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Rdatatable / data.table

R's data.table package extends data.frame:
http://r-datatable.com
Mozilla Public License 2.0
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revdep results #2779

Closed HughParsonage closed 6 years ago

HughParsonage commented 6 years ago

Setup

Runtime: about 7 hrs. Most of the warnings are due to me not updating R to 3.4.4, rather than significant warnings. May filter later, but wanted to save in case I lost.

Platform |setting |value | |:--------|:----------------------------| |version |R version 3.4.3 (2017-11-30) | |system |x86_64, mingw32 | |ui |RStudio (1.1.423) | |language |(EN) | |collate |English_Australia.1252 | |tz |Australia/Sydney | |date |2018-04-21 |
Packages |package |* |version |date |source | |:----------|:--|:-------|:----------|:--------------------------------| |bit64 |* |0.9-7 |2017-05-08 |CRAN (R 3.4.1) | |chron |* |2.3-52 |2018-01-06 |CRAN (R 3.4.4) | |curl | |3.2 |2018-03-28 |CRAN (R 3.4.4) | |data.table |* |1.10.5 |2018-04-21 |local (Rdatatable/data.table@NA) | |knitr | |1.20 |2018-02-20 |CRAN (R 3.4.4) | |reshape2 | |1.4.3 |2017-12-11 |CRAN (R 3.4.3) | |testthat | |2.0.0 |2017-12-13 |CRAN (R 3.4.3) | |xts |* |0.10-2 |2018-03-14 |CRAN (R 3.4.4) | |zoo |* |1.8-1 |2018-01-08 |CRAN (R 3.4.4) |
Check results 148 packages with problems |package |version | errors| warnings| notes| |:------------------|:----------|------:|--------:|-----:| |annovarR |1.0.0 | 1| 0| 1| |antaresProcessing |0.15.1 | 0| 1| 1| |BatchExperiments |1.4.2 | 1| 1| 0| |BatchJobs |1.7 | 0| 1| 0| |BGData |1.0.0 | 0| 1| 0| |biomartr |0.7.0 | 1| 0| 0| |brainGraph |2.0.2 | 1| 0| 0| |bupaR |0.4.0 | 0| 1| 0| |BuyseTest |1.0 | 0| 1| 1| |Causata |4.2-0 | 0| 1| 4| |cdparcoord |1.0.0 | 0| 1| 0| |cffdrs |1.7.6 | 0| 1| 0| |classifierplots |1.3.3 | 0| 1| 0| |clickstream |1.3.0 | 0| 1| 0| |corpustools |0.3.3 | 0| 1| 1| |corregp |2.0.2 | 0| 1| 0| |ctmm |0.4.1 | 0| 1| 0| |cvAUC |1.1.0 | 0| 1| 1| |dartR |1.0 | 1| 0| 0| |dat |0.4.0 | 0| 1| 0| |dataPreparation |0.3.5 | 0| 1| 0| |DCD |0.1.0 | 1| 0| 0| |dfmeta |1.0.0 | 0| 1| 0| |dgo |0.2.14 | 0| 1| 0| |DGVM3D |1.0.0 | 0| 1| 0| |Diderot |0.12 | 0| 1| 0| |difconet |1.0-4 | 0| 1| 0| |drgee |1.1.6 | 0| 1| 1| |dynamichazard |0.5.1 | 1| 0| 2| |easycsv |1.0.7 | 1| 0| 0| |eclust |0.1.0 | 1| 1| 2| |edgeRun |1.0.9 | 1| 0| 0| |EdSurvey |1.0.6 | 0| 1| 0| |eeptools |1.1.1 | 0| 1| 0| |eiCompare |2.1 | 0| 1| 0| |EthSEQ |2.1.2 | 1| 0| 0| |EurosarcBayes |1.1 | 0| 1| 0| |EventStudy |0.34 | 0| 1| 1| |expss |0.8.6 | 2| 1| 0| |fdq |0.2 | 0| 1| 0| |FedData |2.5.2 | 0| 1| 0| |Fgmutils |0.9.4 | 0| 1| 0| |flippant |1.1.0 | 0| 1| 0| |fst |0.8.4 | 1| 0| 1| |genBart |1.0.1 | 1| 0| 0| |GenomicTools |0.2.6 | 1| 0| 0| |GGIR |1.5-18 | 1| 0| 1| |ggswissmaps |0.1.1 | 0| 1| 0| |greport |0.7-1 | 0| 1| 1| |hisse |1.8.5 | 1| 0| 0| |Hmisc |4.1-1 | 0| 1| 1| |hoardeR |0.9.2 | 1| 0| 0| |hypervolume |2.0.8 | 0| 1| 1| |iml |0.3.0 | 2| 0| 0| |installr |0.19.0 | 0| 1| 0| |inTrees |1.2 | 0| 1| 0| |ITGM |0.6 | 0| 1| 0| |itsadug |2.3 | 0| 1| 0| |JWileymisc |0.2.1 | 0| 1| 0| |kangar00 |1.1 | 1| 0| 0| |KRIG |0.1.0 | 1| 0| 0| |LabourMarketAreas |3.2 | 0| 1| 0| |lava |1.6.1 | 1| 0| 1| |lavaSearch2 |1.3.3 | 0| 1| 0| |LSPFP |1.0.0 | 0| 1| 0| |MetamapsDB |0.0.2 | 1| 0| 0| |metaMix |0.2 | 1| 0| 0| |mlr |2.12.1 | 1| 1| 1| |mlrMBO |1.1.1 | 0| 1| 1| |MODIStsp |1.3.3.1 | 1| 0| 0| |MultiABEL |1.1-6 | 0| 1| 1| |NetLogoR |0.3.2 | 0| 1| 1| |networkR |0.1.0-0 | 0| 1| 1| |nlmixr |0.9.0-3 | 0| 1| 1| |NNS |0.3.8.6 | 0| 1| 0| |openEBGM |0.5.0 | 0| 1| 0| |OpenML |1.8 | 0| 1| 0| |openSTARS |1.0.0 | 0| 1| 0| |optiSel |2.0 | 0| 1| 1| |orgR |0.9.0 | 0| 1| 0| |padr |0.4.0 | 1| 0| 1| |partialCI |1.1.1 | 0| 1| 1| |partools |1.1.6 | 0| 1| 0| |pcrsim |1.0.2 | 1| 0| 0| |petro.One |0.1.3 | 1| 0| 0| |PhenotypeSimulator |0.2.0 | 1| 0| 0| |pkggraph |0.2.2 | 0| 1| 0| |plotly |4.7.1 | 0| 1| 0| |popEpi |0.4.4 | 2| 1| 0| |PopGenReport |3.0.0 | 0| 1| 0| |prioritizr |3.0.4 | 0| 1| 2| |ProFound |1.0.1 | 1| 1| 0| |Publish |2018.04.17 | 0| 1| 0| |quickPlot |0.1.3 | 1| 0| 1| |RAM |1.2.1.3 | 0| 1| 2| |rangeMapper |0.3-1 | 0| 1| 0| |RAPIDR |0.1.1 | 1| 0| 0| |Rblpapi |0.3.8 | 1| 0| 0| |readtext |0.50 | 1| 0| 0| |RecordLinkage |0.4-10 | 0| 1| 2| |REIDS |0.0.2 | 1| 0| 0| |reinsureR |0.1.0 | 0| 1| 0| |rGoodData |0.1.1 | 0| 1| 0| |riskRegression |2018.04.21 | 0| 1| 1| |RndTexExams |1.4.1 | 0| 1| 0| |Rnets |0.9.8 | 0| 1| 0| |RNewsflow |1.0.1 | 0| 1| 0| |robCompositions |2.0.7 | 0| 1| 1| |RSauceLabs |0.1.6 | 0| 1| 0| |rstanarm |2.17.4 | 2| 1| 3| |rtop |0.5-14 | 0| 1| 1| |SafeQuant |2.3.1 | 1| 0| 0| |sdcMicro |5.2.0 | 2| 0| 1| |sdcTable |0.22.8 | 1| 0| 0| |SDLfilter |1.0.0 | 0| 1| 0| |seleniumPipes |0.3.7 | 0| 1| 0| |sentometrics |0.3.5 | 0| 1| 1| |simPop |1.1.0 | 0| 1| 1| |SIRItoGTFS |0.2.2 | 1| 0| 0| |sitree |0.1-2 | 0| 1| 0| |socialmixr |0.1.2 | 1| 0| 0| |sommer |3.4 | 0| 1| 0| |SpaDES.core |0.1.1 | 1| 2| 0| |sparseFLMM |0.2.2 | 0| 1| 0| |speaq |2.3.1 | 1| 0| 0| |splitstackshape |1.4.4 | 1| 0| 0| |strataG |2.0.2 | 0| 1| 1| |strvalidator |2.0.0 | 1| 0| 0| |surveyplanning |2.9 | 0| 1| 0| |SWMPr |2.3.0 | 0| 1| 0| |synthACS |1.0.1 | 0| 1| 1| |tcR |2.2.1.11 | 0| 1| 4| |teachingApps |1.0.2 | 0| 1| 1| |textTinyR |1.1.0 | 0| 1| 1| |trelliscope |0.9.8 | 0| 1| 0| |tRophicPosition |0.7.5 | 1| 1| 0| |tstools |0.3.6 | 1| 1| 0| |validateRS |1.0.0 | 0| 1| 0| |vardpoor |0.9.11 | 0| 1| 0| |VIM |4.7.0 | 0| 1| 1| |wally |1.0.9 | 0| 1| 0| |winRatioAnalysis |0.1.0 | 0| 1| 0| |word.alignment |1.0.9 | 0| 1| 0| |xgboost |0.6.4.1 | 0| 1| 1| |yCrypticRNAs |0.99.2 | 1| 0| 0|
Log ## BatchExperiments (1.4.2) Maintainer: Michel Lang Bug reports: https://github.com/tudo-r/BatchExperiments/issues 1 error | 1 warning | 0 notes ``` checking tests ... ERROR Running 'run-all.R' [31s] Running the tests in 'tests/run-all.R' failed. Last 13 lines of output: 5: checkDir(fun.dir, create = TRUE, check.empty = TRUE) 6: stopf("Directory '%s' is not readable/writable!", path) == testthat results ====================================================================================== OK: 930 SKIPPED: 0 FAILED: 4 1. Error: reduceResultsExperimentsParallel (@test_reduceResultsExperimentsParallel.R#13) 2. Error: reduceResultsExperimentsParallel works with default fun (@test_reduceResultsExperimentsParallel.R#107) 3. Error: reduceResultsExperimentsParallel works with ids (@test_reduceResultsExperimentsParallel.R#155) 4. Error: reduceResultsExperimentsParallel applies on missing results (@test_reduceResultsExperimentsParallel.R#169) Error: testthat unit tests failed In addition: Warning messages: 1: package 'BatchJobs' was built under R version 3.4.4 2: package 'BBmisc' was built under R version 3.4.4 Execution halted checking whether package 'BatchExperiments' can be installed ... WARNING Found the following significant warnings: Warning: package 'BatchJobs' was built under R version 3.4.4 Warning: package 'BBmisc' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/BatchExperiments.Rcheck/00install.out' for details. ``` ## ctmm (0.4.1) Maintainer: Christen H. Fleming 0 errors | 1 warning | 0 notes ``` checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 198-210 (variogram.Rmd) Error: processing vignette 'variogram.Rmd' failed with diagnostics: do not know how to convert 'object$timestamp' to class "POSIXct" Execution halted ``` ## dynamichazard (0.5.1) Maintainer: Benjamin Christoffersen Bug reports: https://github.com/boennecd/dynamichazard/issues 1 error | 0 warnings | 2 notes ``` checking tests ... ERROR Running 'testthat.R' [33s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: [34m19. Testing util functions to sim series for tests[39m (@test_test_utils.R#28) - On CRAN == Warnings =============================================================================================== [34m1. Shiny app starts when no arguments are passed[39m (@test_shiny_app.R#6) - package 'shiny' was built under R version 3.4.4 == Failed ================================================================================================= [31m--[39m [31m1. Failure: Posterior gives previous found results with large by length for pbc data with logit (@test_S[39m `f1` not equal to read_to_test("posterior_approx_logit_pbc_large_by"). Component "state_vecs": Mean relative difference: 1.306469e-07 Component "state_vecs": Mean relative difference: 1.306469e-07 == DONE =================================================================================================== Error: Test failures Execution halted checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: data 4.2Mb doc 1.2Mb libs 1.9Mb checking compiled code ... NOTE File 'dynamichazard/libs/x64/dynamichazard.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## easycsv (1.0.7) Maintainer: Dror Bogin Bug reports: https://github.com/bogind/easycsv/issues 1 error | 0 warnings | 0 notes ``` checking examples ... ERROR Running examples in 'easycsv-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fread_folder > ### Title: read multiple csv files into named data frames > ### Aliases: fread_folder > ### Keywords: ~utilities ~misc > > ### ** Examples > > require(easycsv) > require("data.table") > directory = getwd() > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table1.csv")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table2.csv")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table3.txt")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table4.txt")) > fread_folder(directory, extension = "BOTH") Error: isTrueFalse(showProgress) is not TRUE Execution halted ``` ## eclust (0.1.0) Maintainer: Sahir Rai Bhatnagar Bug reports: https://github.com/sahirbhatnagar/eclust/issues 1 error | 1 warning | 2 notes ``` checking examples ... ERROR Running examples in 'eclust-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: s_generate_data > ### Title: Generate linear response data and test and training sets for > ### simulation study > ### Aliases: s_generate_data > ... 18 lines ... + minCor = 0.01, + maxCor = 1, + corPower = 1, + propNegativeCor = 0.3, + backgroundNoise = 0.5, + signed = FALSE, + leaveOut = 1:4) Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'GO.db' Calls: s_modules ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... See example usage at http://sahirbhatnagar.com/eclust/ Quitting from lines 142-168 (eclust.Rmd) Error: processing vignette 'eclust.Rmd' failed with diagnostics: there is no package called 'GO.db' Execution halted checking package dependencies ... NOTE Package suggested but not available for checking: 'ComplexHeatmap' checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: 'ComplexHeatmap' ``` ## expss (0.8.6) Maintainer: Gregory Demin Bug reports: https://github.com/gdemin/expss/issues 2 errors | 1 warning | 0 notes ``` checking examples ... ERROR Running examples in 'expss-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: add_rows > ### Title: Add rows to data.frame/matrix/table > ### Aliases: add_rows add_rows.data.frame %add_rows% .add_rows > > ### ** Examples ... 56 lines ... + am = "Transmission (0 = automatic, 1 = manual)", + am = c(automatic = 0, manual = 1), + gear = "Number of forward gears", + carb = "Number of carburetors" + ) > > tbl_mean = calculate(mtcars, cro_mean(cyl, am)) Error in `[.data.table`(wide_datable, , `:=`(row_labels, paste0(..row_var__, : ..row_var__ in j is looking for row_var__ in calling scope, but a column '..row_var__' exists. Column names should not start with .. Calls: calculate ... FUN -> lapply -> FUN -> format_table -> [ -> [.data.table Execution halted checking tests ... ERROR Running 'testthat.R' [22s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: == testthat results ====================================================================================== OK: 2119 SKIPPED: 1 FAILED: 64 1. Error: (unknown) (@test_add_rows.R#116) 2. Error: (unknown) (@test_cro_fun_df_extended.R#27) 3. Error: (unknown) (@test_cro_fun_extended.R#49) 4. Error: (unknown) (@test_custom_tables.R#25) 5. Error: (unknown) (@test_custom_tables_sig.R#174) 6. Failure: (unknown) (@test_dichotomy.R#192) 7. Error: (unknown) (@test_fre.R#301) 8. Error: (unknown) (@test_htmlTable.R#47) 9. Error: (unknown) (@test_merge.R#181) 1. ... Error: testthat unit tests failed Execution halted checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 79-138 (tables-with-labels.Rmd) Error: processing vignette 'tables-with-labels.Rmd' failed with diagnostics: ..row_var__ in j is looking for row_var__ in calling scope, but a column '..row_var__' exists. Column names should not start with .. Execution halted ``` ## fst (0.8.4) Maintainer: Mark Klik Bug reports: https://github.com/fstpackage/fst/issues 1 error | 0 warnings | 1 note ``` checking tests ... ERROR Running 'testthat.R' [19s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: [31m--[39m [31m5. Failure: preserves time of day (@test_roundtrip.R#95) [39m [31m----------------------------------------------[39m `res` not identical to `x`. target is NULL, current is ITime == testthat results ====================================================================================== OK: 299 SKIPPED: 0 FAILED: 5 1. Error: (unknown) (@test_fst.R#5) 2. Error: (unknown) (@test_meta.R#5) 3. Error: (unknown) (@test_nanotime.R#4) 4. Failure: preserves time of day (@test_roundtrip.R#91) 5. Failure: preserves time of day (@test_roundtrip.R#95) Error: testthat unit tests failed Execution halted checking compiled code ... NOTE File 'fst/libs/x64/fst.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## genBart (1.0.1) Maintainer: Jacob Cardenas 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'limma' 'qusage' Packages suggested but not available for checking: 'DESeq2' 'edgeR' 'SummarizedExperiment' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## GenomicTools (0.2.6) Maintainer: Daniel Fischer 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Package required but not available: 'snpStats' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## GGIR (1.5-18) Maintainer: Vincent T van Hees Bug reports: https://github.com/wadpac/GGIR/issues 1 error | 0 warnings | 1 note ``` checking tests ... ERROR Running 'testthat.R' [194s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 1/1 mismatches [1] 3 - 2 == 1 [31m--[39m [31m2. Failure: chainof5parts (@test_chainof5parts.R#96) [39m [31m--------------------------------------------------[39m `x` not equal to `expected`. 1/1 mismatches [1] 109 - 945 == -836 == testthat results ====================================================================================== OK: 62 SKIPPED: 0 FAILED: 2 1. Failure: chainof5parts (@test_chainof5parts.R#93) 2. Failure: chainof5parts (@test_chainof5parts.R#96) Error: testthat unit tests failed Execution halted checking compiled code ... NOTE File 'GGIR/libs/x64/GGIR.