Package vignette without corresponding tangle output:
  'skellam.rnw'
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
Running 'testthat.r' [172s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("skylight")
  Loading required package: skylight
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     0.67    0.10    0.76
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SLEMI)
  > 
  > test_check("SLEMI")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
  > 
  > proc.time()
     user  system elapsed 
    12.31    0.73   13.03
Running 'testthat.R' [185s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(slippymath)
  > 
  > test_check("slippymath")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 24 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 24 ]
  > 
  > proc.time()
     user  system elapsed 
     7.53    0.46    8.01
Running 'spelling.R' [163s]
  Running 'testthat.R' [212s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE, error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.04    0.23 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SLOPE)
  > 
  > test_check("SLOPE")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 161 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-diagnostics.R:13:3', 'test-plotting.R:24:3',
    'test-plotting.R:57:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 161 ]
  Deleting unused snapshots:
  • plotting/binom-plot-trainedslope-in-test.svg
  • plotting/plot-slope-multinomial-in-test.svg
  • plotting/plot-slope-parameters-in-test.svg
  • plotting/q-plot-trainedslope-in-test.svg
  > 
  > proc.time()
     user  system elapsed 
    52.78    0.64   53.45
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(slouch)
  > 
  > # testsetup <- function(){
  > #   pars <- list(myfunc = myfunc, dummydata = dummydata, model.id.btk = model.id.btk)
  > #   return(pars)
  > # }
  > 
  > test_check("slouch")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     9.89    0.79   10.65
Running 'nacw.R' [178s]
  Running 'pvf.R' [0s]
  Running 'pwi.R' [0s]
  Running 'rankEntropy.R' [0s]
Running the tests in 'tests/nacw.R' failed.
Complete output:
  > library(smaa)
  > 
  > # First alternative beats second on all criteria
  > # --> NA central weights
  > N <- 1E4; m <- 2; n <- 3
  > mnames <- c("A", "B")
  > nnames <- c("a", "b", "c")
  > meas <- array(dim=c(N,m,n))
  > meas[,1,] <- 1
  > meas[,2,] <- 0
  > dimnames(meas) <- list(NULL, mnames, nnames)
  > pref <- matrix(1/3, nrow=N, ncol=n)
  > dimnames(pref) <- list(NULL, nnames)
  > 
  > centroid <- rep(1/3, 3)
  > names(centroid) <- nnames
  > 
  > result <- smaa(meas, pref)
  > stopifnot(all.equal(result$cw[1,], centroid))
  > stopifnot(all(is.na(result$cw[2,])))
  > stopifnot(all.equal(rownames(result$cw), mnames))
  > 
  > ranks <- smaa.ranks(smaa.values(meas, pref))
  > cw <- smaa.cw(ranks, pref)
  > stopifnot(all.equal(cw[1,], centroid))
  > stopifnot(all(is.na(cw[2,])))
  > stopifnot(all.equal(rownames(cw), mnames))
  > 
  > cf <- smaa.cf(meas, cw)
  > stopifnot(all.equal(unname(cf$cf), c(1, NA)))
  > stopifnot(all.equal(names(cf$cf), mnames))
  > 
  > 
  > # First alternative beats second in a single iteration
  > # --> R gives us a vector instead of a matrix (gee, thanks!)
  > meas[1,1,] <- 0
  > meas[1,2,] <- 1
  > 
  > result <- smaa(meas, pref)
  > stopifnot(all.equal(result$cw[1,], centroid))
  > stopifnot(all.equal(result$cw[2,], centroid))
  > 
  > ranks <- smaa.ranks(smaa.values(meas, pref))
  > cw <- smaa.cw(ranks, pref)
  > stopifnot(all.equal(cw[1,], centroid))
  > stopifnot(all.equal(cw[2,], centroid))
  > 
  > proc.time()
     user  system elapsed 
     0.23    0.06    0.28
Running 'testthat.R' [199s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(smallsets)
  > 
  > test_check("smallsets")
  [ FAIL 0 | WARN 53 | SKIP 0 | PASS 31 ]
  
  [ FAIL 0 | WARN 53 | SKIP 0 | PASS 31 ]
  > 
  > proc.time()
     user  system elapsed 
    18.15    0.85   19.40
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smartDesign)
  > 
  > test_check("smartDesign")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
  > 
  > proc.time()
     user  system elapsed 
     0.68    0.14    0.81
Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SmartEDA)
  > 
  > test_check("SmartEDA")
  Classes 'data.table' and 'data.frame':	2 obs. of  3 variables:
   $ am       : num  1 0
   $ Attribute: chr  "mpg" "mpg"
   $ mean     : num  24.4 17.1
   - attr(*, ".internal.selfref")=<externalptr> 
  Classes 'SmartEDA', 'ExpCTable' and 'data.frame':	21 obs. of  5 variables:
   $ Variable  : chr  "cyl" "cyl" "cyl" "cyl" ...
   $ Valid     : chr  "4" "6" "8" "TOTAL" ...
   $ Frequency : num  11 7 14 32 18 14 32 19 13 32 ...
   $ Percent   : num  34.4 21.9 43.8 NA 56.2 ...
   $ CumPercent: num  34.4 56.3 100 NA 56.2 ...
  'data.frame':	3 obs. of  11 variables:
   $ Class: chr  "3" "4" "5"
   $ Out_1: int  0 8 5
   $ Out_0: int  15 4 0
   $ TOTAL: int  15 12 5
   $ Per_1: num  0 0.62 0.38
   $ Per_0: num  0.79 0.21 0
   $ Odds : num  0 6 0
   $ WOE  : num  0 1.08 0
   $ IV   : num  0 0.44 0
   $ Ref_1: chr  "1" "1" "1"
   $ Ref_0: chr  "0" "0" "0"
   - attr(*, "iValue")= num 0.44
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 57 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_expreport.R:8:3', 'test_exptwoplots.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 57 ]
  > 
  > proc.time()
     user  system elapsed 
     3.01    0.60    3.62
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smd)
  > 
  > test_check("smd")
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 68 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test_smd.R:10:5', 'test_smd.R:10:5', 'test_smd.R:10:5',
    'test_smd.R:10:5', 'test_smd.R:10:5', 'test_smd.R:10:5'
  
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 68 ]
  > 
  > proc.time()
     user  system elapsed 
     1.39    0.28    1.67
Running 'tinytest.R' [163s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("smetlite")
  + }
  
  test_smetlite.R...............    0 tests    
  test_smetlite.R...............    0 tests    
  test_smetlite.R...............    1 tests [0;32mOK[0m [0;34m1.0s[0m
  All ok, 1 results (1.0s)
  > 
  > proc.time()
     user  system elapsed 
     1.10    0.17    1.26
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    libs   1.0Mb
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  'mat_list1' 'mat_list2' 'x' 'y' 'return_single'

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  'dists'

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.
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SMITIDvisu)
  > test_check("SMITIDvisu")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 73 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1):
    'D:\RCompile\CRANpkg\local\4.4\SMITIDvisu.Rcheck\tests\testthat\maptt\test-getFeatureDataById.R:74:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 73 ]
  > 
  > proc.time()
     user  system elapsed 
     1.35    0.23    1.56
Running 'testthat.R' [190s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smoothAPC)
  > 
  > test_check("smoothAPC")
  
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   
  |   
  /   
  -   
  \   [ FAIL 0 | WARN 0 | SKIP 5 | PASS 27 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test_twoStepDemogSmooth.R:22:3',
    'test_twoStepDemogSmooth.R:32:3', 'test_twoStepDemogSmooth.R:46:3'
  • empty test (2): 'test_autoDemogSmooth.R:35:1', 'test_demogSmooth.R:36:1'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 27 ]
  > 
  > proc.time()
     user  system elapsed 
    16.45    8.76   25.20
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.3Mb
    libs   1.6Mb
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smoothr)
  
  Attaching package: 'smoothr'
  
  The following object is masked from 'package:stats':
  
      smooth
  
  > 
  > test_check("smoothr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 162 ]
  > 
  > proc.time()
     user  system elapsed 
     9.42    0.51    9.95
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'lseq'
Running 'testthat.r' [161s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("snotelr")
  Loading required package: snotelr
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 0 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test_snotel_functions.r:5:3', 'test_snotel_functions.r:10:3',
    'test_snotel_functions.r:16:3', 'test_snotel_functions.r:21:3',
    'test_snotel_functions.r:26:3', 'test_snotel_functions.r:32:3',
    'test_snotel_functions.r:37:3', 'test_snotel_functions.r:43:3',
    'test_snotel_functions.r:49:3', 'test_snotel_functions.r:56:3',
    'test_snotel_functions.r:62:3', 'test_snotel_functions.r:70:3',
    'test_snotel_functions.r:76:3', 'test_snotel_functions.r:83:3',
    'test_snotel_functions.r:90:3', 'test_snotel_functions.r:97:3',
    'test_snotel_functions.r:109:3'
  
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.29    0.12    1.39
Running 'run_tests.R' [188s]
  Running 'test_functions.R' [0s]
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > #source('/Users/hana/myprojects/snowFT/tests/test_functions.R')
  > source('test_functions.R')
  Loading required package: rlecuyer
  > run.rnorm.sock()
  
  Running rnorm test with SOCK ...
  
  Function performParallel:
     creating cluster ...
  
  Cluster successfully created.
  Cluster size: 5
  Cluster type: SOCKcluster cluster
  Hosts: localhost , localhost , localhost , localhost , localhost , 
     initializing RNG ...
     calling clusterApplyFT ...
  
  Function clusterApplyFT:
     gentype: RNGstream 
     seed:    9523148 8605250 2629207 1781446 1827596 2931860 
     Management files:
       cluster size: .clustersize 
       running processes: .proc 
     clusterApplyFT finished.
     cluster stopped.
     user  system elapsed 
     1.65    2.75    6.15 
  
   OK.
  > run.rnorm.seq()
  
  Running rnorm test sequentially ...
     user  system elapsed 
     0.20    0.05    0.25 
  
   OK.
  > #run.rnorm.sock.cluster.args()
  > #run.rnorm.pvm()
  > #run.rnorm.mpi()
  > check.reproducibility.for.seq.and.par()
  
  Check reproducibility for sequential and parallel runs ... OK.
  
  Check non-reproducibility for sequential and parallel runs ... OK.
  > check.init.workers()
  
  Check initialization of workers ... OK.
  > 
  > proc.time()
     user  system elapsed 
     2.20    2.93    8.54
Running 'testthat.R' [254s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SNPknock)
  > 
  > # Set a random seed for reproducibility when running R CMD CHECK.
  > # Note that this file is not run by devtools::test, so the tests will be truly
  > # random when run from RStudio.
  > set.seed(1234)
  > 
  > # Run the test suite.
  > test_check('SNPknock')
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
  > 
  > # Reset the random seed.
  > rm(.Random.seed)
  > 
  > proc.time()
     user  system elapsed 
    89.01   10.31   99.29
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SNSchart)
  > 
  > test_check("SNSchart")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
  > 
  > proc.time()
     user  system elapsed 
     0.82    0.15    0.96
Running 'testthat.R' [190s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SOAs)
  Loading required package: DoE.base
  Loading required package: grid
  Loading required package: conf.design
  
  Attaching package: 'DoE.base'
  
  The following objects are masked from 'package:stats':
  
      aov, lm
  
  The following object is masked from 'package:graphics':
  
      plot.design
  
  The following object is masked from 'package:base':
  
      lengths
  
  > 
  > test_check("SOAs")
  [ FAIL 0 | WARN 0 | SKIP 16 | PASS 1065 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • On CRAN (16): 'test-OSOAs-regular.R:9:3', 'test-OSOAs.R:10:3',
    'test-OSOAs_LiuLiu.R:18:3', 'test-OSOAs_hadamard.R:9:3', 'test-SOAs.R:3:3',
    'test-SOAs2plus-regular.R:11:3', 'test-SOAs_8level.R:39:3',
    'test-checkStratification.R:17:3', 'test-checkStratification.R:46:3',
    'test-checkStratification.R:117:3', 'test-guide_SOAs.R:38:5',
    'test-guide_SOAs_from_OA.R:45:3', 'test-soa.R:12:3',
    'test-utilitiesCreate.R:5:1', 'test-utilitiesEvaluate.R:17:3',
    'test-utilitiesEvaluate.R:27:3'
  
  [ FAIL 0 | WARN 0 | SKIP 16 | PASS 1065 ]
  > 
  > proc.time()
     user  system elapsed 
    24.81    3.12   27.92
Running 'tests.R' [162s]
Running the tests in 'tests/tests.R' failed.
Complete output:
  > library(sobolnp)
  
  Attaching package: 'sobolnp'
  
  The following object is masked from 'package:graphics':
  
      plot
  
  The following objects are masked from 'package:base':
  
      plot, print
  
  > 
  > ishigami.fun <- function(X) {
  +   A <- 7
  +   B <- 0.1
  +   sin(X[, 1]) + A * sin(X[, 2]) ^ 2 + B * X[, 3] ^ 4 * sin(X[, 1])
  + }
  > 
  > X <- matrix(runif(3 * 10, -pi, pi), ncol = 3)
  > Y <- ishigami.fun(X)
  > 
  > #colnames(X) <- c("1", "2", "3")
  > ss <- sobolnp::sobolnp(
  +   Y = Y,
  +   X = X,
  +   nboot = 2,
  +   mc.cores = 1
  + )
  Estimating non-parametric Sobol indices with cross-validation bandwidth
  
  Multistart 1 of 1 |
  Multistart 1 of 1 |
  Multistart 1 of 1 |
  Multistart 1 of 1 /
  Multistart 1 of 1 |
  Multistart 1 of 1 |
                     
  
  Multistart 1 of 1 |
  Multistart 1 of 1 |
  Multistart 1 of 1 |
  Multistart 1 of 1 /
  Multistart 1 of 1 |
  Multistart 1 of 1 |
                     
  
  Multistart 1 of 1 |
  Multistart 1 of 1 |
  Multistart 1 of 1 |
  Multistart 1 of 1 /
  Multistart 1 of 1 |
  Multistart 1 of 1 |
                     
  Estimating non-parametric Sobol indices with bootstrap bandwidth
  > 
  > print(ss)
  
  Call:
  sobolnp::sobolnp(Y = Y, X = X, nboot = 2, mc.cores = 1)
  
  Number of observations: 10 
  
  Number of variables: 3 
  
  First order indices
              Si CV        bw CV Si Bootstrap bw Bootstrap
  [1,] 3.127548e-01 1.185871e+00 3.183107e-01 1.174020e+00
  [2,] 9.349561e-01 1.294384e-01 9.799105e-01 1.457358e-02
  [3,] 3.335653e-33 1.071725e+08 7.783190e-33 1.071725e+08
  > 
  > plot(ss)
  > 
  > proc.time()
     user  system elapsed 
     3.45    0.25    3.67
Running 'testthat.R' [217s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # nolint start
  > library(testthat)
  > library(socialmixr)
  
  Attaching package: 'socialmixr'
  
  The following object is masked from 'package:utils':
  
      cite
  
  > # nolint end
  > 
  > data.table::setDTthreads(1)
  > test_check("socialmixr")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 136 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-matrix.r:390:3', 'test-surveys.r:4:3',
    'test-surveys.r:11:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 136 ]
  > 
  > proc.time()
     user  system elapsed 
    60.06    3.50   63.59
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sociome)
  > 
  > test_check("sociome")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 4 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • Sys.getenv("CENSUS_API_KEY") == "" is TRUE (1):
    'test_tidycensus_related.R:90:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     3.43    0.70    4.12
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(solartime)
  > 
  > test_check("solartime")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 30 ]
  > 
  > proc.time()
     user  system elapsed 
     0.96    0.29    1.25
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.solveEnv'
Running 'spelling.R' [160s]
  Running 'testthat.R' [25s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if ( requireNamespace("spelling", quietly = TRUE) ) {
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.04    0.23
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
Running 'mmec_examples.R' [0s]
  Running 'testthat.R' [146s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sommer)
  Loading required package: Matrix
  Loading required package: MASS
  Loading required package: crayon
  > 
  > test_check("sommer")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     1.96    0.23    2.18
Documented arguments not in \usage in Rd file 'som.nn.do.train.Rd':
  'model'

Documented arguments not in \usage in Rd file 'som.nn.som.internal.Rd':
  'rlen'

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.
S3 methods shown with full name in Rd file 'plot.predictions.Rd':
  'plot.predictions'

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.
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SOPC)
  > 
  > test_check("SOPC")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.57    0.14    0.70
Running 'spelling.R' [0s]
  Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sortable)
  > 
  > test_check("sortable")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.42    1.90
Documented arguments not in \usage in Rd file 'path2name.Rd':
  'x'

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.
Package suggested but not available for checking: 'SciencesPo'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (require("testthat", quietly = TRUE)) {
  +   library(sourcetools)
  +   test_check("sourcetools")
  + }
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 151 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-tokenize.R:150:3'
  • empty test (1): 'test-tokenize.R:139:1'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 151 ]
  > 
  > proc.time()
     user  system elapsed 
     1.39    0.34    1.71
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
Running 'spelling.R' [175s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.01    0.18
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SP2000)
  Welcome to R Package SP2000 0.2.0 !!!
                                    
