info

checking whether package ‘startR’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/globals/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details.

* installing *source* package ‘startR’ ...
** package ‘startR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘startR’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/startR/new/startR.Rcheck/startR’

* installing *source* package ‘startR’ ...
** package ‘startR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘ncdf4’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘startR’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/startR/old/startR.Rcheck/startR’

stppSim

Version: 1.3.2
GitHub: https://github.com/Manalytics/stppSim
Source code: https://github.com/cran/stppSim
Date/Publication: 2023-10-29 21:20:02 UTC
Number of recursive dependencies: 133

Run revdep_details(, "stppSim") for more info

checking whether package ‘stppSim’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/globals/revdep/checks/stppSim/new/stppSim.Rcheck/00install.out’ for details.

survstan

Version: 0.0.6.1
GitHub: https://github.com/fndemarqui/survstan
Source code: https://github.com/cran/survstan
Date/Publication: 2024-02-05 15:00:02 UTC
Number of recursive dependencies: 127

Run revdep_details(, "survstan") for more info

checking installed package size ... NOTE installed size is 88.9Mb sub-directories of 1Mb or more: libs 88.5Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

synergyfinder

Version: 3.10.3
GitHub: NA
Source code: https://github.com/cran/synergyfinder
Date/Publication: 2024-01-22
Number of recursive dependencies: 202

Run revdep_details(, "synergyfinder") for more info

checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘scales’ Namespaces in Imports field not imported from: ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’ All declared Imports should be used.
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: doc 5.7Mb
checking R code for possible problems ... NOTE .Extract2DrugPlotData: no visible binding for global variable ‘input_type’ .Extract2DrugPlotData: no visible binding for global variable ‘block_id’ .Extract2DrugPlotData: no visible binding for global variable ‘value’ .Extract2DrugPlotData: no visible binding for global variable ‘left’ .Extract2DrugPlotData: no visible binding for global variable ‘right’ .Extract2DrugPlotData: no visible binding for global variable ‘conc1’ .Extract2DrugPlotData: no visible binding for global variable ‘conc2’ .Extract2DrugPlotData: no visible binding for global variable ‘text’ ... response_CI95 response_mean response_origin response_origin_CI95 response_origin_mean response_origin_sd response_origin_sem response_sd response_sem right start synergy t.test text theta value x y Consider adding importFrom("grDevices", "dev.list", "dev.off") importFrom("graphics", "text") importFrom("stats", "end", "predict", "start", "t.test") importFrom("utils", "data", "head") to your NAMESPACE file.
checking Rd files ... NOTE checkRd: (-1) FitDoseResponse.Rd:55: Escaped LaTeX specials: \&

tableschema.r

Version: 1.1.2
GitHub: https://github.com/frictionlessdata/tableschema-r
Source code: https://github.com/cran/tableschema.r
Date/Publication: 2022-09-29 20:00:03 UTC
Number of recursive dependencies: 66

Run revdep_details(, "tableschema.r") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘parsedate’

targeted

Version: 0.5
GitHub: https://github.com/kkholst/targeted
Source code: https://github.com/cran/targeted
Date/Publication: 2024-02-22 10:00:21 UTC
Number of recursive dependencies: 98

Run revdep_details(, "targeted") for more info

checking whether package ‘targeted’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/targeted/new/targeted.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 22.4Mb sub-directories of 1Mb or more: doc 1.1Mb libs 20.9Mb

targets

Version: 1.5.1
GitHub: https://github.com/ropensci/targets
Source code: https://github.com/cran/targets
Date/Publication: 2024-02-15 11:50:02 UTC
Number of recursive dependencies: 166

Run revdep_details(, "targets") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘clustermq’

text

Version: 1.2.0
GitHub: https://github.com/OscarKjell/text
Source code: https://github.com/cran/text
Date/Publication: 2024-02-13 20:51:36 UTC
Number of recursive dependencies: 160

Run revdep_details(, "text") for more info

checking data for non-ASCII characters ... NOTE Note: found 3 marked UTF-8 strings

tglkmeans

Version: 0.5.4
GitHub: https://github.com/tanaylab/tglkmeans
Source code: https://github.com/cran/tglkmeans
Date/Publication: 2024-01-09 14:10:02 UTC
Number of recursive dependencies: 89

Run revdep_details(, "tglkmeans") for more info

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 5.0Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

tidyfit

Version: 0.7.0
GitHub: https://github.com/jpfitzinger/tidyfit
Source code: https://github.com/cran/tidyfit
Date/Publication: 2024-02-26 16:20:02 UTC
Number of recursive dependencies: 188

Run revdep_details(, "tidyfit") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘Accessing_Fitted_Model_Objects.Rmd’ using rmarkdown --- finished re-building ‘Accessing_Fitted_Model_Objects.Rmd’

--- re-building ‘Flowchart.Rmd’ using rmarkdown --- finished re-building ‘Flowchart.Rmd’

--- re-building ‘Predicting_Boston_House_Prices.Rmd’ using rmarkdown --- finished re-building ‘Predicting_Boston_House_Prices.Rmd’