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## greport (0.7-1) Maintainer: Frank E Harrell Jr 0 errors | 1 warning | 1 note ``` checking whether package 'greport' can be installed ... WARNING Found the following significant warnings: Warning: package 'Hmisc' was built under R version 3.4.4 Warning: package 'ggplot2' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/greport.Rcheck/00install.out' for details. checking R code for possible problems ... NOTE accrualReport: multiple local function definitions for 'gg' with different formal arguments ``` ## hisse (1.8.5) Maintainer: Jeremy Beaulieu 1 error | 0 warnings | 0 notes ``` checking whether package 'hisse' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/hisse.Rcheck/00install.out' for details. ``` ## hoardeR (0.9.2) Maintainer: Daniel Fischer 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'Biostrings' 'bamsignals' 'Rsamtools' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## iml (0.3.0) Maintainer: Christoph Molnar Bug reports: https://github.com/christophM/iml/issues 2 errors | 0 warnings | 0 notes ``` checking examples ... ERROR Running examples in 'iml-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Partial > ### Title: Partial Dependence and Individual Conditional Expectation > ### Aliases: Partial > > ### ** Examples ... 53 lines ... + mod = Predictor$new(rf, data = iris, predict.fun = predict.fun, class = 1) + plot(Partial$new(mod, feature = "Sepal.Length")) + } Loading required package: randomForest Warning: package 'randomForest' was built under R version 3.4.4 randomForest 4.6-14 Type rfNews() to see new features/changes/bug fixes. Error in `[.data.table`(results.ice, , list(..y.hat = mean(..y.hat)), : ..y.hat in j is looking for y.hat in calling scope, but a column '..y.hat' exists. Column names should not start with .. Calls: ... -> data.frame -> -> [ -> [.data.table Execution halted checking tests ... ERROR Running 'testthat.R' [22s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 7: `[.data.table`(results.ice, , list(..y.hat = mean(..y.hat)), by = c(self$feature.name, "..class.name")) 8: stop(sym, " in j is looking for ", getName, " in calling scope, but a column '", sym, "' exists. Column names should not start with ..") == testthat results ====================================================================================== OK: 182 SKIPPED: 0 FAILED: 7 1. Error: Partial (pdp only) works for single output and single feature (@test-Partial.R#5) 2. Error: Partial (pdp only) works for single output and 2 features, 2D grid.size (@test-Partial.R#39) 3. Error: Partial (pdp only) works for single output and 2 numerical features, 1D grid.size (@test-Partial.R#59) 4. Error: Partial (pdp only) works for single output and numerical + categorical feature (@test-Partial.R#74) 5. Error: Partial (pdp) works for multiple output (@test-Partial.R#101) 6. Error: Partial (pdp+ice) works for multiple output (@test-Partial.R#114) 7. Error: centered Partial (ice) works for multiple output (@test-Partial.R#158) Error: testthat unit tests failed Execution halted ``` ## kangar00 (1.1) Maintainer: Juliane Manitz 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'KEGGgraph' 'biomaRt' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## KRIG (0.1.0) Maintainer: Pedro Guarderas Bug reports: https://github.com/pedroguarderas/KRIG/issues 1 error | 0 warnings | 0 notes ``` checking whether package 'KRIG' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/KRIG.Rcheck/00install.out' for details. ``` ## lava (1.6.1) Maintainer: Klaus K. Holst Bug reports: https://github.com/kkholst/lava/issues 1 error | 0 warnings | 1 note ``` checking tests ... ERROR Running 'test-all.R' [20s] Running the tests in 'tests/test-all.R' failed. Last 13 lines of output: 2: getExportedValue(pkg, name) 3: asNamespace(ns) 4: getNamespace(ns) 5: tryCatch(loadNamespace(name), error = function(e) stop(e)) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: value[[3L]](cond) == testthat results ====================================================================================== OK: 244 SKIPPED: 8 FAILED: 2 1. Error: Effects (@test-inference.R#27) 2. Error: Graph attributes (@test-model.R#82) Error: testthat unit tests failed Execution halted checking package dependencies ... NOTE Package suggested but not available for checking: 'Rgraphviz' ``` ## MetamapsDB (0.0.2) Maintainer: Wesley GOI 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Package required but not available: 'ShortRead' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## metaMix (0.2) Maintainer: Sofia Morfopoulou 1 error | 0 warnings | 0 notes ``` checking whether package 'metaMix' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/metaMix.Rcheck/00install.out' for details. ``` ## mlr (2.12.1) Maintainer: Bernd Bischl Bug reports: https://github.com/mlr-org/mlr/issues 1 error | 1 warning | 1 note ``` checking tests ... ERROR Running 'run-base.R' [255s] Running the tests in 'tests/run-base.R' failed. Last 13 lines of output: == testthat results ====================================================================================== OK: 3236 SKIPPED: 0 FAILED: 10 1. Error: getHyperPars (@test_base_getHyperPars.R#19) 2. Error: WeightedClassesWrapper, binary (@test_base_imbal_weightedclasses.R#16) 3. Error: WeightedClassesWrapper, multiclass (@test_base_imbal_weightedclasses.R#41) 4. Error: getClassWeightParam (@test_base_imbal_weightedclasses.R#72) 5. Error: measures (@test_base_measures.R#53) 6. Error: check measure calculations (@test_base_measures.R#171) 7. Error: multilabel learning (@test_base_multilabel.R#15) 8. Error: predict preserves rownames (@test_base_predict.R#92) 9. Error: (unknown) (@test_base_prediction_operators.R#5) 10. Error: selectFeatures/sfs works with wrapper (@test_base_selectFeatures.R#64) Error: testthat unit tests failed Execution halted checking whether package 'mlr' can be installed ... WARNING Found the following significant warnings: Warning: package 'ParamHelpers' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/mlr.Rcheck/00install.out' for details. checking compiled code ... NOTE File 'mlr/libs/x64/mlr.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## MODIStsp (1.3.3.1) Maintainer: Lorenzo Busetto Bug reports: https://github.com/lbusett/MODIStsp/issues 1 error | 0 warnings | 0 notes ``` checking whether package 'MODIStsp' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/MODIStsp.Rcheck/00install.out' for details. ``` ## openEBGM (0.5.0) Maintainer: John Ihrie 0 errors | 1 warning | 0 notes ``` checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... NA/NaN function evaluation Warning: package 'ggplot2' was built under R version 3.4.4 Warning: package 'tidyr' was built under R version 3.4.4 Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash, : NA/NaN function evaluation Warning in dnbinom(ni, size = size_f2, prob = prob_f2) : NaNs produced ... 8 lines ... Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash, : NA/NaN function evaluation Warning in log((P * f_star1) + ((1 - P) * f_star2)) : NaNs produced Warning in nlminb(start = as.numeric(theta_init[i, ]), objective = negLLsquash, : NA/NaN function evaluation Warning in theta_hats$guess_num != candidate$guess_num : longer object length is not a multiple of shorter object length Quitting from lines 60-73 (x4_posteriorCalculationVignette.Rmd) Error: processing vignette 'x4_posteriorCalculationVignette.Rmd' failed with diagnostics: (list) object cannot be coerced to type 'double' Execution halted ``` ## padr (0.4.0) Maintainer: Edwin Thoen Bug reports: https://github.com/EdwinTh/padr/issues 1 error | 0 warnings | 1 note ``` checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 1/1 mismatches [1] 2016-10-21 15:39:04 - 2016-10-21 14:39:04 == 1 hours [31m--[39m [31m2. Failure: assure_greater_than_max_x works properly (@test_span.R#98) [39m [31m--------------------------------[39m assure_greater_than_max_x(max_x_posix, end_val_posix, "day") not equal to as.POSIXct("2016-10-21 14:39:04"). 1/1 mismatches [1] 2016-10-21 15:39:04 - 2016-10-21 14:39:04 == 1 hours == testthat results ====================================================================================== OK: 588 SKIPPED: 0 FAILED: 2 1. Failure: assure_greater_than_max_x works properly (@test_span.R#96) 2. Failure: assure_greater_than_max_x works properly (@test_span.R#98) Error: testthat unit tests failed Execution halted checking compiled code ... NOTE File 'padr/libs/x64/padr.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## pcrsim (1.0.2) Maintainer: Oskar Hansson Bug reports: https://github.com/OskarHansson/pcrsim/issues 1 error | 0 warnings | 0 notes ``` checking whether package 'pcrsim' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/pcrsim.Rcheck/00install.out' for details. ``` ## petro.One (0.1.3) Maintainer: Alfonso R. Reyes 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Package required but not available: 'Rgraphviz' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## PhenotypeSimulator (0.2.0) Maintainer: Hannah Meyer Bug reports: https://github.com/HannahVMeyer/PhenotypeSimulator/issues 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Package required but not available: 'snpStats' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## popEpi (0.4.4) Maintainer: Joonas Miettinen Bug reports: https://github.com/WetRobot/popEpi/issues 2 errors | 1 warning | 0 notes ``` checking examples ... ERROR Running examples in 'popEpi-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeWeightsDT > ### Title: Make a 'data.table' of Tabulated, Aggregated Values and Weights > ### Aliases: makeWeightsDT > > ### ** Examples ... 50 lines ... > # enclos = NULL) > > #### formula usage > form <- Surv(fot, factor(from0to1))~gender > dt <- makeWeightsDT(ag, formula = form, Surv.response = TRUE, + adjust = as, values = vs, weights = ws, + enclos = NULL) Error in as.data.table.array(xi, keep.rownames = keep.rownames) : as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used Calls: makeWeightsDT ... Surv2DT -> data.table -> as.data.table -> as.data.table.array Execution halted checking tests ... ERROR Running 'testthat.R' [38s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 4: as.data.table(xi, keep.rownames = keep.rownames) 5: as.data.table.array(xi, keep.rownames = keep.rownames) 6: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used") == testthat results ====================================================================================== OK: 217 SKIPPED: 41 FAILED: 6 1. Error: removing consecutively bad surv.ints is logical w/ & w/out adjusting (@test_survtab_bad_surv_ints.R#16) 2. Error: survtab_ag messages & results due to non-consecutively bad surv.ints are OK (@test_survtab_bad_surv_ints.R#69) 3. Error: surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen (@test_survtab_observed.R#14) 4. Error: survtab works with more complicated estimation (@test_survtab_observed.R#112) 5. Error: relative survivals about the same as relsurv's (@test_survtab_relative.R#57) 6. Error: evalPopFormula & usePopFormula output is stable (@test_utils.R#251) Error: testthat unit tests failed Execution halted checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning: package 'Epi' was built under R version 3.4.4 Quitting from lines 38-67 (survtab_examples.Rmd) Error: processing vignette 'survtab_examples.Rmd' failed with diagnostics: as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used Execution halted ``` ## prioritizr (3.0.4) Maintainer: Richard Schuster Bug reports: https://github.com/prioritizr/prioritizr/issues 0 errors | 1 warning | 2 notes ``` checking whether package 'prioritizr' can be installed ... WARNING Found the following significant warnings: Warning: package 'raster' was built under R version 3.4.4 Warning: package 'sp' was built under R version 3.4.4 Warning: package 'proto' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/prioritizr.Rcheck/00install.out' for details. checking package dependencies ... NOTE Packages suggested but not available for checking: 'gurobi' 'lpsymphony' checking compiled code ... NOTE File 'prioritizr/libs/x64/prioritizr.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## ProFound (1.0.1) Maintainer: Aaron Robotham 1 error | 1 warning | 0 notes ``` checking examples ... ERROR Running examples in 'ProFound-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: FPtest > ### Title: False Positive Reference Data > ### Aliases: FPtest > ### Keywords: datasets > > ### ** Examples > > image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound")) > profound=profoundProFound(image, magzero=30, rotstats=TRUE) Error: The EBImage package is needed for this function to work. Please install it from Bioconductor. Execution halted checking whether package 'ProFound' can be installed ... WARNING Found the following significant warnings: Warning: package 'magicaxis' was built under R version 3.4.4 Warning: package 'mapproj' was built under R version 3.4.4 Warning: package 'maps' was built under R version 3.4.4 Warning: package 'celestial' was built under R version 3.4.4 Warning: package 'RANN' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/ProFound.Rcheck/00install.out' for details. ``` ## quickPlot (0.1.3) Maintainer: Eliot J B McIntire Bug reports: https://github.com/PredictiveEcology/quickPlot/issues 1 error | 0 warnings | 1 note ``` checking tests ... ERROR Running 'test-all.R' [19s] Running the tests in 'tests/test-all.R' failed. Last 13 lines of output: [31m--[39m [31m1. Failure: all exported functions have examples (@test-examples.R#4) [39m [31m---------------------------------[39m `example(x, package = "quickPlot", character.only = TRUE, echo = FALSE)` generated warnings: * package 'rgdal' was built under R version 3.4.4 [31m--[39m [31m2. Failure: all exported functions have examples (@test-examples.R#4) [39m [31m---------------------------------[39m `example(x, package = "quickPlot", character.only = TRUE, echo = FALSE)` generated warnings: * package 'igraph' was built under R version 3.4.4 == testthat results ====================================================================================== OK: 32 SKIPPED: 23 FAILED: 2 1. Failure: all exported functions have examples (@test-examples.R#4) 2. Failure: all exported functions have examples (@test-examples.R#4) Error: testthat unit tests failed Execution halted checking package dependencies ... NOTE Package