  
  To start with the SP2000, please digit:
                                    
  https://cran.r-project.org/package=SP2000(R)
                                    
  https://pypi.org/project/SP2000(Python)
  
  Warning message:
  In Sys.setlocale(category = "LC_ALL", locale = "Chinese") :
    using locale code page other than 65001 ("UTF-8") may cause problems
  > 
  > #All of the tests rely on the API existing and behaving as documented. However,
  > #the API occasionally falls over or stops working which lets to errors on CRAN.
  > #Because we use travis CI we will hear about any test failures as soon as they
  > #happen. So, let's skill all tests on CRAN:
  > 
  > if(identical(Sys.getenv("NOT_CRAN"), "true")){
  +   test_check("SP2000")
  + }
  > 
  > proc.time()
     user  system elapsed 
     1.23    0.26    1.50
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spacejamr)
  > 
  > test_check("spacejamr")
      Density Mean Degree Mean Closeness Mean Betweenness Largest Component Size
  pl        0           0            NaN                0                      1
  apl       0           0            NaN                0                      1
      Density Mean Degree Mean Closeness Mean Betweenness Largest Component Size
  pl        0           0            NaN                0                      1
  apl       0           0            NaN                0                      1
  window: polygonal boundary
  enclosing rectangle: [257656.9, 323005.8] x [4558224, 4654702] units
  PointSim Object
  
  window: polygonal boundary
  enclosing rectangle: [257656.9, 323005.8] x [4558224, 4654702] units
  
  Points:3IGRAPH 54fab75 UN-- 3 0 -- 
  + attr: name (v/c)
  + edges from 54fab75 (vertex names):
  IGRAPH 54fab75 UN-- 3 0 -- 
  + attr: name (v/c)
  + edges from 54fab75 (vertex names):
  Using the projected CRS WGS 84 / UTM zone 19N which uses 'm' for measurement units. Please visit https://spatialreference.org/ref/epsg/32619/ for more information about this CRS.
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 23 ]
  
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
    15.29    1.54   16.81
Running 'basic.R' [2s]
  Comparing 'basic.Rout' to 'basic.Rout.save' ...82,85c82,85
< 2010-08-05 10:00:00   ID_1   ID_2   ID_3
< 2010-08-05 11:00:00   ID_4   ID_5   ID_6
< 2010-08-05 12:00:00   ID_7   ID_8   ID_9
< 2010-08-05 13:00:00  ID_10  ID_11  ID_12
---
> 2010-08-05 10:00:00 "ID_1"  "ID_2"  "ID_3" 
> 2010-08-05 11:00:00 "ID_4"  "ID_5"  "ID_6" 
> 2010-08-05 12:00:00 "ID_7"  "ID_8"  "ID_9" 
> 2010-08-05 13:00:00 "ID_10" "ID_11" "ID_12"
  Running 'over.R' [2s]
  Comparing 'over.Rout' to 'over.Rout.save' ... OK
  Running 'raster.R' [9s]
  Comparing 'raster.Rout' to 'raster.Rout.save' ... OK
  Running 'rw.R' [2s]
  Comparing 'rw.Rout' to 'rw.Rout.save' ... OK
  Running 'stconstruct.R' [2s]
  Comparing 'stconstruct.Rout' to 'stconstruct.Rout.save' ...59,60c59,62
< Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
< Reading layer `nc' from data source `D:\RCompile\CRANpkg\lib\4.4\sf\shape\nc.shp' using driver `ESRI Shapefile'
---
> Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE
> Reading layer `nc' from data source 
>   `/home/edzer/R/x86_64-pc-linux-gnu-library/4.0/sf/shape/nc.shp' 
>   using driver `ESRI Shapefile'
  Running 'subsetting.R' [1s]
  Comparing 'subsetting.Rout' to 'subsetting.Rout.save' ... OK
  Running 'wind.R' [163s]
Running the tests in 'tests/wind.R' failed.
Complete output:
  > ###################################################
  > 
  > proc.time()
     user  system elapsed 
     0.12    0.14    0.20
Package suggested but not available for checking: 'NLMR'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   4.9Mb
Running 'testthat.R' [188s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spaero)
  > 
  > test_check("spaero")
  [ FAIL 0 | WARN 4 | SKIP 7 | PASS 48 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-simulator.R:60:3', 'test-simulator.R:82:3',
    'test-simulator.R:157:3', 'test-simulator.R:190:3', 'test-stats.R:118:3',
    'test-stats.R:237:3', 'test-stats.R:304:3'
  
  [ FAIL 0 | WARN 4 | SKIP 7 | PASS 48 ]
  > 
  > proc.time()
     user  system elapsed 
     6.20    0.68   13.51
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    libs   1.8Mb
Running 'testthat.R' [198s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spant)
  spant 2.19.0
  
  Attaching package: 'spant'
  
  The following object is masked from 'package:stats':
  
      sd
  
  > 
  > test_check("spant")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
  > 
  > proc.time()
     user  system elapsed 
    26.48    6.20   32.68
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(sparkhail)
  > library(sparklyr)
  
  Attaching package: 'sparklyr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > # for travis and devtools
  > if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  +   spark_ver <- Sys.getenv("SPARK_VERSION")
  +   if(spark_ver != "") sparklyr::spark_install(version = spark_ver)
  +   if(sparkhail:::hail_exists() == "") hail_install()
  + }
  > 
  > test_check("sparkhail")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-1-hail_install.R:4:3', 'test-data_frame.R:4:3',
    'test-data_frame.R:23:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.78    0.21    1.98
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparklyr.nested)
  > 
  > test_check("sparklyr.nested")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     1.51    0.20    1.70
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    java   3.8Mb
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparktf)
  > 
  > if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  +   test_check("sparktf")
  +   on.exit({spark_disconnect_all()})
  + }
  > 
  > proc.time()
     user  system elapsed 
     1.18    0.21    1.39
Running 'spelling.R' [0s]
  Running 'testthat.R' [210s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparrpowR)
  
  Welcome to {sparrpowR} version 0.2.8
  > help("sparrpowR") # for documentation
  > citation("sparrpowR") # for how to cite
  
  > 
  > ## WORKAROUND: Avoid R bug 18119 [1] that is trigger when for instance the
  > ## 'tcltk' package is loaded on macOS, or when running in the RStudio Console
  > ## [1] https://bugs.r-project.org/bugzilla/show_bug.cgi?id=18119
  > options(parallelly.makeNodePSOCK.setup_strategy = "sequential")
  > 
  > test_check("sparrpowR")
  
  
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 24 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-test-spatial_plots.R:57:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 24 ]
  > future::plan(future::sequential)
  > 
  > proc.time()
     user  system elapsed 
    11.65    1.01   43.26
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparsebnUtils)
  > 
  > test_check("sparsebnUtils")
  [ FAIL 0 | WARN 2 | SKIP 1 | PASS 391 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-setGraphPackage.R:35:1'
  
  [ FAIL 0 | WARN 2 | SKIP 1 | PASS 391 ]
  > 
  > proc.time()
     user  system elapsed 
     7.48    0.62    8.07
Running 'spelling.R' [0s]
  Running 'testthat.r' [156s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > library(testthat)
  > library(sparsediscrim)
  > 
  > test_check("sparsediscrim")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): 'test-rda-high-dim.r:42:1', 'test-rda-high-dim.r:61:1'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
  > 
  > proc.time()
     user  system elapsed 
     4.09    0.56    4.65
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sparseEigen)
  > 
  > test_check("sparseEigen")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     0.85    0.21    1.07
Running 'test-all.R' [158s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library('SparseGrid')
  > 
  > if(require("testthat", quietly = TRUE)) {
  +     test_package("SparseGrid")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  No installed testthat tests found for SparseGrid
  > 
  > proc.time()
     user  system elapsed 
     0.34    0.15    0.48
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ops <- options("crayon.enabled" = FALSE)
  > library(testthat)
  > require("covr")
  Loading required package: covr
  > 
  > test_check("sparseinv")
  Loading required package: sparseinv
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
  > options(ops)
  > 
  > proc.time()
     user  system elapsed 
     2.45    0.26    2.65
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Running 'spatialCovTests.R' [169s]
Running the tests in 'tests/spatialCovTests.R' failed.
Complete output:
  > library(spatialCovariance)
  > 
  > xVals <- seq(1,10,length=101)
  > yVals <- NULL
  > 
  > nrows <- 1
  > ncols <- 1
  > rowsep <- 0
  > colsep <- 0
  > 
  > for(x in xVals)
  +   {
  +     rowwidth <- x
  +     colwidth <- x
  +     info <- precompute(nrows,ncols,rowwidth,colwidth,rowsep,colsep,cat.level=0)
  +     V <- computeV(info,class="ldt",cat.level=0)
  +     yVals <- c(yVals,V[1,1])  ## should be 
  +   }
  > 
  > cat("Passes",sum((yVals-((25-4*pi-4*log(2))/12-log(xVals)))<1e-12),"of 101 tests\n")
  Passes 101 of 101 tests
  > 
  > nrows <- 2
  > ncols <- 2
  > rowsep <- 0
  > colsep <- 0
  > rowwidth <- 1
  > colwidth <- 10
  > info <- precompute(nrows,ncols,rowwidth,colwidth,rowsep,colsep,cat.level=0)
  > V1 <- computeV(info,class="ldt",cat.level=0)
  > rowwidth <- 10
  > colwidth <- 1
  > info <- precompute(nrows,ncols,rowwidth,colwidth,rowsep,colsep,cat.level=0)
  > V2 <- computeV(info,class="ldt",cat.level=0)
  > cat("Passes", sum(V1 - V2[c(1,3,2,4),c(1,3,2,4)] == 0),"out of 16 additional tests\n")
  Passes 16 out of 16 additional tests
  > 
  > a <- rowwidth
  > b <- colwidth
  > (25*a^2*b^2 - 8 * a* b^3 * atan(a/b) - 8* a^3* b* atan(b/a) - 2*a^4*log(a) -2*b^4*log(b) + (a^4 - 6*a^2*b^2 + b^4)*log(a^2 + b^2))/(12*a^2*b^2)
  [1] -0.8999944
  > V2[1,1]
  [1] -0.8999944
  > 
  > proc.time()
     user  system elapsed 
     0.39    0.07    0.45
Running 'testthat.R' [277s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SpatialDDLS)
  
  Attaching package: 'SpatialDDLS'
  
  The following object is masked from 'package:base':
  
      saveRDS
  
  > 
  > test_check("SpatialDDLS")
     user  system elapsed 
     0.22    0.01    0.23 
     user  system elapsed 
     0.27    0.02    0.29 
     user  system elapsed 
     0.32    0.00    0.33 
     user  system elapsed 
     0.18    0.00    0.17 
     user  system elapsed 
     0.17    0.00    0.17 
     user  system elapsed 
     0.14    0.00    0.14 
  [1] "Check Python dependencies"
  [ FAIL 0 | WARN 0 | SKIP 7 | PASS 125 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • .checkPythonDependencies(alert = "none") is not TRUE (7):
    'test_dnnModel.R:3:1', 'test_evalMetrics.R:3:1',
    'test_plotSpatialCoor.R:3:1', 'test_utils.R:140:5', 'test_utils.R:168:5',
    'test_utils.R:233:5', 'test_utils.R:267:5'
  
  [ FAIL 0 | WARN 0 | SKIP 7 | PASS 125 ]
  > 
  > proc.time()
     user  system elapsed 
    74.53    3.25  112.96
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Running 'testthat.R' [197s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spatialising)
  > 
  > test_check("spatialising")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
  > 
  > proc.time()
     user  system elapsed 
    37.98    0.73   38.67
Running 'testthat.R' [187s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SpatialKDE)
  > 
  > test_check("SpatialKDE")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
  > 
  > proc.time()
     user  system elapsed 
    11.26    0.54   11.76
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    help   1.7Mb
Running 'testthat.R' [324s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(spatialwarnings)
  Loading required package: future
  This is spatialwarnings 3.0.3
  Use plan(multisession) to set up parallel processing
  > if ( require("testthat") ) { 
  +   test_check("spatialwarnings")
  + }
  Loading required package: testthat
  [ FAIL 0 | WARN 5 | SKIP 2 | PASS 114 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-custom_indicator.R:25:3', 'test-workflows.R:33:3'
  
  [ FAIL 0 | WARN 5 | SKIP 2 | PASS 114 ]
  > 
  > proc.time()
     user  system elapsed 
   143.76    5.90  149.71
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spatialwidget)
  > 
  > test_check("spatialwidget")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
  > 
  > proc.time()
     user  system elapsed 
     1.21    0.32    1.53
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SpatMCA)
  Welcome to SpatMCA
  > 
  > test_check("SpatMCA")
  
  warning: solve(): system is singular; attempting approx solution
  Invalid object! Please enter a `spatmca` objectThe input number of cores is invalid - default is  96The number of rows of x1 should be equal to the number of columns of Y1.The number of rows of x2 should be equal to the number of columns of Y2.Number of locations must be larger than 2.Dimension of locations must be less 4.The numbers of sample sizes of both data should be equalNumber of folds must be less than sample size, but got M = 101Welcome to SpatMCA
  Welcome to SpatMCA
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 58 ]
  
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 58 ]
  > 
  > proc.time()
     user  system elapsed 
     8.90    0.39    8.93
Running 'testthat.R' [198s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spatsoc)
  Note: spatsoc has been updated to follow the R-spatial evolution. 
  Package dependencies and some functions have been modified. 
  Please see the NEWS for details: 
  https://docs.ropensci.org/spatsoc/index.html#news
  > library(data.table)
  > library(sf)
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  > data.table::setDTthreads(1)
  > test_check("spatsoc")
  [ FAIL 0 | WARN 12 | SKIP 0 | PASS 291 ]
  
  [ FAIL 0 | WARN 12 | SKIP 0 | PASS 291 ]
  > 
  > proc.time()
     user  system elapsed 
    28.43    1.75   30.23
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running 'circleseg.R' [0s]
  Running 'fmla.R' [169s]
  Running 'indices.R' [171s]
  Running 'numerical.R' [0s]
  Running 'segments.R' [0s]
  Running 'tekst.R' [0s]
Running the tests in 'tests/fmla.R' failed.
Complete output:
  > #'   tests/fmla.R
  > #'
  > #'   Manipulation of formulae
  > 
  > require(spatstat.utils)
  Loading required package: spatstat.utils
  > 
  > #'  code coverage of special cases
  > identical.formulae(y ~ x, NULL)
  [1] FALSE
  > termsinformula(NULL)
  character(0)
  > offsetsinformula(y ~ x)
  character(0)
  > lhs.of.formula(~x)
  NULL
  > rhs.of.formula(y ~ x, tilde=FALSE)
  x
  > f <- ~x
  > lhs.of.formula(f) <- quote(y)
  > print(f)
  y ~ x
  > can.be.formula("y ~ x")
  [1] TRUE
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.04    0.23 
Running the tests in 'tests/indices.R' failed.
Complete output:
  > #' Header for spatstat.utils/tests/*R
  > #'
  > 
  > require(spatstat.utils)
  Loading required package: spatstat.utils
  > ALWAYS <- FULLTEST <- TRUE
  > #' indices.R
  > #' Tests of code for understanding index vectors etc
  > #' $Revision: 1.3 $ $Date: 2020/05/11 01:25:34 $
  > 
  > if(FULLTEST) {
  + local({
  + 
  +   a <- grokIndexVector(c(FALSE,TRUE),         10)
  +   b <- grokIndexVector(rep(c(FALSE,TRUE), 7), 10)
  +   d <- grokIndexVector(c(2,12),               10)
  +   e <- grokIndexVector(letters[4:2], nama=letters)
  +   f <- grokIndexVector(letters[10:1], nama=letters[1:5])
  +   g <- grokIndexVector(-c(2, 5),              10)
  +   h <- grokIndexVector(-c(2, 5, 15),          10)
  + 
  +   Nam <- letters[1:10]
  +   j  <- positiveIndex(-c(2,5), nama=Nam)
  +   jj <- logicalIndex(-c(2,5), nama=Nam)
  +   k  <- positiveIndex(-c(2,5), nama=Nam)
  +   kk <- logicalIndex(-c(2,5), nama=Nam)
  +   mm <- positiveIndex(c(FALSE,TRUE), nama=Nam)
  +   nn <- positiveIndex(FALSE, nama=Nam)
  + })
  + }
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.07    0.25
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data     2.5Mb
    shapes   3.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    help   1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
    etc   1.4Mb
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spdesign)
  Loading required package: stringr
  ┌────────────────────────────────────────────────────────────────────────────────────┐
  │                                                                                    │
  │                                  THANK YOU FOR USING SPDESIGN!                     │
  │                                                                                    │
  │   You are currently using version: 0.0.3                                           │
  │   The latest stable version is:    0.0.3                                           │
  │   Package website with documentation and examples: https://spdesign.edsandorf.me   │
  │   To cite the package:             utils::citation('spdesign')                     │
  │                                                                                    │
  └────────────────────────────────────────────────────────────────────────────────────┘
  
  Attaching package: 'spdesign'
  
  The following object is masked from 'package:stats':
  
      cor
  
  > 
  > test_check("spdesign")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 97 ]
  > 
  > proc.time()
     user  system elapsed 
     1.28    0.48    1.78
Running 'testthat.R' [196s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("spduration")
  > 
  > test_check("spduration")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
  > 
  > proc.time()
     user  system elapsed 
    30.71    1.17   31.89
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SpecsVerification)
  > 
  > test_check('SpecsVerification')
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.81    0.17    0.93
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
  > 
  > proc.time()
     user  system elapsed 
     6.35    0.70    7.04
Documented arguments not in \usage in Rd file 'i_is_index.Rd':
  'max_length'

Documented arguments not in \usage in Rd file 'i_read_asd_spectra.Rd':
  'format'

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.
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("spectrolab")
  spectrolab version: 0.0.18
  
  Please cite:
  Meireles J, Schweiger A, Cavender-Bares J (2017). spectrolab: Class
  and Methods for Spectral Data in R. doi:10.5281/zenodo.3934575
  <https://doi.org/10.5281/zenodo.3934575>, R package version 0.0.18,
  <https://CRAN.R-project.org/package=spectrolab>.DOI: https://doi.org/10.5281/zenodo.3934575
  
  Attaching package: 'spectrolab'
  
  The following objects are masked from 'package:stats':
  
      sd, smooth, var
  
  > 
  > test_check("spectrolab")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 81 ]
  > 
  > proc.time()
     user  system elapsed 
     5.23    0.35    5.57
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spex)
  > 
  > test_check("spex")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 35 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-sf-buf.R:1:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 35 ]
  > 
  > proc.time()
     user  system elapsed 
      8.4     0.5     8.9
Objects in \usage without \alias in Rd file 'add_details.Rd':
  '\S4method{add_details}{spflow_model}'

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.
Running 'countingTest.R' [154s]
  Running 'profileTest.R' [0s]
Running the tests in 'tests/countingTest.R' failed.
Complete output:
  > library(spgs)
  > 
  > #Set random number generator and initialise random seed
  > set.seed(331, kind="Mersenne-Twister", normal.kind="Inversion")
  > 
  > #Simulate a sequence of nucleotides as a Markov chain
  > s <- simulateMarkovChain(500, matrix(0.25, 4, 4), states=c("a", "c", "g", "t"))
  > 
  > #Circular tests
  > pc <- pair.counts(s)
  > tc <- triple.counts(s)
  > qc <- quadruple.counts(s)
  > cc4 <- cylinder.counts(s, 1:4)
  > c2l2c <- spgs:::cyl2lag2.counts(s, 10)
  > circ.res <- c(
  + 	identical(apply(tc, 1:2, sum), apply(tc, 2:3, sum)),
  + 	identical(apply(qc, 1:2, sum), apply(qc, 2:3, sum)),
  + 	identical(apply(qc, 2:3, sum), apply(qc, 3:4, sum)),
  + 	identical(pc, apply(cc4, 1:2, sum)),
  + 	identical(pc, apply(cc4, 2:3, sum)),
  + 	identical(pc, apply(cc4, 3:4, sum)),
  + 	identical(tc, apply(cc4, 1:3, sum)),
  + 	identical(tc, apply(cc4, 2:4, sum)),
  + 	identical(qc, cc4),
  + 	identical(qc, c2l2c[,,,,3])
  + )
  > print(circ.res)
   [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
  > 
  > #Non-circular tests
  > p <- pair.counts(s, circular=FALSE)
  > t <- triple.counts(s, circular=FALSE)
  > q <- quadruple.counts(s, circular=FALSE)
  > c4 <- cylinder.counts(s, 1:4, circular=FALSE)
  > c2l2 <- spgs:::cyl2lag2.counts(s, 10, circular=FALSE)
  > 
  > print(c(sum(p!=pc), sum(t!=tc), sum(q!=qc)))
  [1] 1 2 3
  > 
  > noncirc.res <- c(
  + 	identical(p, cylinder.counts(s, 1:2, circular=FALSE)),
  + 	identical(t, cylinder.counts(s, 1:3, circular=FALSE)),
  + 	identical(q, cylinder.counts(s, 1:4, circular=FALSE)),
  + 	identical(q, c2l2[,,,,3])
  + )
  > print(noncirc.res)
  [1] TRUE TRUE TRUE TRUE
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.09    0.28
Running 'tinytest.R' [173s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("spgwr")
  + }
  Loading required package: sp
  Loading required package: spData
  To access larger datasets in this package, install the spDataLarge
  package with: `install.packages('spDataLarge',
  repos='https://nowosad.github.io/drat/', type='source')`
  NOTE: This package does not constitute approval of GWR
  as a method of spatial analysis; see example(gwr)
  
  test_gwr_0.R..................    0 tests    
  test_gwr_0.R..................    0 tests    
  test_gwr_0.R..................    1 tests [0;32mOK[0m 
  test_gwr_0.R..................    2 tests [0;32mOK[0m 
  test_gwr_0.R..................    3 tests [0;32mOK[0m 
  test_gwr_0.R..................    4 tests [0;32mOK[0m 
  test_gwr_0.R..................    5 tests [0;32mOK[0m 
  test_gwr_0.R..................    6 tests [0;32mOK[0m 
  test_gwr_0.R..................    7 tests [0;32mOK[0m 
  test_gwr_0.R..................    8 tests [0;32mOK[0m [0;34m0.9s[0m
  All ok, 8 results (0.9s)
  > 
  > proc.time()
     user  system elapsed 
     1.15    0.15    1.32
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spider)
  > data(anoteropsis)
  > 
  > test_check("spider")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.15    0.95
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spind)
  > 
  > test_check("spind")
  [ FAIL 0 | WARN 1 | SKIP 23 | PASS 23 ]
  