... --- finished re-building ‘Rolling_Window_Time_Series_Regression.Rmd’

--- re-building ‘Time-varying_parameters_vs_rolling_windows.Rmd’ using knitr --- finished re-building ‘Time-varying_parameters_vs_rolling_windows.Rmd’

SUMMARY: processing the following file failed: ‘Feature_Selection.Rmd’

Error: Vignette re-building failed. Execution halted ```

tidysdm

Version: 0.9.4
GitHub: https://github.com/EvolEcolGroup/tidysdm
Source code: https://github.com/cran/tidysdm
Date/Publication: 2024-03-05 20:30:02 UTC
Number of recursive dependencies: 166

Run revdep_details(, "tidysdm") for more info

checking tests ... ``` Running ‘spelling.R’ Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/BATCH: line 60: 536 Aborted (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: Ranlib: ranlib

Languages:

... dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no Bye... ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: sh: line 1: 2729 Aborted (core dumped) '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --no-echo > '/scratch/henrik/RtmpgjEKuC/filea983a551478' 2>&1 < '/scratch/henrik/RtmpgjEKuC/filea983ad9357b' --- re-building ‘a0_tidysdm_overview.Rmd’ using rmarkdown Warning! HDF5 library version mismatched error The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related ... Bye... --- re-building ‘a3_troubleshooting.Rmd’ using rmarkdown --- finished re-building ‘a3_troubleshooting.Rmd’

SUMMARY: processing the following files failed: ‘a0_tidysdm_overview.Rmd’ ‘a1_palaeodata_application.Rmd’ ‘a2_tidymodels_additions.Rmd’

Error: Vignette re-building failed. Execution halted ```

timetk

Version: 2.9.0
GitHub: https://github.com/business-science/timetk
Source code: https://github.com/cran/timetk
Date/Publication: 2023-10-31 22:30:02 UTC
Number of recursive dependencies: 225

Run revdep_details(, "timetk") for more info

checking data for non-ASCII characters ... NOTE Note: found 2750 marked UTF-8 strings

TreeSearch

Version: 1.4.0
GitHub: https://github.com/ms609/TreeSearch
Source code: https://github.com/cran/TreeSearch
Date/Publication: 2023-08-26 04:50:02 UTC
Number of recursive dependencies: 126

Run revdep_details(, "TreeSearch") for more info

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: datasets 1.6Mb doc 1.2Mb libs 2.5Mb

TriDimRegression

Version: 1.0.2
GitHub: https://github.com/alexander-pastukhov/tridim-regression
Source code: https://github.com/cran/TriDimRegression
Date/Publication: 2023-09-13 14:10:03 UTC
Number of recursive dependencies: 100

Run revdep_details(, "TriDimRegression") for more info

checking whether package ‘TriDimRegression’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/globals/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details.

* installing *source* package ‘TriDimRegression’ ...
** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
** using staged installation
Error in loadNamespace(x) : there is no package called ‘rstantools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: configuration failed for package ‘TriDimRegression’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’

* installing *source* package ‘TriDimRegression’ ...
** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
** using staged installation
Error in loadNamespace(x) : there is no package called ‘rstantools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: configuration failed for package ‘TriDimRegression’
* removing ‘/c4/home/henrik/repositories/globals/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’

txshift

Version: 0.3.8
GitHub: https://github.com/nhejazi/txshift
Source code: https://github.com/cran/txshift
Date/Publication: 2022-02-09 22:30:02 UTC
Number of recursive dependencies: 113

Run revdep_details(, "txshift") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘sl3’

UCSCXenaShiny

Version: 1.1.10
GitHub: https://github.com/openbiox/UCSCXenaShiny
Source code: https://github.com/cran/UCSCXenaShiny
Date/Publication: 2023-02-28 15:32:34 UTC
Number of recursive dependencies: 193

Run revdep_details(, "UCSCXenaShiny") for more info

checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: doc 1.4Mb shinyapp 3.3Mb

updog

Version: 2.1.5
GitHub: https://github.com/dcgerard/updog
Source code: https://github.com/cran/updog
Date/Publication: 2023-11-29 15:50:02 UTC
Number of recursive dependencies: 151

Run revdep_details(, "updog") for more info

checking whether package ‘updog’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/updog/new/updog.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: libs 7.3Mb

variantspark

Version: 0.1.1
GitHub: NA
Source code: https://github.com/cran/variantspark
Date/Publication: 2019-06-13 16:20:03 UTC
Number of recursive dependencies: 57

Run revdep_details(, "variantspark") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

viewpoly

Version: 0.3.2
GitHub: https://github.com/mmollina/viewpoly
Source code: https://github.com/cran/viewpoly
Date/Publication: 2022-11-01 17:30:12 UTC
Number of recursive dependencies: 155