suggested but not available for checking: 'fastshp' ``` ## RAPIDR (0.1.1) Maintainer: Kitty Lo 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'Biostrings' 'Rsamtools' 'GenomicAlignments' Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg19' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## Rblpapi (0.3.8) Maintainer: Dirk Eddelbuettel Bug reports: https://github.com/Rblp/Rblpapi/issues 1 error | 0 warnings | 0 notes ``` checking whether package 'Rblpapi' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/Rblpapi.Rcheck/00install.out' for details. ``` ## readtext (0.50) Maintainer: Kenneth Benoit Bug reports: https://github.com/kbenoit/readtext/issues 1 error | 0 warnings | 0 notes ``` checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: `encoding(rt, verbose = TRUE)` produced unexpected messages. Expected match: Probable encoding: UTF-8 Actual values: * Probable encoding: ISO-8859-2 * == testthat results ====================================================================================== OK: 127 SKIPPED: 11 FAILED: 3 1. Failure: test encoding function on simple text files (@test-encoding.R#7) 2. Failure: test encoding function on simple text files (@test-encoding.R#12) 3. Failure: test encoding function on simple text files (@test-encoding.R#17) Error: testthat unit tests failed Execution halted ``` ## RecordLinkage (0.4-10) Maintainer: Andreas Borg 0 errors | 1 warning | 2 notes ``` checking whether package 'RecordLinkage' can be installed ... WARNING Found the following significant warnings: Warning: package 'DBI' was built under R version 3.4.4 Warning: package 'RSQLite' was built under R version 3.4.4 Warning: package 'ff' was built under R version 3.4.4 Warning: package 'ffbase' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/RecordLinkage.Rcheck/00install.out' for details. checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: [.RLBigData [.RLResult [.RecLinkData [.RecLinkResult See section 'Registering S3 methods' in the 'Writing R Extensions' manual. checking compiled code ... NOTE File 'RecordLinkage/libs/x64/RecordLinkage.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## REIDS (0.0.2) Maintainer: Marijke Van Moerbeke 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'GenomeGraphs' 'biomaRt' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## rstanarm (2.17.4) Maintainer: Ben Goodrich Bug reports: https://github.com/stan-dev/rstanarm/issues 2 errors | 1 warning | 3 notes ``` checking examples ... ERROR Running examples in 'rstanarm-Ex.R' failed The error occurred in: R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. ... 26 lines ... + }, + pos = 'CheckExEnv') > > ### * > library('rstanarm') Loading required package: Rcpp Warning: package 'Rcpp' was built under R version 3.4.4 Error: package or namespace load failed for 'rstanarm' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace 'Matrix' 1.2-12 is being loaded, but >= 1.2.13 is required Execution halted ** found \donttest examples: check also with --run-donttest checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the > # GNU General Public License for more details. > # > # You should have received a copy of the GNU General Public License > # along with this program; if not, write to the Free Software > # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. > > library(testthat) > library(rstanarm) Loading required package: Rcpp Error: package or namespace load failed for 'rstanarm' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace 'Matrix' 1.2-12 is being loaded, but >= 1.2.13 is required In addition: Warning message: package 'Rcpp' was built under R version 3.4.4 Execution halted checking whether package 'rstanarm' can be installed ... WARNING Found the following significant warnings: Warning: package 'Rcpp' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/rstanarm.Rcheck/00install.out' for details. checking installed package size ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: doc 2.8Mb libs 8.2Mb checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. checking compiled code ... NOTE File 'rstanarm/libs/x64/rstanarm.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## SafeQuant (2.3.1) Maintainer: Erik Ahrne 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Package required but not available: 'limma' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## sdcMicro (5.2.0) Maintainer: Matthias Templ 2 errors | 0 warnings | 1 note ``` checking examples ... ERROR Running examples in 'sdcMicro-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: freqCalc > ### Title: Frequencies calculation for risk estimation > ### Aliases: freqCalc > ### Keywords: manip > ... 26 lines ... > ## with missings: > x <- francdat > x[3,5] <- NA > x[4,2] <- x[4,4] <- NA > x[5,6] <- NA > x[6,2] <- NA > f2 <- freqCalc(x, keyVars=c(2,4,5,6),w=8) Error in `[.data.table`(dat_with_na, , `:=`(tmpid, .I)) : Cannot use := to add columns to a null data.table (no columns), currently. You can use := to add (empty) columns to a 0-row data.table (1 or more empty columns), though. Calls: freqCalc -> [ -> [.data.table Execution halted checking tests ... ERROR Running 'globalRecoding_test.R' Running 'microaggregation_test.R' Running 'reporting_test.R' Running 'testhat.R' Running the tests in 'tests/testhat.R' failed. Last 13 lines of output: 6 0.0 0 0 1.00 0.00 9 0.0 0 0 0.00 1.00 Changed observations: variable nrChanges percChanges 1 roof 1 1.08 ---------------------------------------------------------------------- == testthat results ====================================================================================== OK: 5 SKIPPED: 5 FAILED: 2 1. Error: data frame method gives the same as method on sdcMicro object (@test_freqCalc.R#7) 2. Error: method1 frequencies should be 2,2,2,2,1 (@test_freqCalc.R#110) Error: testthat unit tests failed Execution halted checking compiled code ... NOTE File 'sdcMicro/libs/x64/sdcMicro.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## sdcTable (0.22.8) Maintainer: Bernhard Meindl Bug reports: https://github.com/bernhard-da/sdcTable/issues 1 error | 0 warnings | 0 notes ``` checking whether package 'sdcTable' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/sdcTable.Rcheck/00install.out' for details. ``` ## SIRItoGTFS (0.2.2) Maintainer: Dror Bogin Bug reports: https://github.com/bogind/SIRItoGTFS/issues 1 error | 0 warnings | 0 notes ``` checking examples ... ERROR Running examples in 'SIRItoGTFS-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: readGTFS > ### Title: read GTFS files from a folder into R's environment > ### Aliases: readGTFS > ### Keywords: iteration utilities > ... 8 lines ... > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/shapes.txt")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stop_times.txt")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stops.txt")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/translations.txt")) > write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/trips.txt")) > > # now we read just the minimal tables needed for `STG`, > # meaning everything besides shapes and translations > readGTFS(directory, minimal = TRUE, extension = "BOTH") Error: isTrueFalse(showProgress) is not TRUE Execution halted ``` ## socialmixr (0.1.2) Maintainer: Sebastian Funk 1 error | 0 warnings | 0 notes ``` checking tests ... ERROR Running 'testthat.R' [24s] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: @Misc{, title = {POLYMOD social contact data}, author = {Jo ``` ## SpaDES.core (0.1.1) Maintainer: Alex M Chubaty Bug reports: https://github.com/PredictiveEcology/SpaDES.core/issues 1 error | 2 warnings | 0 notes ``` checking tests ... ERROR Running 'test-all.R' [94s] Running the tests in 'tests/test-all.R' failed. Last 13 lines of output: [39m[31m--[39m [31m1. Failure: simList object initializes correctly (@test-simList.R#17) [39m [31m---------------------------------[39m length(out) not equal to 75. 