  ══ Skipped tests (23) ══════════════════════════════════════════════════════════
  • On CRAN (23): 'test_GEE_WRM.R:4:3', 'test_GEE_WRM.R:34:3',
    'test_GEE_WRM.R:59:3', 'test_acfft.R:4:3', 'test_acfft.R:29:3',
    'test_covar_plot.R:11:3', 'test_covar_plot.R:31:3', 'test_mmiGEE.R:4:3',
    'test_mmiGEE.R:44:3', 'test_mmiWMRR.R:4:3', 'test_rvi_plot.R:14:3',
    'test_rvi_plot.R:33:3', 'test_scaleWMRR.R:4:3', 'test_scaleWMRR.R:25:3',
    'test_step_spind.R:5:3', 'test_step_spind.R:29:3', 'test_step_spind.R:55:3',
    'test_step_spind.R:72:3', 'test_thdep_thindep.R:18:3',
    'test_thdep_thindep.R:34:3', 'test_thdep_thindep.R:61:3',
    'test_thdep_thindep.R:75:3', 'test_thdep_thindep.R:83:3'
  
  [ FAIL 0 | WARN 1 | SKIP 23 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
    16.75    1.71   18.43
Running 'spelling.R' [0s]
  Running 'testthat.R' [236s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spinifex)
  Loading required package: tourr
  --------------------------------------------------------
  spinifex --- version 0.3.7.0
  Please share bugs, suggestions, and feature requests at:
  https://github.com/nspyrison/spinifex/issues/
  --------------------------------------------------------
  
  Attaching package: 'spinifex'
  
  The following objects are masked from 'package:tourr':
  
      is_orthonormal, save_history
  
  > 
  > test_check("spinifex")
  
  Attaching package: 'ggplot2'
  
  The following objects are masked from 'package:spinifex':
  
      scale_colour_discrete, scale_fill_discrete
  
  Loading required namespace: hexbin
  `nframes` and `fps` adjusted to match transition
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 149 ]
  
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 149 ]
  > 
  > proc.time()
     user  system elapsed 
    74.17    4.37   73.23
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spiro)
  > 
  > test_check("spiro")
    load step time VO2 VCO2 RR VT VE HR PetO2 PetCO2 VO2_rel VCO2_rel RE RER CHO
  1    0    0    1  NA   NA NA NA NA NA    NA     NA      NA       NA NA  NA  NA
    FO add
  1 NA new
  for pre-measures, interval was set to length of measures (60 seconds)
  for step 23, interval was set to length of step (10 seconds)
  for load steps, interval was set to 30 seconds
  for step 23, interval was set to length of step (10 seconds)
  for load steps, interval was set to 30 seconds
  Last step was excluded from summary calculation due to termination of the test
  For heart rate data, smoothing was based on interpolated values.
  For heart rate data, smoothing was based on interpolated values.
  [ FAIL 0 | WARN 1 | SKIP 20 | PASS 56 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test-add_hr.R:5:3', 'test-add_protocol.R:27:3',
    'test-add_protocol.R:35:3', 'test-spiro.R:22:3', 'test-spiro_get.R:16:3',
    'test-spiro_get.R:25:3', 'test-spiro_get.R:32:3', 'test-spiro_smooth.R:44:3',
    'test-spiro_smooth.R:50:3', 'test-spiro_smooth.R:63:3',
    'test-spiro_smooth.R:70:3', 'test-spiro_smooth.R:77:3',
    'test-spiro_summary.R:5:3', 'test-spiro_summary.R:12:3',
    'test-spiro_summary.R:26:3', 'test_spiro_max.R:7:3', 'test_spiro_max.R:20:3',
    'test_spiro_plot.R:25:3', 'test_spiro_plot.R:32:3', 'test_spiro_plot.R:40:3'
  
  [ FAIL 0 | WARN 1 | SKIP 20 | PASS 56 ]
  Deleting unused snapshots:
  • spiro_plot/bsmooth.svg
  • spiro_plot/color.svg
  • spiro_plot/grid.svg
  • spiro_plot/hr.svg
  • spiro_plot/theme.svg
  • spiro_plot/tsmooth.svg
  • spiro_plot/vertline.svg
  > 
  > proc.time()
     user  system elapsed 
    18.10    1.34   19.45
Invalid package aliases in Rd file 'split_feasibility.Rd':
  'split_feasibility-package'
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SplitGLM)
  > 
  > test_check("SplitGLM")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.14    0.93
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(splitSelect)
  > 
  > test_check("splitSelect")
  Generating 1701 total splits...
  Generating 1050 total splits...
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     2.84    0.20    3.04
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(splitTools)
  > 
  > test_check("splitTools")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ]
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.37    1.82
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spMaps)
  Loading required package: sf
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  Loading required package: sp
  > 
  > test_check("spMaps")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
  > 
  > proc.time()
     user  system elapsed 
     5.50    0.28    5.78
Running 'testthat.R' [240s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spmodel)
  > 
  > test_check("spmodel")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 966 ]
  > 
  > proc.time()
     user  system elapsed 
    68.93    1.93   71.12
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Note that you would never run this file directly. This is used by tools::testInstallPackages()
  > # and other packages like covr.
  > # To actually run the tests, you need to set the working directory then run
  > # devtools::test()
  > 
  > # This line ensures that R CMD check can run tests.
  > # See https://github.com/hadley/testthat/issues/144
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(spongebob)
  > 
  > testthat::test_check('spongebob')
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 218 ]
  Warning message:
  `aes_string()` was deprecated in ggplot2 3.0.0.
  ℹ Please use tidy evaluation idioms with `aes()`.
  ℹ See also `vignette("ggplot2-in-packages")` for more information. 
  > 
  > proc.time()
     user  system elapsed 
     6.54    0.53    7.07
Running 'testthat.R' [188s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("sport")
  Loading required package: sport
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 239 ]
  > 
  > proc.time()
     user  system elapsed 
    16.65    0.65   17.29
Running 'testthat.R' [191s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sportyR)
  > 
  > test_check("sportyR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 129 ]
  > 
  > proc.time()
     user  system elapsed 
    31.00    0.84   31.85
Running 'spelling.R' [160s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.06    0.21
Documented arguments not in \usage in Rd file 'checkFunEvalsDesignSize.Rd':
  'fun' 'upper'

Documented arguments not in \usage in Rd file 'print.spotBOModel.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotGaussianProcessModel.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotLOESS.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotLassoModel.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotLinearModel.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotRSM.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotRandomForest.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotRanger.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotSeverity.Rd':
  'object'

Documented arguments not in \usage in Rd file 'print.spotTreeModel.Rd':
  'object'

Documented arguments not in \usage in Rd file 'simulationSpectral.Rd':
  '...'

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.
Missing or unexported object: 'BalancedSampling::lcubeflightphase'
Error(s) in re-building vignettes:
--- re-building 'spq_userguide.Rmd' using rmarkdown

Quitting from lines 500-501 [unnamed-chunk-24] (spq_userguide.Rmd)
Error: processing vignette 'spq_userguide.Rmd' failed with diagnostics:
Invalid index: field name 'x_start' not found
--- failed re-building 'spq_userguide.Rmd'

SUMMARY: processing the following file failed:
  'spq_userguide.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("spray")
  Loading required package: spray
  
  Attaching package: 'spray'
  
  The following objects are masked from 'package:base':
  
      pmax, pmin
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 230 ]
  > 
  > proc.time()
     user  system elapsed 
     9.28    0.62   10.03
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.2Mb
Argument items with no description in Rd file 'sim.kong.Rd':
  'gamma' 'beta' 'design' 'rho' 'seed' 'impute' 'ppi'
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sptotal)
  > 
  > test_check("sptotal")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
  > 
  > proc.time()
     user  system elapsed 
     1.78    0.20    1.92
Running 'doSvUnit.R' [155s]
Running the tests in 'tests/doSvUnit.R' failed.
Complete output:
  > #! /usr/bin/Rscript --vanilla --default-packages=utils,stats,methods,svUnit
  > pkg <- "sqldf"
  > require(svUnit)  # Needed if run from R CMD BATCH
  Loading required package: svUnit
  > require(pkg, character.only = TRUE)  # Needed if run from R CMD BATCH
  Loading required package: sqldf
  Loading required package: gsubfn
  Loading required package: proto
  Loading required package: RSQLite
  > # unlink("mypkgTest.txt")  # Make sure we generate a new report
  > mypkgSuite <- svSuiteList(pkg, excludeList = NULL)  # List all our test suites
  > runTest(mypkgSuite, name = "svUnit")  # Run them...
  using driver: sqlite 
  > # protocol(Log(), type = "text", file = "mypkgTest.txt")  # ... and write report
  > Log()
  = A svUnit test suite run in less than 0.1 sec with:
  
  * test.all ... OK
  
  
  == test.all (in runit.all.R) run in less than 0.1 sec: OK
  
  //Pass: 28 Fail: 0 Errors: 0//
  
  > 
  > 
  > proc.time()
     user  system elapsed 
     1.43    0.29    1.76
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sqlhelper)
  > 
  > test_check("sqlhelper")
  Note: method with signature 'DBIObject#sf' chosen for function 'dbDataType',
   target signature 'SQLiteConnection#sf'.
   "SQLiteConnection#ANY" would also be valid
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 151 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-read_configs.R:20:3', 'test-read_configs.R:28:3'
  • Requires local SQL Server instance (1): 'test-prepare_sql.R:156:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 151 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     5.75    0.75    6.48
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sqliteutils)
  > 
  > test_check("sqliteutils")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     1.56    0.28    1.79
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sqlscore)
  > 
  > test_check("sqlscore")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 97 ]
  > 
  > proc.time()
     user  system elapsed 
     7.81    0.64    8.43
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(srlars)
  > 
  > test_check("srlars")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     7.20    0.59    7.76
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(srlTS)
  > 
  > test_check("srlTS")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 95 ]
  > 
  > proc.time()
     user  system elapsed 
     6.89    1.65    8.53
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(sr)
  > 
  > test_check("sr")
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 14 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-gamma_histogram.R:2:3', 'test-gamma_test.R:18:3',
    'test-get_Mlist.R:10:3', 'test-increasing_search.R:14:3',
    'test-mask_histogram.R:3:3', 'test-moving_window_search.R:11:3'
  
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 14 ]
  Deleting unused snapshots:
  • gamma_histogram/full-embedding-histogram.svg
  • gamma_test/gamma-test-plot.svg
  • get_Mlist/as-vratio.svg
  • get_Mlist/basic-mlist-works.svg
  • get_Mlist/mlist-on-non-modular-length.svg
  • get_Mlist/mlist-on-vector-input.svg
  • increasing_search/increasing-search-vratios.svg
  • increasing_search/standard-increasing-search.svg
  • mask_histogram/plot-50-bad.svg
  • mask_histogram/plot-50-good.svg
  • moving_window_search/moving-window-vratio.svg
  • moving_window_search/moving-window-works.svg
  > 
  > proc.time()
     user  system elapsed 
     2.06    0.45    2.50
Running 'spelling.R' [166s]
  Running 'testthat.R' [24s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.10    0.12    0.23
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ssc)
  > 
  > test_check("ssc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 178 ]
  > 
  > proc.time()
     user  system elapsed 
    12.92    0.84   13.76
Running 'spelling.R' [171s]
  Running 'testthat.R' [247s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.12    0.06    0.18 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(ssd4mosaic)
  > 
  > test_check("ssd4mosaic")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 69 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-golem-recommended.R:72:5'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 69 ]
  > 
  > proc.time()
     user  system elapsed 
    74.90    2.26   77.20
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.6Mb
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sship)
  > 
  > test_check("sship")
  [ FAIL 0 | WARN 12 | SKIP 0 | PASS 52 ]
  
  [ FAIL 0 | WARN 12 | SKIP 0 | PASS 52 ]
  > 
  > proc.time()
     user  system elapsed 
     2.51    0.29    2.79
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running 'engine.R' [0s]
  Comparing 'engine.Rout' to 'engine.Rout.save' ...4d3
< Linking to libssh v0.10.5
  Running 'spelling.R' [152s]
  Running 'testthat.R' [164s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.12    0.10    0.20 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ssh)
  Linking to libssh v0.10.5
  > 
  > #test_check("ssh")
  > 
  > proc.time()
     user  system elapsed 
     0.42    0.07    0.59
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > require(SSLR)
  Loading required package: SSLR
  > 
  > test_check("SSLR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 153 ]
  > 
  > proc.time()
     user  system elapsed 
    15.64    1.70   17.37
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(ssMRCD)
  > 
  > test_check("ssMRCD")
  No target matrix given. The ssMRCD will use the MCD defaultwise.
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
  > 
  > proc.time()
     user  system elapsed 
     1.89    0.28    2.14
Running 'testthat.R' [279s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(SSN2)
  > 
  > test_check("SSN2")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 349 ]
  > 
  > proc.time()
     user  system elapsed 
   111.93    2.34  114.39
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ssrn)
  > 
  > test_check("ssrn")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ]
  > 
  > proc.time()
     user  system elapsed 
     1.37    0.18    1.56
Running 'spelling.R' [0s]
  Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sss)
  > 
  > test_check("sss")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
  > 
  > proc.time()
     user  system elapsed 
     1.71    0.34    2.04
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stablespec)
  > 
  > test_check("stablespec")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 55 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-modelFitness.R:60:3', 'test-stablespec.R:186:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 55 ]
  > 
  > proc.time()
     user  system elapsed 
     1.56    0.32    1.82
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stabm)
  > 
  > test_check("stabm")
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 300 ]
  
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 300 ]
  > 
  > proc.time()
     user  system elapsed 
    12.75    0.54   13.28
Running 'testthat.R' [150s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stacomirtools)
  Loading required package: RODBC
  Loading required package: DBI
  Loading required package: pool
  > user <- "postgres"
  > password <- "postgres"
  > host <- "localhost"
  > test_check("stacomirtools")
  [ FAIL 0 | WARN 0 | SKIP 19 | PASS 0 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-00-connectionDB.R:6:6', 'test-00-connectionDB.R:22:4',
    'test-00-connectionDB.R:39:4', 'test-00-connectionDB.R:54:4',
    'test-00-connectionDB.R:73:4', 'test-00-connectionDB.R:87:4',
    'test-00-connectionDB.R:97:4', 'test-01-connectionODBC.R:6:7',
    'test-02-requeteDB.R:4:4', 'test-02-requeteDB.R:19:4',
    'test-02-requeteDB.R:31:4', 'test-02-requeteDB.R:52:4',
    'test-02-requeteDB.R:69:4', 'test-03-requeteODBC.R:4:4',
    'test-03-requeteODBC.R:18:7', 'test-04-requeteODBCwhere.R:4:4',
    'test-05-requeteODBCwheredate.R:4:4', 'test-06-requeteDBwhere.R:4:4',
    'test-07-requeteDBwheredate.R:4:4'
  
  [ FAIL 0 | WARN 0 | SKIP 19 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.64    0.29    1.92
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(standardize)
  
   *********************************************************** 
            Loading standardize package version 0.2.2          
       Call standardize.news() to see new features/changes     
   *********************************************************** 
  
  > 
  > test_check("standardize")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 73 ]
  > 
  > proc.time()
     user  system elapsed 
     3.85    0.35    4.15
Running 'testthat.R' [184s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(standardlastprofile)
  > 
  > test_check("standardlastprofile")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 40 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-readme.R:52:3', 'test-readme.R:82:3',
    'test-vignette_examples.R:37:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 40 ]
  > 
  > proc.time()
     user  system elapsed 
     5.28    0.34    5.60
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
Running 'rstan.R' [167s]
Running the tests in 'tests/rstan.R' failed.
Complete output:
  > #Sys.setenv("R_TESTS" = "")
  > #library(rstan)
  > #stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}'
  > #mod <- stan_model(model_code = stancode, verbose = TRUE)
  > #fit <- sampling(mod, data = list(y_mean = 0))
  >   
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.04    0.18
Running 'spelling.R' [0s]
  Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stapler)
  > 
  > test_check("stapler")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
  > 
  > proc.time()
     user  system elapsed 
     2.70    0.31    3.01
Running 'testthat.R' [184s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(starnet)
  > 
  > testthat::test_check(package="starnet",stop_on_warning=FALSE)
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
    13.37    0.62   14.01
Package suggested but not available for checking: 'starsdata'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(starwarsdb)
  > 
  > test_check("starwarsdb")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 33 ]
  Warning messages:
  1: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
  2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
  3: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
  > 
  > proc.time()
     user  system elapsed 
     3.73    1.00    4.62
Running 'spelling.R' [147s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.25    0.00    0.23
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.3Mb
Package suggested but not available for checking: 'asreml'
Running 'testthat.R' [215s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(statgenGxE)
  > 
  > test_check("statgenGxE")
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 448 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3',
    'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3',
    'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3',
    'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3',
    'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3',
    'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3',
    'test-report.R:41:3', 'test-summaries.R:75:3'
  
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 448 ]
  > 
  > proc.time()
     user  system elapsed 
    40.59    1.14   41.73
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/statmod.Rcheck/00install.out' for details.
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Running 'skip-download.R' [166s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/skip-download.R' failed.
Complete output:
  > # To run download functions you need an internet connection.
  > # pref a fast one
  > skip_download = function() {
  +   if(!curl::has_internet() |
  +      identical(Sys.getenv("DONT_DOWNLOAD_ANYTHING"), "true"))
  +     skip("No connection to run download function.")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.01    0.20
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
Running 'spelling.R' [156s]
  Running 'testthat.R' [157s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.01    0.18 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(statsr)
  Loading required package: BayesFactor
  Loading required package: coda
  Loading required package: Matrix
  ************
  Welcome to BayesFactor 0.9.12-4.7. If you have questions, please contact Richard Morey (richarddmorey@gmail.com).
  
  Type BFManual() to open the manual.
  ************
  
  Attaching package: 'BayesFactor'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("statsr")
  Single numerical variable
  n = 28, y-bar = 55.5239, s = 23.254
  (Assuming proper prior:  mu | sigma^2 ~ N(35, *sigma^2/25)
  (Assuming proper prior: 1/sigma^2 ~ G(24/2,156.25*24/2)
  
  Joint Posterior Distribution for mu and 1/sigma^2:
   N(45.8428, sigma^2/53) G(52/2, 8.6769*52/2)
  
  Marginal Posterior for mu:
  Student t with posterior mean = 45.8428, posterior scale = 2.9457 on 52 df
  
  95% CI: (39.9319 , 51.7537)
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     2.45    0.46    2.92
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stcov)
  > 
  > test_check("stcov")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     0.68    0.14    0.75
Running 'testthat.R' [224s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stdmod)
  > 
  > test_check("stdmod")
  
  Number of valid bootstrap estimates: 91
  [ FAIL 0 | WARN 0 | SKIP 9 | PASS 153 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test_plotmod.R:1:1',
    'test_plotmod_percentile_more_levels.R:1:1', 'test_plotmod_tumble.R:1:1',
    'test_plotmod_user_value.R:1:1', 'test_stdmod_lavaan_2.R:1:1',
    'test_stdmod_selected_boot.R:1:1', 'test_stdmod_selected_boot_fac.R:1:1',
    'test_stdmod_selected_vcov.R:1:1'
  • Test in interactive sessions (1): 'test_stdmod_selected_print_summary.R:1:1'
  
  [ FAIL 0 | WARN 0 | SKIP 9 | PASS 153 ]
  > 
  > proc.time()
     user  system elapsed 
    54.23    3.23   57.42
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(StempCens)
  > 
  > test_check("StempCens")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.25    0.31    2.54
Running 'testthat.R' [150s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stencilaschema)
  
  Attaching package: 'stencilaschema'
  
  The following objects are masked from 'package:methods':
  
      Math, Quote
  
  > 
  > test_check("stencilaschema")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 74 ]
  > 
  > proc.time()
     user  system elapsed 
     1.03    0.21    1.21
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(STEPCAM) 
  > test_check("STEPCAM")
  [ FAIL 0 | WARN 0 | SKIP 22 | PASS 0 ]
  
  ══ Skipped tests (22) ══════════════════════════════════════════════════════════
  • On CRAN (22): 'test-ABC_SMC.R:4:3', 'test-ABC_SMC.R:229:3',
    'test-GenerateValues.R:4:3', 'test-GenerateValues.R:59:3',
    'test-STEPCAM.R:4:3', 'test-STEPCAM_ABC.R:4:3', 'test-TernPlot.R:4:3',
    'test-TernPlot.R:40:3', 'test-calcSD.R:4:3', 'test-calcSD.R:45:3',
    'test-generateFrequencies.R:4:3', 'test-generateFrequencies.R:14:3',
    'test-getRandomVals.R:4:3', 'test-normalizeWeights.R:4:3',
    'test-ordinationAxes.R:4:3', 'test-ordinationAxes.R:153:3',
    'test-perturb.R:4:3', 'test-plotSMC.R:4:3', 'test-plotSTEPCAM.R:4:3',
    'test-scaleSpeciesValues.R:4:3', 'test-scaleSpeciesValues.R:29:3',
    'test-strippeddbFD.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 22 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.79    0.23    3.01
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stepSplitReg)
  > 
  > test_check("stepSplitReg")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     1.73    0.21    1.89
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(stickyr)
  
  Attaching package: 'stickyr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > 
  > test_check("stickyr")
  Adding missing grouping variables: `name`
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
     1.56    0.23    1.73
Running 'testthat.R' [191s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(STMr)
  > 
  > test_check("STMr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1836 ]
  > 
  > proc.time()
     user  system elapsed 
    11.53    3.10   14.75
Running 'spelling.R' [0s]
  Running 'testthat.R' [189s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stochLAB)
  > 
  > test_check("stochLAB")
  
  -- Stochastic CRM for Migratory birds --
  
  i Checking for manditory arguments
  v Checking for manditory arguments [21ms]
  
  i Data validation
  v Data validation [49ms]
  
  i Sampling data
  v Sampling data [53ms]
  
  i Running simulation...
  v Running simulation... [2s]
  
  i Creating outputs
  v Creating outputs [27ms]
  
  -- Stochastic CRM --
  
  i Checking inputs
  v Checking inputs [21ms]
  
  i Preparing data
  v Preparing data [54ms]
  
  i Sampling parameters
  v Sampling parameters [48ms]
  
  \ Calculating collisions | 3/1000 iterations
  v Calculating collisions | 1000/1000 iterations [2.4s]
  
  i Sorting outputs
  v Sorting outputs [934ms]
  
  v Job done!
  