Run revdep_details(, "viewpoly") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 5. │ └─shinydashboard:::tagAssert(body, type = "div", class = "content-wrapper") 6. ├─shinydashboard::dashboardBody(...) 7. │ ├─htmltools::div(...) 8. │ │ └─rlang::dots_list(...) 9. │ └─tags$section(class = "content", ...)
1. │ └─rlang::dots_list(...) ... [ FAIL 1 | WARN 3 | SKIP 2 | PASS 27 ] Deleting unused snapshots: • tetra_example/effects-bar.svg • tetra_example/effects-circle.svg • tetra_example/effects-digenic.svg • tetra_example/linkage-map-draw-names.svg • tetra_example/plot-map-list.svg • tetra_example/qtl-plot.svg Error: Test failures Execution halted ```

vip

Version: 0.4.1
GitHub: https://github.com/koalaverse/vip
Source code: https://github.com/cran/vip
Date/Publication: 2023-08-21 09:20:02 UTC
Number of recursive dependencies: 105

Run revdep_details(, "vip") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'C50', 'caret', 'Cubist', 'earth', 'gbm', 'glmnet', 'h2o', 'lightgbm', 'mixOmics', 'mlr', 'mlr3', 'neuralnet', 'parsnip', 'partykit', 'pls', 'randomForest', 'ranger', 'rpart', 'RSNNS', 'sparklyr', 'tidymodels', 'workflows', 'xgboost'
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘randomForest’, ‘glmnet’, ‘C50’, ‘Cubist’, ‘caret’, ‘partykit’, ‘earth’, ‘gbm’, ‘h2o’, ‘sparklyr’, ‘ranger’, ‘rpart’, ‘xgboost’, ‘lightgbm’

vmeasur

Version: 0.1.4
GitHub: NA
Source code: https://github.com/cran/vmeasur
Date/Publication: 2021-11-11 19:00:02 UTC
Number of recursive dependencies: 119

Run revdep_details(, "vmeasur") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

WeightedCluster

Version: 1.6-4
GitHub: NA
Source code: https://github.com/cran/WeightedCluster
Date/Publication: 2023-07-07 07:50:02 UTC
Number of recursive dependencies: 43

Run revdep_details(, "WeightedCluster") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘WeightedCluster.Rnw’ using knitr --- finished re-building ‘WeightedCluster.Rnw’

--- re-building ‘WeightedClusterFR.Rnw’ using knitr --- finished re-building ‘WeightedClusterFR.Rnw’

--- re-building ‘WeightedClusterPreview.Rnw’ using knitr Error: processing vignette 'WeightedClusterPreview.Rnw' failed with diagnostics: Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed. ... l.85 \usepackage {tikz}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘WeightedClusterPreview.Rnw’

SUMMARY: processing the following file failed: ‘WeightedClusterPreview.Rnw’

Error: Vignette re-building failed. Execution halted ```

wru

Version: 3.0.1
GitHub: https://github.com/kosukeimai/wru
Source code: https://github.com/cran/wru
Date/Publication: 2024-02-28 04:20:02 UTC
Number of recursive dependencies: 96

Run revdep_details(, "wru") for more info

checking whether package ‘wru’ can be installed ... WARNING Found the following significant warnings: /c4/home/henrik/repositories/globals/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] /c4/home/henrik/repositories/globals/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] See ‘/c4/home/henrik/repositories/globals/revdep/checks/wru/new/wru.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: data 3.5Mb help 1.9Mb libs 2.0Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘future’ ‘tidyr’ All declared Imports should be used.

XNAString

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/XNAString
Date/Publication: 2023-10-24
Number of recursive dependencies: 106

Run revdep_details(, "XNAString") for more info

checking compiled code ... WARNING ``` File ‘XNAString/libs/XNAString.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘./ViennaRNA/utils/utils.o’ Found ‘sprintf’, possibly from ‘sprintf’ (C) Objects: ‘./ViennaRNA/part_func_up.o’, ‘./ViennaRNA/RNAstruct.o’, ‘./ViennaRNA/model.o’ Found ‘srand’, possibly from ‘srand’ (C) Object: ‘./ViennaRNA/utils/utils.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 11.2Mb sub-directories of 1Mb or more: doc 1.0Mb libs 9.5Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.

HenrikBengtsson/globals documentation built on March 12, 2024, 12:30 p.m.

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HenrikBengtsson/globals Identify Global Objects in R Expressions

revdep/problems.md In HenrikBengtsson/globals: Identify Global Objects in R Expressions

agcounts

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AIPW

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AlpsNMR

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altdoc

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amapGeocode

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aroma.core

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BAMBI

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bamm

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batchtools

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bayesmove

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BEKKs

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bigDM

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bistablehistory

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blavaan

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BPrinStratTTE

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Installation

Devel

CRAN

brms

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broom.mixed

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bsitar

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ceRNAnetsim

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Name: find_node_perturbation

Title: Calculates average expression changes of all (or specified)

nodes except trigger and finds the perturbed node count for all (or

specified) nodes in system.

Aliases: find_node_perturbation

** Examples

cft

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Installation

Devel

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ChromSCape

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clickR

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clustermq

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codebook

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collinear

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colocr

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corporaexplorer

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cSEM

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CSGo

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cuda.ml

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cytomapper

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deseats

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dipsaus

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HenrikBengtsson/globals
Identify Global Objects in R Expressions

revdep/problems.md
In HenrikBengtsson/globals: Identify Global Objects in R Expressions