1/1 mismatches [1] 73 - 75 == -2 [34m Using cached copy of burn event in fireSpread module [39m== testthat results ====================================================================================== OK: 391 SKIPPED: 33 FAILED: 1 1. Failure: simList object initializes correctly (@test-simList.R#17) Error: testthat unit tests failed In addition: Warning messages: 1: package 'quickPlot' was built under R version 3.4.4 2: package 'reproducible' was built under R version 3.4.4 Execution halted checking whether package 'SpaDES.core' can be installed ... WARNING Found the following significant warnings: Warning: package 'quickPlot' was built under R version 3.4.4 Warning: package 'reproducible' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/SpaDES.core.Rcheck/00install.out' for details. checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': ... 8 lines ... Attaching package: 'reproducible' The following object is masked from 'package:igraph': %>% Warning: package 'SpaDES.tools' was built under R version 3.4.4 Error: processing vignette 'ii-modules.Rmd' failed with diagnostics: node stack overflow Execution halted ``` ## speaq (2.3.1) Maintainer: Charlie Beirnaert 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'MassSpecWavelet' 'impute' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ``` ## splitstackshape (1.4.4) Maintainer: Ananda Mahto Bug reports: http://github.com/mrdwab/splitstackshape/issues 1 error | 0 warnings | 0 notes ``` checking examples ... ERROR Running examples in 'splitstackshape-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cSplit_f > ### Title: Split Concatenated Cells in a data.frame or a data.table > ### Aliases: cSplit_f > > ### ** Examples ... 22 lines ... 6 6 9-3 U.C.G x_m_k_r 7 7 9-8 A.I.M y_s_a_u 8 8 4-2 M.N.T r_z_j_c 9 9 8-3 T.R.C q_j_w_s 10 10 10-2 S.K.W b_u_i_k > > cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_")) Error in fread(x, sep[i], header = FALSE) : You can provide 'input=' or 'file=', not both. Calls: cSplit_f -> fread Execution halted ``` ## strvalidator (2.0.0) Maintainer: Oskar Hansson Bug reports: https://github.com/OskarHansson/strvalidator/issues 1 error | 0 warnings | 0 notes ``` checking whether package 'strvalidator' can be installed ... ERROR Installation failed. See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/strvalidator.Rcheck/00install.out' for details. ``` ## tcR (2.2.1.11) Maintainer: Vadim Nazarov Bug reports: https://github.com/imminfo/tcr/issues 0 errors | 1 warning | 4 notes ``` checking whether package 'tcR' can be installed ... WARNING Found the following significant warnings: Warning: package 'ggplot2' was built under R version 3.4.4 Warning: package 'gridExtra' was built under R version 3.4.4 Warning: package 'igraph' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/tcR.Rcheck/00install.out' for details. checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: data 1.2Mb doc 3.9Mb checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: slice.fun See section 'Registering S3 methods' in the 'Writing R Extensions' manual. checking Rd \usage sections ... NOTE S3 methods shown with full name in documentation object 'top.fun': 'slice.fun' The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. checking compiled code ... NOTE File 'tcR/libs/x64/tcR.dll': Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols' It is good practice to register native routines and to disable symbol search. See 'Writing portable packages' in the 'Writing R Extensions' manual. ``` ## tRophicPosition (0.7.5) Maintainer: Claudio Quezada-Romegialli Bug reports: https://groups.google.com/d/forum/trophicposition-support 1 error | 1 warning | 0 notes ``` checking examples ... ERROR Running examples in 'tRophicPosition-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: TPmodel > ### Title: Function to create a JAGS-based Bayesian model to calculate > ### trophic position > ### Aliases: TPmodel > > ### ** Examples > > isotopeData <- generateTPData() > model.string <- jagsBayesianModel() > model <- TPmodel(data = isotopeData, model.string = model.string, + n.adapt = 500) Error: .onLoad failed in loadNamespace() for 'rjags', details: call: fun(libname, pkgname) error: Failed to locate any version of JAGS version 4 The rjags package is just an interface to the JAGS library Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from http://www.sourceforge.net/projects/mcmc-jags/files Execution halted checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 108-110 (Multiple_model_calculation_of_trophic_position_in_R.Rmd) Error: processing vignette 'Multiple_model_calculation_of_trophic_position_in_R.Rmd' failed with diagnostics: .onLoad failed in loadNamespace() for 'rjags', details: call: fun(libname, pkgname) error: Failed to locate any version of JAGS version 4 The rjags package is just an interface to the JAGS library Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from http://www.sourceforge.net/projects/mcmc-jags/files Execution halted ``` ## tstools (0.3.6) Maintainer: Matthias Bannert 1 error | 1 warning | 0 notes ``` checking tests ... ERROR Running 'testthat.R' Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 6: fread(file, sep = sep, stringsAsFactors = FALSE, colClasses = "numeric") [31m--[39m [31m2. Error: differing lengths work (@testWriteTimeseries.R#282) [39m [31m-----------------------------------------[39m Attempt to override column 1 <> of inherent type 'string' down to 'float64' which will lose accuracy. If this was intended, please coerce to the lower type afterwards. Only overrides to a higher type are permitted. 1: read_ts("faulty.csv") at testthat/testWriteTimeseries.R:282 2: read_ts.csv(file) 3: fread(file, sep = sep, stringsAsFactors = FALSE, colClasses = "numeric") == testthat results ====================================================================================== OK: 32 SKIPPED: 0 FAILED: 2 1. Error: imports work (@testWriteTimeseries.R#232) 2. Error: differing lengths work (@testWriteTimeseries.R#282) Error: testthat unit tests failed Execution halted checking whether package 'tstools' can be installed ... WARNING Found the following significant warnings: Warning: package 'zoo' was built under R version 3.4.4 See 'C:/Users/hughp/Documents/Rdatatable/data.table/revdep/checks/tstools.Rcheck/00install.out' for details. ``` ## yCrypticRNAs (0.99.2) Maintainer: Nicole Uwimana Bug reports: https://bitbucket.org/nuwimana/ycrypticrnas/issues 1 error | 0 warnings | 0 notes ``` checking package dependencies ... ERROR Packages required but not available: 'biomaRt' 'Rsamtools' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ```
mattdowle commented 6 years ago