  -- Stochastic CRM --
  
  i Checking inputs
  v Checking inputs [21ms]
  
  i Preparing data
  v Preparing data [46ms]
  
  i Sampling parameters
  v Sampling parameters [59ms]
  
  \ Calculating collisions | 3/1000 iterations
  | Calculating collisions | 652/1000 iterations
  v Calculating collisions | 1000/1000 iterations [2.7s]
  
  i Sorting outputs
  v Sorting outputs [696ms]
  
  v Job done!
  
  -- Stochastic CRM --
  
  i Checking inputs
  v Checking inputs [20ms]
  
  i Preparing data
  v Preparing data [57ms]
  
  i Sampling parameters
  v Sampling parameters [73ms]
  
  \ Calculating collisions | 3/1000 iterations
  | Calculating collisions | 414/1000 iterations
  v Calculating collisions | 1000/1000 iterations [2.7s]
  
  i Sorting outputs
  v Sorting outputs [642ms]
  
  v Job done!
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 96 ]
  > 
  > proc.time()
     user  system elapsed 
    16.78    1.07   17.85
Argument items with no description in Rd file 'd.sum.of.mixtures.EXPLN.Rd':
  'p.vector'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Running 'lint.R' [166s]
  Running 'spelling.R' [0s]
  Running 'testthat.R' [1s]
Running the tests in 'tests/lint.R' failed.
Complete output:
  > library("testthat")
  > 
  > proc.time()
     user  system elapsed 
     0.32    0.12    0.40
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stoRy)
  > 
  > test_check("stoRy")
  [ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]
  
  [ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     2.40    0.34    2.73
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(strand)
  The tzdb package is not installed. Timezones will not be available to Arrow compute functions.
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("strand")
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 89 ]
  
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 89 ]
  > 
  > proc.time()
     user  system elapsed 
    19.53    0.78   20.31
Running 'spelling.R' [167s]
  Running 'testthat.R' [10s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.14    0.07    0.20
Running 'spelling.R' [169s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.01    0.18
Package suggested but not available for checking: 'StrathE2E2examples'
Running 'testthat.R' [228s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > #
  > # A few long running tests make use of the testthat::skip_on_cran() mechanism so that they don't run when on CRAN
  > #
  > # This skip function relies on devtools package setting an environment variable NOT_CRAN, so if you want to run the tests
  > # locally you must either use devtools or set this variable explicitly yourself:
  > #
  > # cd StrathE2E2
  > # R
  > # > library(StrathE2E2)
  > # > Sys.setenv(NOT_CRAN="true")
  > # > testthat::test_dir("tests")
  > #
  > 
  > library(testthat)
  > library(StrathE2E2)
  > 
  > test_check("StrathE2E2")
  [ FAIL 0 | WARN 0 | SKIP 10 | PASS 91 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-Monte-Carlo.R:3:1',
    'test-annealing-ACTmult-HRtarg.R:3:1',
    'test-annealing-ACTmult-ecotarg.R:3:1', 'test-annealing-HRscale.R:3:1',
    'test-annealing-ecology.R:3:1', 'test-internal.R:2:1', 'test-internal.R:9:1',
    'test-plots.R:3:9', 'test-sensitivity_analysis_code.R:3:1',
    'test-sensitivity_analysis_code.R:28:1'
  
  [ FAIL 0 | WARN 0 | SKIP 10 | PASS 91 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
    62.78    1.53   64.28
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(strat)
  > 
  > test_check("strat")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.59    0.12    0.71
Running 'testthat.R' [186s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(streambugs)
  > 
  > test_check("streambugs")
  streambugs
  ----------
  number of state variables: 234
  number of inputs:          0
  number of parameters:      2526
  running C version of streambugs ...
  simulation completed
     user  system elapsed 
     4.73    0.03    4.77 
  streambugs
  ----------
  number of state variables: 54
  number of inputs:          1
  number of parameters:      105
  running R version of streambugs ...
  simulation completed
     user  system elapsed 
     4.78    0.01    4.82 
  streambugs
  ----------
  number of state variables: 54
  number of inputs:          1
  number of parameters:      105
  running C version of streambugs ...
  simulation completed
     user  system elapsed 
     0.27    0.00    0.26 
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
  > 
  > proc.time()
     user  system elapsed 
    25.06    1.50   27.07
Running 'testthat.R' [191s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stressor)
  > 
  > test_check("stressor")
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 82 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • Python is not available (6): 'test-create_virtualenv.R:5:3',
    'test-create_virtualenv.R:11:3', 'test-cv.R:23:3', 'test-mlm.R:2:3',
    'test-mlm.R:18:3', 'test-predict_mlm_stressor.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 82 ]
  > 
  > proc.time()
     user  system elapsed 
     4.23    1.03   23.28
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stressr)
  > 
  > test_check("stressr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
  > 
  > proc.time()
     user  system elapsed 
     2.84    0.26    3.03
Documented arguments not in \usage in Rd file 'get_groups.Rd':
  'groups'

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.
Running 'test-all.R' [170s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("stringb")
  Loading required package: stringb
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 182 ]
  > 
  > proc.time()
     user  system elapsed 
     1.82    0.50    2.31
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.0Mb
Running 'stringmagic_tests.R' [171s]
Running the tests in 'tests/stringmagic_tests.R' failed.
Complete output:
  > 
  > library(stringmagic)
  > 
  > stringmagic:::run_tests(source = TRUE)
  PLURAL 
  
  STRING_MAGIC 
  
  TOOLS 
  
  NULL
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.76    0.06    0.81
Running 'realtest.R' [175s]
Running the tests in 'tests/realtest.R' failed.
Complete output:
  > # This file is part of the 'stringx' project.
  > # Copyleft (c) 2021-2022, Marek Gagolewski <https://www.gagolewski.com>
  > 
  > # Runs all unit tests for the package
  > 
  > this_package <- "stringx"
  > 
  > set.seed(123)
  > library(this_package, character.only=TRUE)
  
  Attaching package: 'stringx'
  
  The following objects are masked from 'package:base':
  
      casefold, chartr, endsWith, gregexec, gregexpr, grep, grepl, gsub,
      ISOdate, ISOdatetime, nchar, nzchar, paste, paste0, regexec,
      regexpr, sprintf, startsWith, strftime, strptime, strrep, strsplit,
      strtrim, strwrap, sub, substr, substr<-, substring, substring<-,
      Sys.time, tolower, toupper, trimws, xtfrm, xtfrm.default
  
  > if (require("realtest", quietly=TRUE)) {
  +     f <- file.path(path.package(this_package), "realtest")
  +     r <- test_dir(f, ".*\\.R$")
  +     x <- summary(r)
  + 
  +     names(r) <- row.names(x)
  +     fails <- x[x[["match"]] == "fail", , drop=FALSE]
  +     if (nrow(fails) > 0) {
  +         fails2 <- as.data.frame(fails[,
  +             !(names(fails) %in% ".expr") & !sapply(fails, function(x) all(is.na(x))),
  +             drop=FALSE])
  +         for (i in row.names(fails2)) {
  +             cat(sprintf("%s:%d:\n", fails2[i, ".file"], fails2[i, ".line"]))
  +             cat("    value: "); str(r[[i]][["object"]][["value"]], indent.str="    ")
  +             cat("    sides: "); str(r[[i]][["object"]][["sides"]], indent.str="    ")
  +         }
  + 
  +         if (require("stringi", quietly=TRUE))
  +             cat(sprintf("%s; %s\n", stri_info(TRUE), Sys.getlocale()))
  + 
  +         stop("some tests failed")
  +     }
  + }
  > 
  > proc.time()
     user  system elapsed 
     1.85    0.06    1.90
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
S3 methods shown with full name in Rd file 'size.penalize.Rd':
  'size.penalize'

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.
Documented arguments not in \usage in Rd file 'subsamp.Rd':
  'x:' 'y:' 's:' 'm:' 'qnum:' 'wplot:'

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.
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(summariser)
  > 
  > test_check("summariser")
  [ FAIL 0 | WARN 1 | SKIP 1 | PASS 17 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_calculations.R:29:3'
  
  [ FAIL 0 | WARN 1 | SKIP 1 | PASS 17 ]
  > 
  > proc.time()
     user  system elapsed 
     1.21    0.34    1.54
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sunburstR)
  > 
  > test_check("sunburstR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
     7.01    0.39    7.40
Auto-generated content requiring editing in Rd file 'supcluster-package.Rd':
  \references: '~~ Literature or other references for background information ~~'
Running 'testthat.R' [187s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("superb")
  Loading required package: superb
  ==> THIS IS A TEST OF runDebug <==
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 190 ]
  > 
  > proc.time()
     user  system elapsed 
    29.14    1.48   30.67
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(SuperGauss)
  
  Attaching package: 'SuperGauss'
  
  The following object is masked from 'package:base':
  
      %*%
  
  > library(testthat)
  > 
  > test_check("SuperGauss")
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 844 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-Circulant-basics.R:27:3',
    'test-Circulant-determinant.R:6:3', 'test-Circulant-product.R:6:3',
    'test-Circulant-solve.R:6:3', 'test-NormalCirculant-grad_full.R:7:3',
    'test-NormalCirculant-logdens.R:6:3', 'test-fft.R:31:3', 'test-fft.R:44:3'
  
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 844 ]
  > 
  > proc.time()
     user  system elapsed 
     4.71    0.48    5.15
Running 'testthat.R' [235s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(superheat)
  > 
  > test_check("superheat")
  [ FAIL 0 | WARN 258 | SKIP 40 | PASS 18 ]
  
  ══ Skipped tests (40) ══════════════════════════════════════════════════════════
  • empty test (40): 'test-labels.R:10:1', 'test-labels.R:17:1',
    'test-labels.R:23:1', 'test-labels.R:29:1', 'test-labels.R:35:1',
    'test-labels.R:42:1', 'test-labels.R:48:1', 'test-labels.R:54:1',
    'test-labels.R:61:1', 'test-labels.R:68:1', 'test-labels.R:76:1',
    'test-labels.R:83:1', 'test-layout-examples.R:9:1',
    'test-layout-examples.R:15:1', 'test-layout-examples.R:22:1',
    'test-layout-examples.R:28:1', 'test-layout-examples.R:37:1',
    'test-layout-examples.R:45:1', 'test-layout-examples.R:51:1',
    'test-layout-examples.R:59:1', 'test-layout-examples.R:67:1',
    'test-layout-examples.R:74:1', 'test-layout-examples.R:82:1',
    'test-layout-examples.R:90:1', 'test-layout-examples.R:99:1',
    'test-layout-examples.R:107:1', 'test-layout-examples.R:120:1',
    'test-layout-examples.R:127:1', 'test-layout-examples.R:135:1',
    'test-layout-examples.R:143:1', 'test-layout-examples.R:153:1',
    'test-layout-examples.R:162:1', 'test-layout-examples.R:171:1',
    'test-layout-examples.R:183:1', 'test-layout-examples.R:190:1',
    'test-layout-examples.R:198:1', 'test-layout-examples.R:206:1',
    'test-layout-examples.R:216:1', 'test-layout-examples.R:225:1',
    'test-layout-examples.R:234:1'
  
  [ FAIL 0 | WARN 258 | SKIP 40 | PASS 18 ]
  > 
  > proc.time()
     user  system elapsed 
    76.35    2.95   79.32
Package suggested but not available for checking: 'extraTrees'
Running 'test_miscs.R' [0s]
  Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(superml)
  Loading required package: R6
  > 
  > test_check("superml")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.23    1.01
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SuperpixelImageSegmentation)
  > 
  > test_check("SuperpixelImageSegmentation")
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 3 ]
  
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     2.60    0.45    3.04
Running 'spelling.R' [0s]
  Running 'testthat.R' [202s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Superpower)
  > 
  > 
  > test_check("Superpower")
  [ FAIL 0 | WARN 18 | SKIP 13 | PASS 399 ]
  
  ══ Skipped tests (13) ══════════════════════════════════════════════════════════
  • On CRAN (13): 'test-ANOVA_compromise.R:45:3', 'test-anova_exact.R:152:3',
    'test-anova_power.R:93:3', 'test-anova_power.R:119:3',
    'test-anova_power.R:160:3', 'test-anova_power.R:193:3',
    'test-anova_power.R:232:3', 'test-emmeans_power.R:44:3',
    'test-justifieR.R:29:3', 'test-plot_power.R:43:3', 'test-plot_power.R:102:3',
    'test-plot_power.R:148:3', 'test-plot_power.R:169:3'
  
  [ FAIL 0 | WARN 18 | SKIP 13 | PASS 399 ]
  > 
  > proc.time()
     user  system elapsed 
    43.06    2.31   45.37
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/SuppDists.Rcheck/00install.out' for details.
surfaceSimulate : phytransform: no visible global function definition
  for 'rescale'
Undefined global functions or variables:
  rescale
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(SurfaceTortoise)
  > 
  > test_check("SurfaceTortoise")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     5.82    0.40    6.17
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.1Mb
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(surveyCV)
  > 
  > test_check("surveyCV")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
  > 
  > proc.time()
     user  system elapsed 
     2.07    0.25    2.32
Running 'spelling.R' [0s]
  Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(surveydata)
  
  Attaching package: 'surveydata'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("surveydata")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 220 ]
  > 
  > proc.time()
     user  system elapsed 
     3.59    0.67    4.18
Running 'spelling.R' [158s]
  Running 'testthat.R' [15s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.06    0.25
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(surveygraph)
  > 
  > test_check("surveygraph")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.14    0.90
Running 'testthat.R' [205s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(survivalMPLdc)
  > 
  > test_check("survivalMPLdc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
    39.17    5.23   44.43
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(survminer)
  Loading required package: ggplot2
  Loading required package: ggpubr
  > 
  > test_check("survminer")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     2.75    0.43    3.14
Running 'spelling.R' [153s]
  Running 'testthat.R' [57s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.04    0.18
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(susographql)
  
  Attaching package: 'susographql'
  
  The following objects are masked from 'package:base':
  
      endsWith, startsWith
  
  > 
  > test_check("susographql")
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-suso_gql_assignments.R:2:3',
    'test-suso_gql_credentials.R:2:3', 'test-suso_gql_credentials.R:8:3',
    'test-suso_gql_interviews.R:2:3', 'test-suso_gql_questionnaires.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.14    0.93
Running 'spelling.R' [0s]
  Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("svDialogs")
  Loading required package: svDialogs
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
     0.73    0.14    0.89
Running 'spelling.R' [169s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +     skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.06    0.23
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(svglite)
  > 
  > test_check("svglite")
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 105 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On Windows (2): 'test-text-fonts.R:7:3', 'test-text.R:33:3'
  • empty test (4): 'test-clip.R:1:1', 'test-clip.R:11:1', 'test-scale.R:8:1',
    'test-text.R:79:1'
  
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 105 ]
  > 
  > proc.time()
     user  system elapsed 
     2.18    0.56    2.78
Running 'spelling.R' [166s]
  Running 'testthat.R' [1s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.12    0.07    0.18
Found the following significant warnings:
  D:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/emmintrin.h:169:19: warning: 'void* __builtin_memcpy(void*, const void*, long long unsigned int)' reading 16 or more bytes from a region of size 8 [-Wstringop-overread]
See 'd:/Rcompile/CRANpkg/local/4.4/svines.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 13.2.0'
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(svplots)
  > 
  > test_check("svplots")
  [ FAIL 0 | WARN 21 | SKIP 0 | PASS 56 ]
  
  [ FAIL 0 | WARN 21 | SKIP 0 | PASS 56 ]
  > 
  > proc.time()
     user  system elapsed 
     7.09    0.40    7.48
Running 'testthat.R' [211s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(svrep)
  > 
  > test_check("svrep")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 213 ]
  Warning message:
  call dbDisconnect() when finished working with a connection 
  > 
  > proc.time()
     user  system elapsed 
    34.57    4.71   39.31
Running 'spelling.R' [0s]
  Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("svSweave")
  Loading required package: svSweave
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
  > 
  > proc.time()
     user  system elapsed 
     0.71    0.17    0.87
Running 'spelling.R' [0s]
  Running 'test-with-svUnit.R' [157s]
Running the tests in 'tests/test-with-svUnit.R' failed.
Complete output:
  > # Note that the message in case of error is not explicit enough.Moreover,
  > # nothing is printed in case of success, while we would like a succinct report
  > # TODO: check if warnings are not converted into errors during R CMD check tests
  > library(svUnit)
  > clearLog()
  > res <- capture.output(runTest(svSuite("package:svUnit"), "svUnit"))
  > errorLog()
  > 
  > proc.time()
     user  system elapsed 
     0.28    0.04    0.31
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(swaprinc)
  > 
  > test_check("swaprinc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 53 ]
  > 
  > proc.time()
     user  system elapsed 
     5.06    0.57    5.62
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(swaRm)
  > 
  > test_check("swaRm")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.54    0.12    0.65
Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(swdft)
  > 
  > test_check("swdft")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     6.04    0.35    6.39
Package suggested but not available for checking: 'swephRdata'
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## inhibit overloading of ephemeris provided by
  > ## swephR and swephRdata
  > Sys.setenv(SE_EPHE_PATH = "")
  > 
  > library(testthat)
  > library(swephR)
  > 
  > test_check("swephR")
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 187 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • swephRdata cannot be loaded (8): 'test-calculation.R:21:5',
    'test-calculation.R:49:5', 'test-calculation.R:79:5', 'test-misc.R:56:5',
    'test-misc.R:64:5', 'test-misc.R:221:3', 'test-misc.R:229:3',
    'test-misc.R:237:3'
  
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 187 ]
  > 
  > proc.time()
     user  system elapsed 
     2.00    0.31    2.25
Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(swfscAirDAS)
  > 
  > test_check("swfscAirDAS")
  [ FAIL 0 | WARN 45 | SKIP 0 | PASS 50 ]
  
  [ FAIL 0 | WARN 45 | SKIP 0 | PASS 50 ]
  > 
  > proc.time()
     user  system elapsed 
    10.04    0.37   10.48
Running 'testthat.R' [199s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(swfscDAS)
  > 
  > test_check("swfscDAS")
  [ FAIL 0 | WARN 116 | SKIP 0 | PASS 47 ]
  
  [ FAIL 0 | WARN 116 | SKIP 0 | PASS 47 ]
  > 
  > proc.time()
     user  system elapsed 
    46.68    0.84   47.54
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
Running 'test-all.R' [172s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)
  +   test_check("swirl")
  + }
  Loading required package: swirl
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 13 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On Windows (1): 'test-encoding.R:10:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 13 ]
  > 
  > proc.time()
     user  system elapsed 
     0.98    0.23    1.21
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
Running 'degenerate_cases.r' [168s]
  Running 'readability.r' [0s]
  Running 'sylcount.r' [161s]
Running the tests in 'tests/degenerate_cases.r' failed.
Complete output:
  > library(sylcount)
  > 
  > test = readability("", nthreads=1)
  > truth = 
  + data.frame(
  +   chars = 0L,
  +   wordchars = 0L,
  +   words = 0L,
  +   nonwords = 0L,
  +   sents = 0L,
  +   sylls = 0L,
  +   polys = 0L,
  +   re = NaN,
  +   gl = NaN,
  +   ari = NA_integer_,
  +   smog = NaN,
  +   cl = NaN
  + )
  > 
  > stopifnot(identical(test, truth))
  > 
  > 
  > 
  > test = doc_counts("", nthreads=1)
  > truth = truth[, 1:7]
  > stopifnot(identical(test, truth))
  > 
  > 
  > 
  > test = sylcount("")
  > truth = list(NA_integer_)
  > stopifnot(identical(test, truth))
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.04    0.23 
Running the tests in 'tests/sylcount.r' failed.
Complete output:
  > library(sylcount)
  > 
  > a = "I am the very model of a modern major general."
  > b = "I have information vegetable, animal, and mineral."
  > x = c(a, b)
  > y = paste0(a, b, collapse=" ")
  > 
  > 
  > 
  > test = sum(sylcount(a)[[1]])
  > truth = 16L
  > stopifnot(identical(truth, test))
  > 
  > test = sum(sylcount(b)[[1]])
  > truth = 17L
  > stopifnot(identical(truth, test))
  > 
  > 
  > 
  > test = sylcount(x)
  > truth = list(
  +   as.integer(c(1, 1, 1, 2, 2, 1, 1, 2, 2, 3)),
  +   as.integer(c(1, 1, 4, 4, 3, 1, 3))
  + )
  > stopifnot(identical(test, truth))
  > 
  > test = sylcount(y)[[1]]
  > stopifnot(identical(test, unlist(truth)))
  > 
  > 
  > 
  > truth <- data.frame(
  +   word=c("I", "am", "the", "very", "model", "of", "a", "modern", "major", "general", "I", "have", "information", "vegetable", "animal", "and", "mineral"),
  +   syllables = test,
  +   stringsAsFactors=FALSE
  + )
  > test = sylcount(y, counts.only=FALSE)
  > stopifnot(identical(truth, test[[1]]))
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.04    0.21
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(syllabifyr)
  > 
  > test_check("syllabifyr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 77 ]
  > 
  > proc.time()
     user  system elapsed 
     4.34    0.32    4.67
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./tests
  > 
  > library(testthat)
  > library(sylly)
  
  Attaching package: 'sylly'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("sylly")
  Changed
  
    syll                         word
  1    8 in-com-pre-hens-ib-il-it-ies
  
    into
  
    syll                            word
  1   11 in-co-mp-re-he-ns-ib-il-it-ie-s
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
  > 
  > proc.time()
     user  system elapsed 
     0.84    0.15    0.98
Running 'tinytest.R' [165s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +     tinytest::test_package("symDMatrix")
  + }
  
  test-as.symDMatrix.R..........    0 tests    
  test-as.symDMatrix.R..........    1 tests [0;32mOK[0m 
  test-as.symDMatrix.R..........    2 tests [0;32mOK[0m [0;34m0.2s[0m
  
  test-blockIndex.R.............    0 tests    
  test-blockIndex.R.............    1 tests [0;32mOK[0m [0;36m51ms[0m
  
  test-blockSize.R..............    0 tests    
  test-blockSize.R..............    1 tests [0;32mOK[0m 
  test-blockSize.R..............    2 tests [0;32mOK[0m 
  test-blockSize.R..............    3 tests [0;32mOK[0m [0;36m51ms[0m
  
  test-diag.R...................    0 tests    
  test-diag.R...................    1 tests [0;32mOK[0m [0;36m45ms[0m
  
  test-nBlocks.R................    0 tests    
  test-nBlocks.R................    1 tests [0;32mOK[0m [0;36m95ms[0m
  
  test-symDMatrix.R.............    0 tests    
  test-symDMatrix.R.............    1 tests [0;32mOK[0m 
  test-symDMatrix.R.............    1 tests [0;32mOK[0m 
  test-symDMatrix.R.............    2 tests [0;32mOK[0m 
  test-symDMatrix.R.............    3 tests [0;32mOK[0m 
  test-symDMatrix.R.............    4 tests [0;32mOK[0m 
  test-symDMatrix.R.............    4 tests [0;32mOK[0m 
  test-symDMatrix.R.............    4 tests [0;32mOK[0m 
  test-symDMatrix.R.............    5 tests [0;32mOK[0m 
  test-symDMatrix.R.............    5 tests [0;32mOK[0m 
  test-symDMatrix.R.............    6 tests [0;32mOK[0m 
  test-symDMatrix.R.............    6 tests [0;32mOK[0m 
  test-symDMatrix.R.............    7 tests [0;32mOK[0m 
  test-symDMatrix.R.............    8 tests [0;32mOK[0m 
  test-symDMatrix.R.............    9 tests [0;32mOK[0m [0;36m96ms[0m
  All ok, 17 results (0.6s)
  > 
  > proc.time()
     user  system elapsed 
     0.87    0.21    1.03
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(symengine)
  SymEngine Version: 0.11.2
   _____           _____         _         
  |   __|_ _ _____|   __|___ ___|_|___ ___ 
  |__   | | |     |   __|   | . | |   | -_|
  |_____|_  |_|_|_|_____|_|_|_  |_|_|_|___|
        |___|               |___|          
  > 
  > test_check("symengine")
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 647 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-basic_parser.R:222:5'
  • empty test (8): 'test-basic_language_conversion.R:16:1',
    'test-symengine_is_working.R:15:1', 'test-symengine_is_working.R:19:1',
    'test-symengine_is_working.R:23:1', 'test-vecbasic_constructors.R:73:1',
    'test-vecbasic_constructors.R:76:1', 'test-vecbasic_constructors.R:80:1',
    'test-vecbasic_s4bindings.R:9:1'
  • symengine_have_component("llvm") is not TRUE (2):
    'test-double_visitor.R:23:5', 'test-double_visitor.R:34:5'
  
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 647 ]
  > 
  > proc.time()
     user  system elapsed 
     4.76    1.45   21.03
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(symSEM)
  Loading required package: caracas
  
  Attaching package: 'caracas'
  
  The following objects are masked from 'package:base':
  
      %*%, det, diag, diag<-
  
  > 
  > test_check("symSEM")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_utilities.R:2:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.56    0.64   12.36
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SyncRNG)
  > 
  > test_check("SyncRNG")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2016 ]
  > 
  > proc.time()
     user  system elapsed 
     4.03    0.37    4.34
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(synr)
  > 
  > test_check("synr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 189 ]
  > 
  > proc.time()
     user  system elapsed 
     3.09    0.37    3.43
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(syntaxr)
  > 
  > test_check("syntaxr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
  > 
  > proc.time()
     user  system elapsed 
     0.81    0.14    0.93
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(synthesis)
  > 
  > proc.time()
     user  system elapsed 
     0.29    0.17    0.42
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(synthesisr)
  > 
  > test_check("synthesisr")
  Reading file D:\temp\Rtmp46qUQN\eviatlas278145e2ff6 ... done
  Reading file D:\temp\Rtmp46qUQN\litsearchr278147f1420d6 ... done
  Reading file D:\temp\Rtmp46qUQN\res_synth2781468ad5a83 ... done
  Reading file D:\temp\Rtmp46qUQN\eviatlas278145e2ff6 ... done
  Reading file D:\temp\Rtmp46qUQN\litsearchr278147f1420d6 ... done
  Reading file D:\temp\Rtmp46qUQN\res_synth2781468ad5a83 ... done
  Reading file D:\temp\Rtmp46qUQN\file2781476e0225b ... done
  Reading file D:\temp\Rtmp46qUQN\eviatlas278145ba743a ... done
  Reading file D:\temp\Rtmp46qUQN\litsearchr27814360f6312 ... done
  Reading file D:\temp\Rtmp46qUQN\res_synth278144f4133c ... done
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     1.10    0.15    1.20
Running 'spelling.R' [162s]
  Running 'testthat.R' [8s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly=TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.14    0.04    0.17
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(syt)
  > 
  > test_check("syt")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
  > 
  > proc.time()
     user  system elapsed 
     1.81    0.28    2.07
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.unsetenv("R_TESTS") # Becasue https://github.com/hadley/testthat/issues/144
  > 
  > library(testthat)
  > library(syuzhet)
  > 
  > test_check("syuzhet")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
    23.98    1.81   29.20
Running examples in 'T2DFitTailor-Ex.R' failed
The error most likely occurred in:

> ### Name: TailorExercisePlan
> ### Title: Tailor Exercise Plan for T2D Patients
> ### Aliases: TailorExercisePlan
> 
> ### ** Examples
> 
> # Create a demo dataframe
> set.seed(16)
> df <- data.frame(
+ Age = sample(39:77, 8, replace = TRUE),
+ Sex = sample(0:1, 8, replace = TRUE),
+ BMI = sample(18:31, 8, replace = TRUE),
+ Duration_T2D = sample(1:26, 8, replace = TRUE),
+ HDL = sample(1:1.7, 8, replace = TRUE),
+ PCS = sample(27:54, 8, replace = TRUE),
+ WHtR = sample(0.4:0.6, 8, replace = TRUE)
+ )
> rownames(df) <- c("xiaoming", "xiaohong", "xiaohua", "xiaogang",
+                   "xiaoli", "zhangsan", "lisi", "wangwu")
> colnames(df) <- c("Age", "Sex", "BMI", "Duration_T2D (year)",
+                   "HDL (mmol/L)", "PCS", "WHtR")
> # Run the TailorExercisePlan function
> demo_result <- TailorExercisePlan(df)
Note: Sample_ID and the rownames of input data correspond on a one-to-one basis.
Error: lexical error: invalid char in json text.
                                       Please check your data format!
                     (right here) ------^
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.4Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tabledown)
  > 
  > test_check("tabledown")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.67    0.43    3.09
Running 'testthat.R' [187s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(table.express)
  
  Attaching package: 'table.express'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:table.express':
  
      matches
  
  > 
  > # old reporter for CMD checks
  > options(testthat.default_reporter = "summary")
  > 
  > #' To test in a local machine:
  > #' Sys.setenv(NOT_CRAN = "true"); test_dir("tests/testthat/")
  > #' OR
  > #' devtools::test()
  > #'
  > testthat::test_check("table.express")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 615 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-90-namespace.R:4:5'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 615 ]
  > 
  > proc.time()
     user  system elapsed 
    12.32    0.89   13.21
Documented arguments not in \usage in Rd file 'table_params_circle.Rd':
  'd'

Documented arguments not in \usage in Rd file 'table_params_rect.Rd':
  'd' 'scale_breaks' 'r_max'

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.
Running 'testthat.R' [236s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv(R_TESTS = "")
  > library(testthat)
  > library(tableschema.r)
  > 
  > test_check("tableschema.r")
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 529 ]
  
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 529 ]
  > 
  > proc.time()
     user  system elapsed 
    25.48    4.87   69.25
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tablexlsx)
  > 
  > test_check("tablexlsx")
  [ FAIL 0 | WARN 0 | SKIP 14 | PASS 50 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • On CRAN (14): 'test-add_table.R:8:3', 'test-add_table.R:21:3',
    'test-add_table.R:34:3', 'test-add_table.R:47:3', 'test-add_table.R:61:3',
    'test-add_table.R:75:3', 'test-add_table.R:93:3', 'test-add_table.R:113:3',
    'test-add_table.R:133:3', 'test-asserts.R:24:3', 'test-asserts.R:35:3',
    'test-asserts.R:55:3', 'test-asserts.R:78:3', 'test-asserts.R:91:3'
  
  [ FAIL 0 | WARN 0 | SKIP 14 | PASS 50 ]
  > 
  > proc.time()
     user  system elapsed 
     3.37    0.73    4.17
Running 'spelling.R' [170s]
  Running 'testthat.R' [10s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.04    0.23
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tabulate)
  > 
  > test_check("tabulate")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 7 ]
  
  == Skipped tests (3) ===========================================================
  * On CRAN (3): 'test-table.R:6:3', 'test-table.R:40:3', 'test-table.R:54:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 7 ]
  > 
  > proc.time()
     user  system elapsed 
     1.12    0.14    1.25
Running 'spelling.R' [166s]
  Running 'testthat.R' [172s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.03    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tactile)
  Loading required package: lattice
  > 
  > test_check("tactile")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     2.12    0.43    2.71
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tagtools)
  
  Attaching package: 'tagtools'
  
  The following object is masked from 'package:stats':
  
      smooth
  
  > 
  > test_check("tagtools")
   num -0.395
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 103 ]
  > 
  > proc.time()
     user  system elapsed 
     5.17    0.95    6.12
Running 'testthat.R' [149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(taipan)
  > 
  > test_check("taipan")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • Testing shiny apps is not working due to tmpdir issues (2):
    'test-inputs.R:26:3', 'test-taipan.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.06    0.25    1.29
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tame)
  > 
  > test_check("tame")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
  > 
  > proc.time()
     user  system elapsed 
     1.59    0.37    1.95
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(TangledFeatures)
  > 
  > test_check("TangledFeatures")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     2.31    0.31    2.56
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tangram)
  Loading required package: R6
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Loading required package: knitr
  > 
  > test_check("tangram")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 241 ]
  > 
  > proc.time()
     user  system elapsed 
     4.23    0.51    4.75
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tardis)
  > 
  > test_check("tardis")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
  > 
  > proc.time()
     user  system elapsed 
     7.06    0.35    7.42
Running 'test-all.R' [163s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > suppressPackageStartupMessages(library("testthat"))
  > test_check("targeted")
  Loading required package: targeted
  Loading required package: lava
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
  > 
  > proc.time()
     user  system elapsed 
     2.31    0.39    2.68
Package suggested but not available for checking: 'tashudata'
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tauturri)
  > 
  > # Only run tests if API details are available
  > if (Sys.getenv("tautulli_url") != "" & Sys.getenv("tautulli_apikey") != "") {
  +   test_check("tauturri")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.82    0.12    0.93
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(taxalight)
  > 
  > test_check("taxalight")
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 7 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-tl.R:5:3', 'test-tl_create.R:4:3', 'test-tl_create.R:37:3'
  • takes a long time (2): 'test-import_all.R:3:3', 'test-import_all.R:14:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 7 ]
  > 
  > proc.time()
     user  system elapsed 
     1.34    0.31    1.93
Running 'spelling.R' [134s]
  Running 'testthat.R' [12s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.01    0.21
Running 'testthat.R' [339s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tboot)
  > 
  > test_check("tboot")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
  > 
  > proc.time()
     user  system elapsed 
   157.84   17.82  175.65
Running 'spelling.R' [157s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.04    0.23
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tcgaViz)
  > 
  > test_check("tcgaViz")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 6 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-golem-recommended.R:24:9'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 6 ]
  > 
  > proc.time()
     user  system elapsed 
     2.46    0.56    2.98
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tci)
  > 
  > test_check("tci")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.00    0.29    1.28
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Tcomp)
  > 
  > test_check("Tcomp")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2645 ]
  > 
  > proc.time()
     user  system elapsed 
    11.68    0.84   12.54
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tcpl)
  tcpl (v3.1.0) loaded with the following settings:
    TCPL_DB:    D:/RCompile/CRANpkg/lib/4.4/tcpl/csv
    TCPL_USER:  NA
    TCPL_HOST:  NA
    TCPL_DRVR:  tcplLite
  Default settings stored in tcpl config file. See ?tcplConf for more information.
  > 
  > test_check("tcpl")
  [ FAIL 0 | WARN 4 | SKIP 5 | PASS 55 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-tcplDefine.R:3:3', 'test-tcplDefine.R:9:3',
    'test-tcplDefine.R:19:3', 'test-tcplPlot.R:175:3', 'test-tcplPlot.R:196:3'
  
  [ FAIL 0 | WARN 4 | SKIP 5 | PASS 55 ]
  > 
  > proc.time()
     user  system elapsed 
     5.26    0.68    5.92
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.1Mb
Running 'testthat.R' [274s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TDApplied)
  > 
  > test_check("TDApplied")
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 166 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • T is TRUE (5): 'test-python.R:7:3', 'test-python.R:19:3',
    'test-python.R:43:3', 'test-python.R:78:3', 'test-python.R:90:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 166 ]
  > 
  > proc.time()
     user  system elapsed 
     6.53    0.85  104.48
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(TDCM)
  > 
  > test_check("TDCM")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
  > 
  > proc.time()
     user  system elapsed 
     1.07    0.21    1.28
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > testthat::test_check("tdcmStan")
  Loading required package: tdcmStan
  [ FAIL 0 | WARN 14 | SKIP 0 | PASS 3 ]
  
  [ FAIL 0 | WARN 14 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     2.79    0.39    3.17
Running 'spelling.R' [0s]
  Running 'test-all.R' [137s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("tdigest")
  Loading required package: tdigest
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
     1.17    0.10    1.25
Running 'tinytest.R' [156s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("td")
  + }
  Attaching td version 0.0.6. No config file or environment variable found: API access unlikely.
  
  test_td.R.....................    0 tests    
  test_td.R.....................    0 tests    
  test_td.R.....................    0 tests    
  test_td.R.....................    0 tests    [0;36m63ms[0m
  All ok, 0 results (67ms)
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.23    0.09    0.31
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tdsc)
  > library(tuneR)
  > 
  > test_check("tdsc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
  > 
  > proc.time()
     user  system elapsed 
     4.01    0.56    4.56
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > pkg_name <- "teal.code"
  > library(pkg_name, character.only = TRUE)
  > testthat::test_check(pkg_name)
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
  > 
  > proc.time()
     user  system elapsed 
     1.65    0.25    1.89
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > pkg_name <- "teal.data"
  > library(pkg_name, character.only = TRUE)
  Loading required package: teal.code
  > testthat::test_check(pkg_name)
  [1] 1
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 245 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • This is not urgent and can be ommitted with @linksto tag. (1):
    'test-get_code.R:424:3'
  • We will not resolve this, as this requires code evaluation. (1):
    'test-get_code.R:250:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 245 ]
  > 
  > proc.time()
     user  system elapsed 
     5.07    0.48    5.53
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > pkg_name <- "teal.transform"
  > library(pkg_name, character.only = TRUE)
  > testthat::test_check(pkg_name)
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 659 ]
  > 
  > proc.time()
     user  system elapsed 
    14.75    0.73   15.50
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > pkg_name <- "teal.widgets"
  > library(pkg_name, character.only = TRUE)
  > testthat::test_check(pkg_name)
  Error in initialize(...) : Invalid path to Chrome
  Error in pag_indices_inner(pagdf = mf_rinfo(mpf), rlpp = calc_rlpp(pg_size_spec,  : 
    Lines of repeated context (plus header materials) larger than specified lines per page
  Error in initialize(...) : Invalid path to Chrome
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 203 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • `shinytest2::AppDriver` can not be initialized as {chromote} can not be
    started (2): 'test-plot_with_settings_ui.R:10:3',
    'test-table_with_settings_ui.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 203 ]
  Deleting unused snapshots:
  • app_pws_ui/plot_with_settings_ui/pws-download_menu.png
  • app_pws_ui/plot_with_settings_ui/pws-hidden.png
  • app_pws_ui/plot_with_settings_ui/pws-resize_menu.png
  • app_pws_ui/plot_with_settings_ui/pws-visible.png
  • app_tws_ui/table_with_settings_ui/tws-final_values.json
  > 
  > proc.time()
     user  system elapsed 
    11.42    1.20   12.93
Running 'spelling.R' [171s]
  Running 'testthat.R' [158s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.10    0.14    0.20 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tehtuner)
  > 
  > test_check("tehtuner")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     2.28    0.39    2.62
Running 'testthat.R' [182s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(telefit)
  > 
  > test_check("telefit")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
    10.60    1.07   11.70
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Temporal)
  > 
  > test_check("Temporal")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 35 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-comparison.R:5:3', 'test-gengamma.R:5:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 35 ]
  > 
  > proc.time()
     user  system elapsed 
     2.20    0.23    2.43
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tensorflow)
  > 
  > if (identical(Sys.getenv("NOT_CRAN"), "true"))
  +   test_check("tensorflow")
  > 
  > proc.time()
     user  system elapsed 
     1.75    0.18    1.93
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  > library("TensorTest2D")
  > test_check("TensorTest2D")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
     9.06    1.90   10.95
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(terminaldigits)
  > 
  > test_check("terminaldigits")
  [ FAIL 0 | WARN 1 | SKIP 1 | PASS 32 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-full_functions.R:8:3'
  