This is great -- thanks for this! 148 spurious package installation errors to be worked through then! Welcome to my world. I tend to get down to under 10 quite quickly. Then the last 4 or 5 can take a few days to resolve. You're on Windows though which should help a lot given compiled packages. (On Ubuntu, I have to compile them all!)

There are lots of errors like this one : "Packages required but not available: 'MassSpecWavelet' 'impute'" Which command did you use to run this, and why doesn't it install the required packages?

The code I use is here : https://github.com/Rdatatable/data.table/blob/master/CRAN_Release.cmd#L310

I can see two non-spurious by the looks of it, both fread related. So there's at least some work to do then: either communication with those maintainers, or fixes to avoid the breakage.

HughParsonage commented 6 years ago

This was simply devtools::revdep(dependencies = c("Depends", "Imports")). I think those packages are on Bioconductor. Sometimes a package just fails too: connection drops out at an inopportune time.

I'll go through it and keep culling the spurious ones: some other main ones I see are due to ITime and ..x.

MichaelChirico commented 6 years ago

Bravo sir. I've got some time I could spare today (Singapore time = GMT+8) if you'd like an extra pair of hands/eyes 👍

HughParsonage commented 6 years ago

Sure! You go from the bottom? My plan is to just edit the issue OP until only the genuine ones remain.

mattdowle commented 6 years ago

I ran the code in CRAN_Release.cmd overnight and got this : 

> status()
CRAN:
 ERROR   :  16 : AFM easycsv expss fst iml mlr PhenotypeSimulator popEpi prediction sdcMicro SIRItoGTFS socialmixr SpaDES.core splitstackshape tstools yCrypticRNAs 
 WARNING :   2 : optiSel xgboost 
 NOTE    : 148 
 OK      : 307 
 TOTAL   : 473 / 473 
 RUNNING :   0 :  

BIOC:
 ERROR   :  30 : CAGEr ccmap cellbaseR ChIPexoQual COMPASS CONFESS crossmeta CytoML fgsea flowWorkspace genomation ggcyto GGtools GOTHiC ImmuneSpaceR LowMACA maftools metagene metavizr methylPipe minfi MinimumDistance pepStat PGA psichomics rTANDEM RTCGA SNPhood TCGAbiolinks VanillaICE 
 WARNING :  56 : ABAEnrichment amplican anamiR AUCell basecallQC BASiCS biobroom BPRMeth branchpointer bsseq CEMiTool Chicago CopywriteR CRISPRseek dada2 DEFormats diffloop geneXtendeR GenoGAM GenomicDataCommons GenomicTuples GUIDEseq iGC IrisSpatialFeatures LOLA MAST MethylMix MIGSA MIRA MSnID MSstats OmicsMarkeR Onassis OncoSimulR openCyto paxtoolsr phyloseq Prostar PureCN Pviz QUALIFIER R3CPET r3Cseq rfPred RiboProfiling RTN S4Vectors scater SCnorm SISPA SWATH2stats TCGAbiolinksGUI TitanCNA TPP transcriptogramer yamss 
 NOTE    :  23 
 OK      :   2 
 TOTAL   : 111 / 111 
 RUNNING :   0 :

Took 7.5 hours using 8 cores on laptop. The error rate on CRAN is very low. Given that, the Bioc result is likely mostly spurious. Will look.