  [ FAIL 0 | WARN 1 | SKIP 1 | PASS 32 ]
  > 
  > proc.time()
     user  system elapsed 
     9.50    2.26   11.78
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(term)
  > 
  > test_check("term")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 546 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-print.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 546 ]
  > 
  > proc.time()
     user  system elapsed 
     6.82    0.78    7.60
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running 'spelling.R' [173s]
  Running 'testthat.R' [170s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE, error = TRUE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.06    0.20 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("Ternary")
  > 
  > test_check("Ternary")
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 108 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-Annotate.R:20:3', 'test-Contours.R:60:3',
    'test-Contours.R:236:3', 'test-Contours.R:246:3', 'test-Holdridge.R:27:3',
    'test-axis-rotate.R:66:3', 'test-axis-rotate.R:88:3', 'test-ternary.R:66:3',
    'test-ternary.R:127:3', 'test-ternary.R:132:3', 'test-ternary.R:144:3'
  
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 108 ]
  Deleting unused snapshots:
  • Annotate/annotate-auto-locate.svg
  • Contours/contours-skiwiff.svg
  • Contours/density-contours-2.svg
  • Contours/density-contours-3.svg
  • Contours/density-contours.svg
  • Contours/filledcontours.svg
  • Contours/lo-res-density-contours.svg
  • ternary/blank-down-anticlockwise.svg
  • ternary/blank-down.svg
  • ternary/blank-le-anticlockwise.svg
  • ternary/blank-le.svg
  • ternary/blank-right-anticlockwise.svg
  • ternary/blank-right.svg
  • ternary/blank-up-anticlockwise.svg
  • ternary/blank-up.svg
  • ternary/cartesian.svg
  • ternary/colours-and-water.svg
  • ternary/padding.svg
  • ternary/plot-to-ternary-y.svg
  > 
  > proc.time()
     user  system elapsed 
     3.75    0.43    4.14
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/terra.Rcheck/00install.out' for details.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       8.1Mb
    tessdata  14.0Mb
Running 'spelling.R' [159s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.03    0.21
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(testdat)
  
  Attaching package: 'testdat'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("testdat")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 185 ]
  > 
  > proc.time()
     user  system elapsed 
     6.18    0.64    6.81
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(TestDimorph)
  
  Type 'citation("TestDimorph")' for citing this R package in publications.
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library("testthat")
  + } else {
  +   message("'testthat' not available")
  + }
  > test_check("TestDimorph")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
  > 
  > proc.time()
     user  system elapsed 
     6.85    0.57    7.43
Package vignette with \VignetteEngine{} not specifying an engine package:
  'tester_introduction.Rnw'
Engines should be specified as \VignetteEngine{PKG::ENG}.
Running 'testthat.R' [151s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(testthatmulti)
  > 
  > test_check("testthatmulti")
  [1] 2
  [1] 5
  [1] 3
  [1] 2
  [1] 1
  [1] 2
  [1] 4
  [1] 4
  [1] 4
  [1] 1
  [1] 5
  [1] 5
  [1] 1
  [1] 5
  [1] 6
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ]
  > 
  > proc.time()
     user  system elapsed 
     1.29    0.21    1.45
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("testthis")
  Loading required package: testthis
  ✔ Setting active project to '<no active project>'
  ✔ Setting active project to '<no active project>'
  ✔ Setting active project to '<no active project>'
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 67 ]
  > 
  > proc.time()
     user  system elapsed 
     2.81    0.68    3.53
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("texreg")
  Version:  1.39.3
  Date:     2023-11-09
  Author:   Philip Leifeld (University of Essex)
  
  Consider submitting praise using the praise or praise_interactive functions.
  Please cite the JSS article in your publications -- see citation("texreg").
  > 
  > test_check("texreg")
  [ FAIL 0 | WARN 0 | SKIP 33 | PASS 212 ]
  
  ══ Skipped tests (33) ══════════════════════════════════════════════════════════
  • On CRAN (32): 'test-extract.R:6:3', 'test-extract.R:28:3',
    'test-extract.R:67:3', 'test-extract.R:90:3', 'test-extract.R:162:3',
    'test-extract.R:193:3', 'test-extract.R:214:3', 'test-extract.R:239:3',
    'test-extract.R:280:3', 'test-extract.R:305:3', 'test-extract.R:328:3',
    'test-extract.R:367:3', 'test-extract.R:415:3', 'test-extract.R:441:3',
    'test-extract.R:467:3', 'test-extract.R:501:3', 'test-extract.R:543:3',
    'test-extract.R:591:3', 'test-extract.R:615:3', 'test-extract.R:651:3',
    'test-extract.R:738:3', 'test-extract.R:761:3', 'test-extract.R:783:3',
    'test-extract.R:817:3', 'test-extract.R:846:3', 'test-extract.R:881:3',
    'test-extract.R:934:3', 'test-extract.R:956:3', 'test-extract.R:985:3',
    'test-extract.R:1009:3', 'test-extract.R:1041:3', 'test-extract.R:1133:3'
  • biglm cannot be loaded (1): 'test-plotreg.R:39:3'
  
  [ FAIL 0 | WARN 0 | SKIP 33 | PASS 212 ]
  > 
  > proc.time()
     user  system elapsed 
     6.54    0.82    7.36
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(text2sdg)
  > 
  > test_check("text2sdg")
  
  Running Elsevier
  [ FAIL 0 | WARN 0 | SKIP 15 | PASS 12 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-crosstab_sdg.R:3:3', 'test-crosstab_sdg.R:19:3',
    'test-crosstab_sdg.R:26:3', 'test-crosstab_sdg.R:34:3',
    'test-crosstab_sdg.R:42:3', 'test-crosstab_sdg.R:51:3',
    'test-crosstab_sdg.R:60:3', 'test-crosstab_sdg.R:67:3',
    'test-crosstab_sdg.R:75:3', 'test-detect_any.R:59:3',
    'test-detect_any.R:83:3', 'test-detect_any.R:103:3',
    'test-detect_sdg_systems.R:39:3', 'test-ensemble.R:15:3',
    'test-ensemble.R:37:3'
  
  [ FAIL 0 | WARN 0 | SKIP 15 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
     3.70    0.31    4.03
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(text2speech)
  > 
  > test_check("text2speech")
  Error in ms_fetch_key(api_key = api_key, error = TRUE) : 
    Microsoft Cognitive Services Text To Speech (TTS) API Key not found please set option('ms_tts_key') for general use or set environment variable MS_TTS_API_KEY, to be accessed by Sys.getenv('MS_TTS_API_KEY')
  Error in ms_fetch_key(api_key = api_key, error = TRUE) : 
    Microsoft Cognitive Services Text To Speech (TTS) API Key not found please set option('ms_tts_key') for general use or set environment variable MS_TTS_API_KEY, to be accessed by Sys.getenv('MS_TTS_API_KEY')
  [ FAIL 0 | WARN 8 | SKIP 8 | PASS 0 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-tts.R:3:38', 'test-tts.R:3:38', 'test-tts.R:3:38',
    'test-tts.R:3:38', 'test-tts_voices.R:6:38', 'test-tts_voices.R:6:38',
    'test-tts_voices.R:6:38', 'test-tts_voices.R:21:13'
  
  [ FAIL 0 | WARN 8 | SKIP 8 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.06    0.39    3.32
Running 'spelling.R' [0s]
  Running 'testthat.R' [209s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(textmineR)
  Loading required package: Matrix
  
  Attaching package: 'textmineR'
  
  The following object is masked from 'package:Matrix':
  
      update
  
  The following object is masked from 'package:stats':
  
      update
  
  > 
  > test_check("textmineR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 113 ]
  > 
  > proc.time()
     user  system elapsed 
    19.59    0.85   51.54
Running 'testthat.R' [201s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tfevents)
  > 
  > test_check("tfevents")
  [ FAIL 0 | WARN 140 | SKIP 12 | PASS 70 ]
  
  ══ Skipped tests (12) ══════════════════════════════════════════════════════════
  • inherits(try(reticulate::import("tbparse"), silent = TRUE), "try-error") is
    TRUE (12): 'test-audio.R:10:3', 'test-audio.R:36:3', 'test-audio.R:58:3',
    'test-histogram.R:10:3', 'test-histogram.R:37:3', 'test-hparams.R:1:1',
    'test-image.R:14:3', 'test-image.R:53:3', 'test-tensor.R:2:3',
    'test-tensor.R:29:3', 'test-tensor.R:45:3', 'test-text.R:8:3'
  
  [ FAIL 0 | WARN 140 | SKIP 12 | PASS 70 ]
  > 
  > proc.time()
     user  system elapsed 
    16.18    1.73   36.14
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tfprobability)
  > 
  > if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  +   test_check("tfprobability")
  + }
  > 
  > proc.time()
     user  system elapsed 
     1.40    0.32    1.71
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tfrmtbuilder)
  > 
  > test_check("tfrmtbuilder")
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 0 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-mod_load.R:3:3', 'test-mod_load.R:59:3',
    'test-mod_load.R:89:3', 'test-mod_titles.R:4:3', 'test-mod_titles.R:41:3'
  • interactive() is not TRUE (6): 'test-e2e-auto.R:3:3',
    'test-mod_body_plan-shinytest2.R:5:3',
    'test-mod_body_plan-shinytest2.R:49:3',
    'test-mod_datamapping-shinytest2.R:7:3',
    'test-mod_datamapping_inputs-shinytest2.R:4:3',
    'test-mod_datamapping_inputs-shinytest2.R:50:3'
  
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.20    0.39    2.59
Running 'testthat.R' [207s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tfrmt)
  > 
  > test_check("tfrmt")
  Writing json file out to:
  test.json
  The following rows of the given dataset have no format applied to them 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36
  The following rows of the given dataset have no format applied to them 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
  [ FAIL 0 | WARN 0 | SKIP 10 | PASS 546 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-JSON.R:4:3', 'test-JSON.R:39:3', 'test-JSON.R:58:3',
    'test-JSON.R:94:3', 'test-JSON.R:268:3', 'test-JSON.R:287:3',
    'test-JSON.R:346:3', 'test-JSON.R:446:3', 'test-JSON.R:478:3',
    'test-make_mock_data.R:226:3'
  
  [ FAIL 0 | WARN 0 | SKIP 10 | PASS 546 ]
  > 
  > proc.time()
     user  system elapsed 
    51.12    2.57   53.84
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tgamtheme)
  > 
  > test_check("tgamtheme")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     0.76    0.09    0.79
Running 'skip-download.R' [156s]
  Running 'testthat.R' [168s]
Running the tests in 'tests/skip-download.R' failed.
Complete output:
  > # To run download functions you need an internet connection.
  > # pref a fast one
  > skip_download = function() {
  +   if(!curl::has_internet() |
  +      identical(Sys.getenv("DONT_DOWNLOAD_ANYTHING"), "true"))
  +     skip("No connection to run download function.")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.04    0.17 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tgver)
  
  Attaching package: 'tgver'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  The following object is masked from 'package:utils':
  
      help
  
  The following object is masked from 'package:base':
  
      version
  
  > 
  > # disable browserURL
  > Sys.setenv(R_BROWSER = FALSE)
  > test_check("tgver")
  Running plumber at: http://127.0.0.1/8000
  Running plumber at: http://127.0.0.1/8000
  Attempting to browse TGVE from: D:\temp\RtmpAziRfV/tgve
   [1] "tooltipColumns"     "defaultURL"         "geographyURL"      
   [4] "geographyColumn"    "column"             "data"              
   [7] "layerName"          "dark"               "viewport"          
  [10] "hideChartGenerator" "hideCharts"        
  Attempting to serve TGVE instance from: D:\temp\RtmpAziRfV/tgve
  Running plumber at: http://127.0.0.1/8000
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 46 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-explore_dir.R:10:3', 'test-tgve.R:8:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 46 ]
  > 
  > proc.time()
     user  system elapsed 
     1.98    0.39    2.37
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Running 'testthat.R' [151s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(theftdlc)
  Loading required package: theft
  This is version 0.6.1 of theft. All analysis and visualisation functions (plus a host of new ones!) have been moved to the {theftdlc} package
  and subsequently renamed and refactored.
  You can install {theftdlc} via install.packages('theftdlc').
  Please see https://hendersontrent.github.io/theftdlc/ for more.
  > 
  > test_check("theftdlc")
  No IDs removed. All value vectors good for feature extraction.
  Running computations for catch22...
  
  Calculations completed for catch22.
  [ FAIL 0 | WARN 4 | SKIP 4 | PASS 1 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-classify.R:4:3', 'test-classify.R:11:3',
    'test-compare_features.R:4:3', 'test-compare_features.R:11:3'
  
  [ FAIL 0 | WARN 4 | SKIP 4 | PASS 1 ]
  Warning message:
  There was 1 warning in `dplyr::reframe()`.
  ℹ In argument: `Rcatch22::catch22_all(.data$values, catch24 = catch24)`.
  ℹ In group 1: `id = "Gaussian Noise_1"` and `group = "Gaussian Noise"`.
  Caused by warning:
  ! As of 0.1.14 the feature 'CO_f1ecac' returns a double instead of int
  This warning is displayed once per session. 
  > 
  > proc.time()
     user  system elapsed 
     4.17    0.35    4.51
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(theft)
  This is version 0.6.1 of theft. All analysis and visualisation functions (plus a host of new ones!) have been moved to the {theftdlc} package
  and subsequently renamed and refactored.
  You can install {theftdlc} via install.packages('theftdlc').
  Please see https://hendersontrent.github.io/theftdlc/ for more.
  > 
  > test_check("theft")
  No IDs removed. All value vectors good for feature extraction.
  Running computations for catch22...
  
  Calculations completed for catch22.
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-calculate_features.R:10:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2 ]
  Warning messages:
  1: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
  ℹ Please use `"id"` instead of `.data$id` 
  2: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
  ℹ Please use `"timepoint"` instead of `.data$timepoint` 
  3: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
  ℹ Please use `"values"` instead of `.data$values` 
  4: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
  ℹ Please use `"group"` instead of `.data$group` 
  5: There was 1 warning in `dplyr::reframe()`.
  ℹ In argument: `Rcatch22::catch22_all(.data$values, catch24 = catch24)`.
  ℹ In group 1: `id = "Gaussian Noise_1"` and `group = "Gaussian Noise"`.
  Caused by warning:
  ! As of 0.1.14 the feature 'CO_f1ecac' returns a double instead of int
  This warning is displayed once per session. 
  > 
  > proc.time()
     user  system elapsed 
     3.59    0.64    4.14
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(thematic)
  > 
  > test_check("thematic")
  `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
  [ FAIL 0 | WARN 1 | SKIP 16 | PASS 27 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • On CRAN (13): 'test-base.R:9:3', 'test-ggplot.R:31:3', 'test-ggplot.R:149:3',
    'test-ggplot.R:225:3', 'test-ggthemes.R:12:3', 'test-ggthemes.R:27:3',
    'test-ggthemes.R:56:3', 'test-lattice.R:15:3',
    'test-sequential-gradient.R:14:3', 'test-shinytest.R:3:1',
    'test-state.R:5:3', 'test-state.R:27:3', 'test-state.R:43:3'
  • gridExtra cannot be loaded (1): 'test-ggplot.R:202:3'
  • patchwork cannot be loaded (1): 'test-ggplot.R:213:3'
  • rgdal cannot be loaded (1): 'test-ggplot.R:177:3'
  
  [ FAIL 0 | WARN 1 | SKIP 16 | PASS 27 ]
  > 
  > proc.time()
     user  system elapsed 
     9.39    0.90   10.59
Documented arguments not in \usage in Rd file 'witcher.Rd':
  'palettes'

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.
Documented arguments not in \usage in Rd file 'poisson_likelihood.Rd':
  'rate_exp' 'rate_ref' 'rate_pla'

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.
Running 'threejs.R' [148s]
Running the tests in 'tests/threejs.R' failed.
Complete output:
  > library(threejs)
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > # scatterplots
  > z <- seq(-10, 10, 0.1)
  > x <- cos(z)
  > y <- sin(z)
  > scatterplot3js(x, y, z, color=rainbow(length(z)))
  > scatterplot3js(x, y, z, color=rainbow(length(z)), axisLabels=c("a", "b", "c"))
  > 
  > # globes
  > data(flights, package="threejs")
  > dest   <- factor(sprintf("%.2f:%.2f", flights[, 3], flights[, 4]))
  > freq <- sort(table(dest), decreasing=TRUE)
  > frequent_destinations <- names(freq)[1:10]
  > idx <- dest %in% frequent_destinations
  > frequent_flights <- flights[idx, ]
  > ll <- unique(frequent_flights[, 3:4])
  > globejs(lat=ll[, 1], long=ll[, 2], arcs=frequent_flights,
  +         arcsHeight=0.3, arcsLwd=2, arcsColor="#ffff00", arcsOpacity=0.15,
  +         atmosphere=TRUE, color="#00aaff", pointsize=0.5)
  > 
  > # graphs
  > data(LeMis, package="threejs")
  > g <- graphjs(LeMis, main="Les Mis&eacute;rables")
  This graph was created by an old(er) igraph version.
    Call upgrade_graph() on it to use with the current igraph version
    For now we convert it on the fly...
  > g <- graphjs(LeMis, main="Les Mis&eacute;rables", brush=TRUE)
  > 
  > proc.time()
     user  system elapsed 
     0.82    0.25    1.04
Running 'testthat.R' [193s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #! /usr/bin/env Rscript
  > 
  > library(testthat)
  > library(thriftr)
  > 
  > test_check("thriftr")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 272 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • empty test (3): 'test.test_parser.R:7:1',
    'test.test_protocol_binary.R:158:1', 'test.test_socket.R:32:1'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 272 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
    44.06    0.90   44.96
Running 'testthat.R' [193s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("tibble")
  Loading required package: tibble
  Starting 2 test processes
  [ FAIL 0 | WARN 0 | SKIP 41 | PASS 902 ]
  
  ══ Skipped tests (41) ══════════════════════════════════════════════════════════
  • On CRAN (40): 'test-vignette-formats.R:5:3', 'test-add.R:313:3',
    'test-enframe.R:120:3', 'test-error.R:16:3', 'test-as_tibble.R:166:3',
    'test-as_tibble.R:180:3', 'test-as_tibble.R:235:3', 'test-as_tibble.R:269:3',
    'test-as_tibble.R:278:3', 'test-as_tibble.R:333:3', 'test-as_tibble.R:606:3',
    'test-as_tibble.R:713:3', 'test-names.R:18:3', 'test-new.R:132:3',
    'test-print.R:11:3', 'test-msg.R:12:3', 'test-rownames.R:101:3',
    'test-str.R:2:3', 'test-subsetting-matrix.R:21:3', 'test-tbl_df.R:77:3',
    'test-tbl_sum.R:2:3', 'test-tibble.R:245:3', 'test-tidy_names.R:7:3',
    'test-tidy_names.R:14:3', 'test-tidy_names.R:39:3', 'test-tidy_names.R:46:3',
    'test-tidy_names.R:53:3', 'test-tidy_names.R:60:3', 'test-tidy_names.R:69:3',
    'test-tidy_names.R:76:3', 'test-tribble.R:230:3',
    'test-utils-msg-format.R:24:3', 'test-utils-tick.R:2:3',
    'test-vignette-digits.R:2:3', 'test-vignette-extending.R:2:3',
    'test-vignette-invariants.R:5:3', 'test-vignette-numbers.R:2:3',
    'test-vignette-tibble.R:5:3', 'test-vignette-types.R:2:3',
    'test-subsetting.R:762:3'
  • On Windows (1): 'test-print.R:56:3'
  
  [ FAIL 0 | WARN 0 | SKIP 41 | PASS 902 ]
  Deleting unused snapshots:
  • vignette-digits/digits.md
  • vignette-extending/extending.md
  • vignette-formats/formats.md
  • vignette-invariants/invariants.md
  • vignette-numbers/numbers.md
  • vignette-types/types.md
  > 
  > proc.time()
     user  system elapsed 
     5.70    0.39   35.68
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tibbletime)
  
  Attaching package: 'tibbletime'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tibbletime")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 145 ]
  > 
  > proc.time()
     user  system elapsed 
     3.03    0.56    3.57
Running 'testthat.R' [189s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tictoc)
  > 
  > test_check("tictoc")
  [1] "Average elapsed time: 1.032 sec"
  1: 1.03 sec elapsed
  2: 1.04 sec elapsed
  3: 1.03 sec elapsed
  4: 1.03 sec elapsed
  5: 1.03 sec elapsed
  6: 1.03 sec elapsed
  7: 1.03 sec elapsed
  8: 1.03 sec elapsed
  9: 1.03 sec elapsed
  10: 1.04 sec elapsed
  Starting outer...
  Starting middle...
  Starting inner...
  INFO: inner: 3.1 seconds elapsed
  INFO: middle: 5.16 seconds elapsed
  INFO: outer: 6.19 seconds elapsed
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 73 ]
  > 
  > proc.time()
     user  system elapsed 
     1.20    0.28   26.17
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TideCurves)
  > 
  > test_check("TideCurves")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > 
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
     9.28    0.51    9.73
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidier)
  > 
  > test_check(package = "tidier")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 20 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 20 ]
  > 
  > proc.time()
     user  system elapsed 
     5.45    0.60    6.06
Running 'spelling.R' [168s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.01    0.18
Running 'spelling.R' [174s]
  Running 'testthat.R' [164s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = TRUE,
  +                              skip_on_cran = TRUE)
  NULL
  > # spelling::spell_check_package()
  > # spelling::update_wordlist()
  > 
  > proc.time()
     user  system elapsed 
     0.14    0.10    0.23 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyCDISC)
  > library(shinyjs)
  
  Attaching package: 'shinyjs'
  
  The following objects are masked from 'package:methods':
  
      removeClass, show
  
  > 
  > test_check("tidyCDISC")
  [ FAIL 0 | WARN 1 | SKIP 15 | PASS 98 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • empty test (15): 'test-mod_tableGen_fct_anova.R:3:1',
    'test-mod_tableGen_fct_anova.R:7:1', 'test-mod_tableGen_fct_chg.R:5:1',
    'test-mod_tableGen_fct_chg.R:9:1', 'test-tableGen_fct_mean.R:3:1',
    'test-tableGen_fct_mean.R:7:1', 'test-tableGen_fct_mean.R:11:1',
    'test-tableGen_fct_mean.R:15:1', 'test-tableGen_fct_methods.R:21:1',
    'test-tableGen_fct_nested_freq.R:33:1',
    'test-tableGen_fct_nested_freq.R:40:1',
    'test-tableGen_fct_non_missing.R:27:1',
    'test-tableGen_fct_non_missing.R:33:1', 'test-tableGen_fct_y_freq.R:28:1',
    'test-tableGen_fct_y_freq.R:35:1'
  
  [ FAIL 0 | WARN 1 | SKIP 15 | PASS 98 ]
  > 
  > proc.time()
     user  system elapsed 
     9.39    0.90   10.35
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidycharts)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Loading required package: knitr
  > 
  > test_check("tidycharts")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 77 ]
  > 
  > proc.time()
     user  system elapsed 
     4.25    1.26    4.40
Running 'testthat.R' [195s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyclust)
  > 
  > test_check("tidyclust")
  [ FAIL 0 | WARN 0 | SKIP 48 | PASS 177 ]
  
  ══ Skipped tests (48) ══════════════════════════════════════════════════════════
  • On CRAN (48): 'test-arguments.R:27:3', 'test-arguments.R:35:3',
    'test-arguments.R:41:3', 'test-augment.R:31:3',
    'test-cluster_metric_set.R:24:3', 'test-cluster_metric_set.R:35:3',
    'test-cluster_metric_set.R:47:3', 'test-control.R:19:3',
    'test-engines.R:2:3', 'test-extract_centroids.R:4:3',
    'test-extract_centroids.R:15:3', 'test-extract_centroids.R:27:3',
    'test-extract_centroids.R:39:3', 'test-extract_cluster_assignment.R:4:3',
    'test-extract_cluster_assignment.R:15:3',
    'test-extract_cluster_assignment.R:27:3',
    'test-extract_cluster_assignment.R:39:3', 'test-extract_fit_summary.R:61:3',
    'test-fiting.R:7:3', 'test-hier_clust.R:29:3', 'test-hier_clust.R:179:3',
    'test-hier_clust.R:188:3', 'test-k_means-clustMixType.R:104:3',
    'test-k_means.R:40:3', 'test-k_means.R:108:3', 'test-k_means.R:117:3',
    'test-k_means.R:168:3', 'test-metric-silhouette.R:23:3',
    'test-metric-silhouette.R:32:3', 'test-metric-sse.R:4:3',
    'test-metric-sse.R:13:3', 'test-metric-sse.R:22:3', 'test-metric-sse.R:31:3',
    'test-predict.R:4:3', 'test-predict.R:15:3', 'test-predict.R:27:3',
    'test-predict.R:39:3', 'test-reconcile_clusterings.R:26:3',
    'test-reconcile_clusterings.R:48:3', 'test-tune_cluster.R:194:3',
    'test-tune_cluster.R:255:3', 'test-tune_cluster.R:283:3',
    'test-tune_cluster.R:295:3', 'test-tune_cluster.R:380:3',
    'test-tune_cluster.R:440:3', 'test-workflows.R:18:3',
    'test-workflows.R:41:3', 'test-workflows.R:65:3'
  
  [ FAIL 0 | WARN 0 | SKIP 48 | PASS 177 ]
  > 
  > proc.time()
     user  system elapsed 
    41.31    1.85   43.23
Running 'version.R' [165s]
Running the tests in 'tests/version.R' failed.
Complete output:
  > pkg <- "tidyCpp"
  > nrdfile <- system.file("NEWS.Rd", package = pkg)
  > isCI <- (Sys.getenv("CI") == "true") || (Sys.getenv("TRAVIS") == "true") || (Sys.getenv("CONTINUOUS_INTEGRATION") == "true") || (Sys.getenv("CODECOV_TOKEN") != "")
  > if (file.exists(nrdfile)) {
  +     nrd <- readLines(nrdfile)
  +     ver <- as.package_version(gsub(".* ([0-9\\.]+) .*", "\\1", nrd[grepl("\\{Changes", nrd)]))
  +     dcf <- read.dcf(system.file("DESCRIPTION", package = pkg))
  +     cur <- as.package_version(dcf[[1,"Version"]])
  +     if (cur != ver[1] && !isCI) stop("Expected NEWS entry for ", cur, " saw ", ver[1], call. = FALSE)
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.14    0.09    0.20
Running 'testthat.R' [233s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tidydann)
  > 
  > test_check("tidydann")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 35 ]
  > 
  > proc.time()
     user  system elapsed 
    70.45    0.90   71.43
Running 'testthat.R' [220s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(EdSurvey)
  Loading required package: car
  Loading required package: carData
  Loading required package: lfactors
  lfactors v1.0.4
  
  Loading required package: Dire
  Dire v2.2.0
  
  EdSurvey v4.0.4
  
  > library(tidyEdSurvey)
  tidyEdSurvey v0.1.2
  A package for using 'dplyr' and 'ggplot2' with student level data in an edsurvey.data.frame. To work with teacher or school level data, see ?EdSurvey::getData
  
  Attaching package: 'tidyEdSurvey'
  
  The following object is masked from 'package:base':
  
      attach
  
  > test_check('tidyEdSurvey')
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 12 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-dplyr-TIMSS.R:1:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
    50.59    2.06   52.64
Running 'spelling.R' [170s]
  Running 'testthat.R' [8s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE,
  +     error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.14    0.06    0.18
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tidyfinance)
  > 
  > test_check("tidyfinance")
  Downloaded WRDS dummy database to D:\temp\RtmpO6sLLW\file2802479416b1.sqlite.
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 45 ]
  > 
  > proc.time()
     user  system elapsed 
     1.42    0.43    1.90
Running 'testthat.R' [151s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidyformula)
  > 
  > test_check("tidyformula")
  [ FAIL 0 | WARN 39 | SKIP 0 | PASS 20 ]
  
  [ FAIL 0 | WARN 39 | SKIP 0 | PASS 20 ]
  > 
  > proc.time()
     user  system elapsed 
     2.54    0.26    2.76
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidygeoRSS)
  > 
  > test_check("tidygeoRSS")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     1.67    0.25    1.90
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tidygraph)
  
  Attaching package: 'tidygraph'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tidygraph")
  Ungrouping `.data`...
  Splitting by nodes
  Unfocusing graph...
  `focus()` selected all nodes. Returning unfocused graph
  `focus()` didn't select any nodes. Returning unfocused graph
  Unfocusing graph...
  Unfocusing prior to grouping
  Unfocusing prior to morphing
  Unfocusing graph...
  Joining with `by = join_by(from, to)`
  Joining with `by = join_by(from, to)`
  Joining with `by = join_by(from, to)`
  Joining with `by = join_by(from, to)`
  Joining with `by = join_by(from, to)`
  Joining with `by = join_by(from, to)`
  Ungrouping `.data`...
  Subsetting by nodes
  Splitting by nodes
  Unfocusing prior to morphing
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 431 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-random-walk.R:19:3'
  • On Windows (7): 'test-centrality.R:17:3', 'test-centrality.R:35:3',
    'test-centrality.R:53:3', 'test-centrality.R:71:3', 'test-group.R:29:3',
    'test-group.R:49:3', 'test-group.R:69:3'
  
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 431 ]
  > 
  > proc.time()
     user  system elapsed 
    11.25    1.07   12.31
Running 'testthat.R' [207s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyHeatmap)
  ========================================
  tidyHeatmap version 1.8.1
  If you use tidyHeatmap in published research, please cite:
  1) Mangiola et al. tidyHeatmap: an R package for modular heatmap production 
    based on tidy principles. JOSS 2020.
  2) Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.
  This message can be suppressed by:
    suppressPackageStartupMessages(library(tidyHeatmap))
  ========================================
  
  
  Attaching package: 'tidyHeatmap'
  
  The following object is masked from 'package:stats':
  
      heatmap
  
  > 
  > test_check("tidyHeatmap")
  [ FAIL 0 | WARN 4 | SKIP 21 | PASS 15 ]
  
  ══ Skipped tests (21) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'tests.R:18:2', 'tests.R:38:2', 'tests.R:54:2', 'tests.R:90:2',
    'tests.R:110:2', 'tests.R:128:2', 'tests.R:281:2', 'tests.R:301:2',
    'tests.R:319:2', 'tests.R:335:2', 'tests.R:378:2', 'tests.R:439:2',
    'tests.R:525:2', 'tests.R:549:2', 'tests.R:568:2', 'tests.R:587:2',
    'tests.R:606:2', 'tests.R:625:2', 'tests.R:644:2', 'tests.R:664:2'
  • empty test (1): 'tests.R:443:1'
  
  [ FAIL 0 | WARN 4 | SKIP 21 | PASS 15 ]
  Deleting unused snapshots:
  • tests/scale-both.svg
  • tests/scale-column.svg
  • tests/scale-none.svg
  > 
  > proc.time()
     user  system elapsed 
    35.45    0.98   36.40
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyheatmaps)
  > 
  > test_check("tidyheatmaps")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     1.35    0.32    1.62
Running 'spelling.R' [0s]
  Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidylda)
  tidylda is under active development. The API and behavior may change.
  > 
  > test_check("tidylda")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 203 ]
  > 
  > proc.time()
     user  system elapsed 
     9.73    0.56   10.28
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("tidylog")
  
  Attaching package: 'tidylog'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tidylog")
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 303 ]
  
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 303 ]
  > 
  > proc.time()
     user  system elapsed 
     3.46    0.45    3.93
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyMC)
  > 
  > test_check("tidyMC")
  Running single test-iteration for each parameter combination...
  
   Test-run successfull: No errors occurred!
  Running whole simulation: Overall 12 parameter combinations are simulated ...
  
   Simulation was successfull!
   Running time: 00:00:00.334366
  Running single test-iteration for each parameter combination...
  
   Test-run successfull: No errors occurred!
  Running whole simulation: Overall 6 parameter combinations are simulated ...
  
   Simulation was successfull!
   Running time: 00:00:00.114955
  Running single test-iteration for each parameter combination...
  Running single test-iteration for each parameter combination...
  Running single test-iteration for each parameter combination...
  
   Test-run successfull: No errors occurred!
  Running whole simulation: Overall 6 parameter combinations are simulated ...
  
   Progress: ─────────────────────────────────────────────────────────────    100%
   Simulation was successfull!
   Running time: 00:00:00.634863
  Running single test-iteration for each parameter combination...
  
   Test-run successfull: No errors occurred!
  Running whole simulation: Overall 6 parameter combinations are simulated ...
  
   Simulation was successfull!
   Running time: 00:00:00.130783
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 59 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 59 ]
  > 
  > proc.time()
     user  system elapsed 
     5.68    0.50   19.59
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TidyMultiqc)
  > 
  > test_check("TidyMultiqc")
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
  > 
  > proc.time()
     user  system elapsed 
     5.73    1.12    6.87
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidypaleo)
  > 
  > test_check("tidypaleo")
  [ FAIL 0 | WARN 3 | SKIP 18 | PASS 208 ]
  
  ══ Skipped tests (18) ══════════════════════════════════════════════════════════
  • On CRAN (18): 'test-age_depth_model.R:120:3',
    'test-ggstrat-plot_addons.R:25:3', 'test-ggstrat-plot_addons.R:53:5',
    'test-ggstrat-plot_addons.R:100:5', 'test-ggstrat.R:39:3',
    'test-ggstrat.R:175:3', 'test-ggstrat.R:231:3', 'test-ggstrat.R:256:3',
    'test-ggstrat.R:275:3', 'test-ggstrat.R:315:3', 'test-ggstrat.R:357:3',
    'test-ggstrat.R:393:3', 'test-ggstrat.R:430:5', 'test-ggstrat.R:502:5',
    'test-nested_chclust.R:56:5', 'test-nested_chclust.R:100:3',
    'test-nested_chclust.R:146:3', 'test-nested_chclust.R:191:3'
  
  [ FAIL 0 | WARN 3 | SKIP 18 | PASS 208 ]
  > 
  > proc.time()
     user  system elapsed 
    16.21    0.62   17.07
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyplus)
  > 
  > test_check("tidyplus")
  Coalesced 'x' from: 'x'
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 128 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On Windows (2): 'test-replace-na-if.R:10:3', 'test-unite-str.R:47:3'
  • get unite_str working with symbol! (1): 'test-unite-str.R:11:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 128 ]
  Deleting unused snapshots:
  • replace-na-if/works.csv
  • unite-str/notremove.csv
  > 
  > proc.time()
     user  system elapsed 
     2.87    0.57    3.43
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidypmc)
  > 
  > test_check("tidypmc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
  > 
  > proc.time()
     user  system elapsed 
     2.04    0.37    2.40
Running 'testthat.R' [204s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyquery)
  > 
  > test_check("tidyquery")
  The tzdb package is not installed. Timezones will not be available to Arrow compute functions.
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  Joining with `by = join_by(office_id)`
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 235 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • Error only affects rlang 0.4.11 and earlier (1): 'test-errors.R:96:3'
  • currently does not fail as expected (1): 'test-arrow-dataset.R:75:3'
  • currently fails because dbplyr does not yet accept `multiple` argument to
    join functions (1): 'test-dbplyr.R:39:3'
  • currently returns columns in wrong order (1): 'test-aggregate.R:294:3'
  
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 235 ]
  > 
  > proc.time()
     user  system elapsed 
    45.48    2.50   50.26
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyqwi)
  Loading required package: future
  > 
  > test_check("tidyqwi")
  [ FAIL 0 | WARN 1 | SKIP 1 | PASS 20 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test.R:45:3'
  
  [ FAIL 0 | WARN 1 | SKIP 1 | PASS 20 ]
  > 
  > proc.time()
     user  system elapsed 
     1.31    0.25    1.56
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyREDCap)
  > 
  > test_check("tidyREDCap")
  Reading metadata about your project....
  Reading variable labels for your variables....
  Reading your data....
  ℹ This may take a while if your dataset is large.
  [ FAIL 0 | WARN 8 | SKIP 0 | PASS 14 ]
  
  [ FAIL 0 | WARN 8 | SKIP 0 | PASS 14 ]
  > 
  > proc.time()
     user  system elapsed 
     2.79    0.50    5.56
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyRSS)
  > 
  > test_check("tidyRSS")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ]
  > 
  > proc.time()
     user  system elapsed 
     3.60    0.39    6.31
Running 'testthat.R' [186s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyrules)
  > 
  > test_check("tidyrules")
  [1] "Bldg_Type == 'OneFam' & House_Style == 'One_and_Half_Unf' & Sale_Type == 'WD'"
  [1] "`Bldg Type` == 'OneFam' & `House Style` == 'One_and_Half_Unf' & Sale_Type == 'WD'"
  integer(0)
  integer(0)
  integer(0)
  integer(0)
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 46 ]
  > 
  > proc.time()
     user  system elapsed 
    16.00    0.96   16.93
Running 'spelling.R' [0s]
  Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidysmd)
  
  Attaching package: 'tidysmd'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("tidysmd")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 89 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-geom_love.R:30:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 89 ]
  Deleting unused snapshots:
  • geom_love/love-plot-works.svg
  > 
  > proc.time()
     user  system elapsed 
     3.37    0.48    3.85
Running 'spelling.R' [153s]
  Running 'testthat.R' [154s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.03    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidysq)
  
  Attaching package: 'tidysq'
  
  The following object is masked from 'package:base':
  
      paste
  
  > 
  > test_check("tidysq")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 805 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • warning handling on C++ side is poorly implemented (1):
    'test-warnings.R:39:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 805 ]
  > 
  > proc.time()
     user  system elapsed 
     9.07    1.37   10.40
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidysynth)
  > 
  > test_check("tidysynth")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 87 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 87 ]
  > 
  > proc.time()
     user  system elapsed 
    15.23    0.46   15.70
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidytable)
  
  Attaching package: 'tidytable'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      dt, filter, lag
  
  The following object is masked from 'package:base':
  
      %in%
  
  > 
  > test_check("tidytable")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1327 ]
  > 
  > proc.time()
     user  system elapsed 
    14.95    2.90   17.90
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidytree)
  If you use the ggtree package suite in published research, please cite
  the appropriate paper(s):
  
  S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
  Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
  visualization of richly annotated phylogenetic data. Molecular Biology
  and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166
  
  Guangchuang Yu. Using ggtree to visualize data on tree-like structures.
  Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
  
  Attaching package: 'tidytree'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tidytree")
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 113 ]
  
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 113 ]
  > 
  > proc.time()
     user  system elapsed 
     3.40    0.48    3.89
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidytuesdayR)
  > 
  > test_check("tidytuesdayR")
  [ FAIL 0 | WARN 3 | SKIP 48 | PASS 35 ]
  