Logs from the 18 CRAN fails attached : 

find . -name 00check.log | grep -E
'AFM|easycsv|expss|fst|iml|mlr|PhenotypeSimulator|popEpi|prediction|sdcMicro|SIRItoGTFS|socialmixr|SpaDES.core|splitstackshape|tstools|yCrypticRNAs|optiSel|xgboost'
| xargs grep -H . > /tmp/out.log

out.log

mattdowle commented 6 years ago

I installad CRAN version data.table_1.10.4-3 and reran CRAN fails.

> status()
CRAN:
 ERROR   :   5 : AFM expss mlr prediction yCrypticRNAs 
 WARNING :   2 : optiSel xgboost 
 NOTE    : 154 
 OK      : 310 
 TOTAL   : 471 / 471 
 RUNNING :   0 :

NB: 2 packages removed from CRAN overnight (readability and syllable) hence 473 => 471.

So those 7 are either spurious local fails to be resolved, or already in fail status on CRAN.

That leaves 18-7 = 11 CRAN packages that are broken by the data.table update. 11/471 = 2.3%.

( Ticked means it's either resolved on data.table side, or the maintainer has been been contacted. )

MichaelChirico commented 6 years ago

For both easycsv and SIRItoGTFS, the error comes from changing showProgress = getOption("datatable.showProgress") to showProgress = interactive() (more specifically from, deleting the default datatable.showProgress argument) in fread. I don't see this change mentioned in the NEWS, perhaps this should be remedied before notifying easycsv and SIRItoGTFS Issue trackers (note: both are the same author).

I'm also not seeing anything in NEWS that would suggest the change to sdcMicro, which was relying on being able to assing to a data.table with no columns. I recall this being discussed but don't remember the specific issue.

klmr commented 6 years ago

HannahVMeyer/PhenotypeSimulator#7 is due to a breaking change/regression in {data.table}: specifying skip='string' would previously skip lines up to and including the line with the specified string. As of 1.10.5, that line itself isn’t skipped. I can file a new issue with an MWE, if desired.

MichaelChirico commented 6 years ago

@klmr thanks. Based on verbose output it looks like fread attempts to determine whether that row is a header using the auto-detect rules that have been around for a while. It's hinted at in the NEWS but I don't see the specific issue:

People appear to be using skip="string" or skip=nrow to find the header row exactly, which is retained and simpler.

Filed #2786

HughParsonage commented 6 years ago

fst looks like a genuine change:

# fst
library(fst)
library(data.table)

# Convenience method to tests on different versions of the package
# Not used in the CRAN release
fstwriteproxy <- function(x, path, compress = 0, uniform.encoding = TRUE) {
  write_fst(x, path, compress, uniform.encoding)  # use current version of fst package
}

fstreadproxy <- function(path, columns = NULL, from = 1, to = NULL, as.data.table = FALSE) {
  read_fst(path, columns, from, to, as.data.table)
}

fstmetaproxy <- function(path) {
  metadata_fst(path)
}

roundtrip_vector <- function(x) {
  df <- data.frame(x = x, stringsAsFactors = FALSE)
  roundtrip(df)$x
}

roundtrip <- function(df) {
  temp <- tempfile()
  fstwriteproxy(df, temp)
  on.exit(unlink(temp))

  fstreadproxy(temp)
}

roundtrip_vector_dt <- function(x) {
  dt <- data.table(x = x, stringsAsFactors = FALSE)
  roundtrip(dt)$x
}

# ITime
test_that("preserves time of day", {
  x <- as.ITime(c(1:10, NA), origin = "1970-01-01")
  res <- roundtrip_vector_dt(x)
  expect_identical(res, x)

  mode(x) <- "double"
  res <- roundtrip_vector_dt(x)
  expect_identical(res, x)
})
# Error: Test failed: 'preserves time of day'
# * `res` not identical to `x`.
# Classes differ: integer is not ITime
# * `res` not identical to `x`.
# Classes differ: numeric is not ITime
MichaelChirico commented 6 years ago

@HughParsonage I get a different error?

Error: Test failed: 'preserves time of day'
* `res` not identical to `x`.
target is NULL, current is ITime
* `res` not identical to `x`.
target is NULL, current is ITime
HughParsonage commented 6 years ago

Yes difference in versions. Looks okay now.

fst data.table result
cran cran X
cran dev X
dev cran X
dev dev OK
HughParsonage commented 6 years ago

For SpaDES.core I can't work out what the error is, I get a node overflow error due to testthat::capture_warnings, but I have no idea why.

jangorecki commented 6 years ago

@HughParsonage make extra check to confirm that error is not present on 1.10.4, if it happens there then it is likely not the issue on our side, but other package dependency.

christophM commented 6 years ago

Fixed for the iml package: https://github.com/christophM/iml/issues/11 Will submit to CRAN the next days

mattdowle commented 6 years ago

Current status : 

CRAN:
 ERROR   :  11 : easycsv expss fst mlr PhenotypeSimulator popEpi prediction sdcMicro SIRItoGTFS SpaDES.core splitstackshape 
 WARNING :   5 : emil optiSel r2glmm simPH xgboost 
 NOTE    : 139 
 OK      : 320 
 TOTAL   : 475 / 475 
 RUNNING :   0 :  

BIOC:
 ERROR   :   8 : COMPASS CytoML ImmuneSpaceR LowMACA maftools MinimumDistance PGA VanillaICE 
 WARNING :  16 : CEMiTool CONFESS crossmeta IrisSpatialFeatures MethylMix methylPipe MSstats openCyto QUALIFIER R3CPET RiboProfiling rTANDEM S4Vectors SISPA TCGAbiolinksGUI TitanCNA 
 NOTE    :  74 
 OK      :  13 
 TOTAL   : 111 / 111 
 RUNNING :   0 :

All of the CRAN 11+5 are either fixed in data.table, or communicated. Yay! BIOC 8+16 are unrelated to data.table, other than the following 6.

mattdowle commented 6 years ago

CRAN rev dep checks match our results. There were two packages (batchtools and metaMix) that unexpectedly failed with the update, but those turned out to be unrelated to data.table. v1.11.0 is now on CRAN.