  ══ Skipped tests (48) ══════════════════════════════════════════════════════════
  • On CRAN (48): 'test-00-github_api.R:5:3', 'test-00-github_api.R:22:3',
    'test-00-github_api.R:37:3', 'test-00-github_api.R:47:3',
    'test-00-github_api.R:59:3', 'test-00-github_api.R:68:3',
    'test-00-github_api.R:77:3', 'test-00-github_api.R:97:3',
    'test-01-tt_master_file.R:5:3', 'test-01-tt_master_file.R:21:3',
    'test-01-tt_master_file.R:41:3', 'test-02-tt_available.R:5:3',
    'test-02-tt_available.R:16:3', 'test-02-tt_available.R:27:3',
    'test-02-tt_available.R:43:3', 'test-02-tt_available.R:68:3',
    'test-02-tt_available.R:94:3', 'test-03-tt_check_date.R:4:3',
    'test-03-tt_check_date.R:12:3', 'test-03-tt_check_date.R:21:3',
    'test-03-tt_check_date.R:31:3', 'test-04-tt_compile.R:4:3',
    'test-04-tt_compile.R:30:3', 'test-05-tt_load_gh.R:12:3',
    'test-05-tt_load_gh.R:25:3', 'test-05-tt_load_gh.R:37:3',
    'test-05-tt_load_gh.R:45:5', 'test-05-tt_load_gh.R:56:3',
    'test-05-tt_load_gh.R:66:5', 'test-05-tt_load_gh.R:80:3',
    'test-05-tt_load_gh.R:93:3', 'test-05-tt_load_gh.R:103:3',
    'test-05-tt_load_gh.R:113:3', 'test-05-tt_load_gh.R:121:3',
    'test-05-tt_load_gh.R:139:3', 'test-06-tt_parse_blob.R:119:3',
    'test-07-tt_read_data.R:5:3', 'test-07-tt_read_data.R:34:3',
    'test-07-tt_read_data.R:60:3', 'test-07-tt_read_data.R:75:3',
    'test-08-tt_load.R:11:3', 'test-08-tt_load.R:36:3', 'test-10-utils.R:42:3',
    'test-11-last_tuesday.R:3:3', 'test-11-last_tuesday.R:33:3',
    'test-12-encoding.R:6:5', 'test-12-encoding.R:17:5',
    'test-12-encoding.R:28:5'
  
  [ FAIL 0 | WARN 3 | SKIP 48 | PASS 35 ]
  > 
  > proc.time()
     user  system elapsed 
     3.32    0.51    3.84
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(tidyverse)
  ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
  ✔ dplyr     1.1.4     ✔ readr     2.1.5
  ✔ forcats   1.0.0     ✔ stringr   1.5.1
  ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
  ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
  ✔ purrr     1.0.2     
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
  > 
  > test_check("tidyverse")
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 2 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-attach.R:2:3', 'test-attach.R:7:3', 'test-attach.R:13:3',
    'test-conflicts.R:2:3'
  • On Windows (1): 'test-logo.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     2.04    0.35    2.37
Running 'spelling.R' [153s]
  Running 'testthat.R' [175s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE, error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.12    0.15    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidywikidatar)
  > 
  > test_check("tidywikidatar")
  [ FAIL 0 | WARN 0 | SKIP 12 | PASS 3 ]
  
  ══ Skipped tests (12) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-cache.R:4:3', 'test-cache.R:20:5', 'test-get.R:4:3',
    'test-get.R:33:3', 'test-get_image.R:5:3', 'test-get_image.R:42:3',
    'test-get_image.R:92:3', 'test-get_many.R:4:3',
    'test-get_property_same_length.R:4:3', 'test-get_qualifiers.R:4:3',
    'test-get_qualifiers.R:35:3', 'test-tw_get_p_wide.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 12 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     5.48    0.43    5.86
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tigris)
  To enable caching of data, set `options(tigris_use_cache = TRUE)`
  in your R script or .Rprofile.
  > 
  > test_check("tigris")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
  > 
  > proc.time()
     user  system elapsed 
     1.23    0.29    1.51
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (nchar(Sys.getenv("R_TESTS")) == 0) {
  +   library(testthat)
  +   library(tikzDevice)
  + 
  +   test_check("tikzDevice")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.04    0.20
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(timbr)
  > 
  > test_check("timbr")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Matching, by = c("key1", "key2", "key3")
  Matching, by = c("key1", "key2", "key3")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
     2.20    0.39    2.59
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(timeR)
  > 
  > test_check("timeR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.53    0.07    0.60
Invalid package aliases in Rd file 'timeSeq_1.0.4-package.Rd':
  'timeSeq_1.0.4-package'
Running 'testthat.R' [149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(time.slots)
  > 
  > test_check("time.slots")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
  > 
  > proc.time()
     user  system elapsed 
     1.35    0.31    1.67
Running 'spelling.R' [166s]
  Running 'testthat.R' [154s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.06    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(timevarcorr)
  timevarcorr loaded; type ?tcor for help on this package.
  
  > 
  > test_check("timevarcorr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     0.70    0.12    0.81
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tinsel)
  > 
  > test_check("tinsel")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 62 ]
  > 
  > proc.time()
     user  system elapsed 
     1.12    0.23    1.34
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tinter)
  > 
  > test_check("tinter")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
  > 
  > proc.time()
     user  system elapsed 
     0.75    0.26    1.00
Running 'simple.R' [169s]
Running the tests in 'tests/simple.R' failed.
Complete output:
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())
  > 
  > ## process html -- should work everywhere
  > ## but doesn't: CRAN's macOS and Solaris have seriously outdated pandoc binaries
  > ## replace with test from rmarkdown itself
  > ## old: asTRUE(unname(Sys.info()["sysname"]) %in% c("Linux","Windows"))) {
  > if (rmarkdown::pandoc_available("1.12.3")) {
  +     file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  +     rmarkdown::render("simpleHtml.Rmd")
  + }
  
  
  processing file: simpleHtml.Rmd
  output file: simpleHtml.knit.md
  
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS simpleHtml.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output simpleHtml.html --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --section-divs --template "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\Rtmpy2igap\rmarkdown-strf7fc1453113a.html" 
  
  Output created: simpleHtml.html
  > 
  > ## pdf requires a fairly complete latex installation so make this conditional
  > #if (isTRUE(unname(Sys.info()["user"])=="edd")) {
  > #    file.copy(system.file("examples", "simplePdf.Rmd", package="tint"), "simplePdf.Rmd")
  > #    rmarkdown::render("simplePdf.Rmd")
  > #}
  > 
  > proc.time()
     user  system elapsed 
     0.90    0.23    1.62
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("tinylabels")
  > 
  > test_check("tinylabels")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 74 ]
  > 
  > proc.time()
     user  system elapsed 
     1.39    0.34    1.79
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tinyProject)
  > 
  > test_check("tinyProject")
  [ FAIL 0 | WARN 5 | SKIP 0 | PASS 87 ]
  
  [ FAIL 0 | WARN 5 | SKIP 0 | PASS 87 ]
  > 
  > proc.time()
     user  system elapsed 
     1.46    0.31    1.73
Running 'tinytest.R' [164s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE) && isTRUE(Sys.getenv("R_NOT_CRAN") == "true")) {
  +     tinytest::test_package("tinysnapshot")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.04    0.21
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tipr)
  > 
  > test_check("tipr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 64 ]
  > 
  > proc.time()
     user  system elapsed 
     1.70    0.17    1.86
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
Found the following significant warnings:
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:317:29: warning: format '%d' expects argument of type 'int', but argument 2 has type 'DWORD' {aka 'long unsigned int'} [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.6Mb
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("tmod")
  Loading required package: tmod
  For tmod user guide, type `vignette("tmod")`
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 122 ]
  > 
  > proc.time()
     user  system elapsed 
     4.85    1.39    6.21
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./testthat
  > 
  > require(testthat)
  Loading required package: testthat
  > # tm is only imported
  > require(tm)
  Loading required package: tm
  Loading required package: NLP
  > test_check("tm.plugin.koRpus")
  Loading required package: tm.plugin.koRpus
  Loading required package: koRpus
  Loading required package: sylly
  
  Attaching package: 'sylly'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  For information on available language packages for 'koRpus', run
  
    available.koRpus.lang()
  
  and see ?install.koRpus.lang()
  
  
  Attaching package: 'koRpus'
  
  The following object is masked from 'package:tm':
  
      readTagged
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
  > 
  > proc.time()
     user  system elapsed 
     4.37    0.42    4.78
Running 'import.R' [174s]
Running the tests in 'tests/import.R' failed.
Complete output:
  > library(tm)
  Loading required package: NLP
  > library(tm.plugin.lexisnexis)
  > 
  > # English example
  > file <- system.file("texts", "lexisnexis_test_en.html",
  +                     package = "tm.plugin.lexisnexis")
  > corpus <- Corpus(LexisNexisSource(file))
  > 
  > # French example
  > file <- system.file("texts", "lexisnexis_test_fr.html",
  +                     package = "tm.plugin.lexisnexis")
  > corpus <- Corpus(LexisNexisSource(file))
  > 
  > # Two malformed examples: one which can be parsed but with a missing copyright
  > # notice (and with a warning), and one which should be dropped (with a warning).
  > # We suppress warnings to avoid breaking the build, then test the consequences.
  > file <- system.file("texts", "lexisnexis_test_copyright_error.html",
  +                     package = "tm.plugin.lexisnexis")
  > corpus <- suppressWarnings(Corpus(LexisNexisSource(file)))
  > stopifnot(length(corpus) == 1,
  +           corpus[[1]]$meta$id == "resize201812311",
  +           length(corpus[[1]]$meta$rights) == 0)
  > 
  > proc.time()
     user  system elapsed 
     0.65    0.10    0.73
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tm)
  Loading required package: NLP
  > 
  > test_check("tm")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 17 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • latin1 locale not available (1): 'test-Transformation.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 17 ]
  > 
  > proc.time()
     user  system elapsed 
     0.87    0.31    1.17
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tmsens)
  > 
  > 
  > test_check("tmsens")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-tm_bias.R:3:1', 'test-tmf.R:3:1'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.65    0.18    0.78
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TNC)
  Welcome to TNC, a package to calculate centrality measures in temporal networks.
  > 
  > test_check("TNC")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
  > 
  > proc.time()
     user  system elapsed 
     0.81    0.26    1.03
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tntpr)
  NOTE: The 'Halyard Display' font is the default font for the tntp_style() theme. This font is not currently installed on your system. 
  
        To install 'Halyard Display', follow the directions in the TNTP Visualization Cookbook at the following link:
  
        https://tntp.github.io/tntpr/articles/visualization-cookbook.html#setting-font-family-and-font-sizes
  > 
  > test_check("tntpr")
  i Changed the following columns to factors: `a`
  
  Attaching package: 'janitor'
  
  The following objects are masked from 'package:stats':
  
      chisq.test, fisher.test
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 0 | WARN 10 | SKIP 0 | PASS 95 ]
  
  [ FAIL 0 | WARN 10 | SKIP 0 | PASS 95 ]
  > 
  > proc.time()
     user  system elapsed 
     5.09    0.60    5.70
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tokenizers)
  > 
  > test_check("tokenizers")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 219 ]
  > 
  > proc.time()
     user  system elapsed 
     3.00    0.29    3.28
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tok)
  > 
  > test_check("tok")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 8 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-encoding.R:2:3', 'test-tokenizer.R:30:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     1.20    0.18    1.31
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("toOrdinal")
  Loading required package: toOrdinal
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
  > 
  > proc.time()
     user  system elapsed 
     0.84    0.18    1.03
Running 'spelling.R' [157s]
  Running 'testthat.R' [174s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.10    0.14    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(topdowntimeratio)
  
  Attaching package: 'topdowntimeratio'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  > 
  > test_check("topdowntimeratio")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-tsiter.R:119:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
     1.17    0.28    1.43
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(testthat)
  > library(torchaudio)
  > 
  > if (Sys.getenv("TORCH_TEST", unset = 0) == 1)
  +   test_check("torchaudio")
  > 
  > proc.time()
     user  system elapsed 
     0.37    0.09    0.45
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(torchdatasets)
  > 
  > if (Sys.getenv("TORCH_TEST", unset = 0) == 1)
  +   test_check("torchdatasets")
  > 
  > proc.time()
     user  system elapsed 
     1.03    0.28    1.29
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(torchopt)
  > test_check("torchopt")
  [ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-optimizers.R:46:5', 'test-optimizers.R:66:5',
    'test-optimizers.R:81:5', 'test-optimizers.R:96:5',
    'test-optimizers.R:112:5', 'test-optimizers.R:127:5',
    'test-optimizers.R:142:5', 'test-optimizers.R:157:5',
    'test-optimizers.R:172:5', 'test-utils-testopt.R:2:5'
  
  [ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     1.04    0.17    1.20
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.7Mb
    include   1.8Mb
    libs     17.2Mb
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(torch)
  > 
  > if (Sys.getenv("TORCH_TEST", unset = 0) == 1) {
  +   test_check("torch")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.92    0.25    1.17
Running 'spelling.R' [156s]
  Running 'testthat.R' [152s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.07    0.18 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tor)
  > 
  > test_check("tor")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
  > 
  > proc.time()
     user  system elapsed 
     3.07    0.60    3.51
Package suggested but not available for checking: 'toscaData'
Running 'spelling.R' [174s]
  Running 'testthat.R' [453s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.06    0.37
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("TotalCopheneticIndex")
  > 
  > test_check("TotalCopheneticIndex")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
  > 
  > proc.time()
     user  system elapsed 
     1.12    0.26    1.37
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(toxEval)
  For more information:
  https://doi-usgs.github.io/toxEval/
  ToxCast database: version 3.5
  > test_check("toxEval")
  [ FAIL 0 | WARN 4 | SKIP 20 | PASS 23 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test_utils.R:4:3', 'test_utils.R:43:3',
    'tests_endpoint.R:21:3', 'tests_endpoint.R:35:3', 'tests_endpoint.R:57:3',
    'tests_endpoint.R:89:3', 'tests_summary.R:43:3', 'tests_summary.R:57:3',
    'tests_summary.R:85:3', 'tests_summary.R:113:3', 'tests_summary.R:141:3',
    'tests_summary.R:169:3', 'tests_summary.R:195:3', 'tests_summary.R:208:3',
    'tests_summary.R:230:3', 'tests_summary.R:270:3', 'tests_summary.R:310:3',
    'tests_summary.R:331:3', 'tests_summary.R:358:3', 'tests_summary.R:372:3'
  
  [ FAIL 0 | WARN 4 | SKIP 20 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
    10.48    1.18   11.64
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Running 'testthat.R' [183s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TPCselect)
  > 
  > test_check("TPCselect")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
  > 
  > proc.time()
     user  system elapsed 
     7.64    1.18    9.07
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tqk)
  > 
  > test_check("tqk")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 3 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-code_get.R:3:3', 'test-tqk_get.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     1.10    0.26    1.34
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(trackdf)
  
  Attaching package: 'trackdf'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("trackdf")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     1.29    0.34    1.59
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trafo)
  > 
  > test_check("trafo")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 84 ]
  > 
  > proc.time()
     user  system elapsed 
     1.04    0.31    1.34
Running 'spelling.R' [146s]
  Running 'testthat.R' [163s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.03    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(traipse)
  > 
  > test_check("traipse")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
     1.48    0.29    1.76
Package suggested but not available for checking: 'taxidata'
Running 'testthat.R' [187s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trajr)
  > 
  > test_check("trajr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 277 ]
  > 
  > proc.time()
     user  system elapsed 
    19.84    3.21   22.57
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.3Mb
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(transformer)
  > 
  > test_check("transformer")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.92    0.12    1.03
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TransPhylo)
  > 
  > test_check("TransPhylo")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
  > 
  > proc.time()
     user  system elapsed 
     7.37    2.26    9.65
Running 'spelling.R' [0s]
  Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(transplantr)
  > 
  > test_check("transplantr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 77 ]
  > 
  > proc.time()
     user  system elapsed 
     1.21    0.28    1.45
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(transport)
  > 
  > test_check("transport")
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 36 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-main.R:163:3', 'test-main.R:185:3', 'test-main.R:194:3',
    'test-main.R:220:3'
  
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 36 ]
  > 
  > proc.time()
     user  system elapsed 
     2.04    0.29    2.32
Packages which this enhances but not available for checking:
  'fwelnet', 'doMC'
Running 'testthat.R' [211s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(transreg)
  > 
  > testthat::test_check(package="transreg",stop_on_warning=FALSE)
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 9 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 9 ]
  > 
  > proc.time()
     user  system elapsed 
    38.31    1.89   40.23
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(traudem)
  > 
  > test_check("traudem")
  [ FAIL 0 | WARN 0 | SKIP 12 | PASS 0 ]
  
  ══ Skipped tests (12) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-aaa-sitrep.R:2:3', 'test-aaa-sitrep.R:10:3',
    'test-aaa-sitrep.R:18:3', 'test-aaa-sitrep.R:25:3', 'test-aread8.R:2:3',
    'test-d8flowdir.R:2:3', 'test-moveoutletstostrm.R:2:3',
    'test-pitremove.R:2:3', 'test-pitremove.R:20:3', 'test-pitremove.R:36:3',
    'test-taudem_threshold.R:2:3', 'test-threshold.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 12 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.03    0.25    1.23
Running 'testthat.R' [145s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(treasury)
  > 
  > test_check("treasury")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
  > 
  > proc.time()
     user  system elapsed 
     1.09    0.14    1.21
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TreeBUGS)
  > 
  > test_check("TreeBUGS")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 25 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_fitModelCpp.R:7:5', 'test_fitModelCpp.R:24:5'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
     1.35    0.18    1.53
Documented arguments not in \usage in Rd file 'correct_continuous.Rd':
  'x'

Documented arguments not in \usage in Rd file 'tc_correlation.Rd':
  'p'

Documented arguments not in \usage in Rd file 'tc_efunc.Rd':
  'p'

Documented arguments not in \usage in Rd file 'tc_mfunc.Rd':
  'p'

Documented arguments not in \usage in Rd file 'tc_response.Rd':
  'p'

Documented arguments not in \usage in Rd file 'truncate_input.Rd':
  'moving'

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.
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TreeDiagram)
  > 
  > test_check("TreeDiagram")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     1.20    0.17    1.35
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TreeDimensionTest)
  Loading required package: mlpack
  
  Attaching package: 'mlpack'
  
  The following object is masked from 'package:stats':
  
      kmeans
  
  The following object is masked from 'package:base':
  
      det
  
  > 
  > test_check("TreeDimensionTest")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
  > 
  > proc.time()
     user  system elapsed 
     2.07    0.34    2.40
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.1Mb
Running 'spelling.R' [171s]
  Running 'testthat.R' [19s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(vignettes = TRUE, error = TRUE,
  +                              skip_on_cran = TRUE)
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
      0.1     0.1     0.2
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (C) 2020  Momoko Hayamizu <hayamizu@ism.ac.jp>
  > #
  > # This program is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # 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, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  > library(treefit)
  > 
  > test_check("treefit")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
  > 
  > proc.time()
     user  system elapsed 
     6.26    0.75    7.00
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tree.interpreter)
  > 
  > test_check("tree.interpreter")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 122 ]
  > 
  > proc.time()
     user  system elapsed 
     6.14    1.28    6.92
Running 'spelling.R' [156s]
  Running 'testthat.R' [152s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.04    0.25 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(treemapify)
  > 
  > test_check("treemapify")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_plots.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
  Deleting unused snapshots:
  • plots/colour-is-drawn-correctly-in-legend.svg
  • plots/correct-colours-for-subgroup-text-differently.svg
  • plots/correct-colours-for-subgroup-text.svg
  • plots/fixed-layout.svg
  • plots/scol-layout.svg
  • plots/squarified-layout-starting-from-top-right.svg
  • plots/srow-layout-starting-from-bottom-right-with-subgroups.svg
  • plots/srow-layout.svg
  • plots/understands-variants-of-centre-with-subgroups.svg
  • plots/understands-variants-of-centre.svg
  > 
  > proc.time()
     user  system elapsed 
     4.75    0.32    5.07
Auto-generated content requiring editing in Rd file 'treemisc-package.Rd':
  \references: 'This optional section can contain literature or other refere...'
  \seealso: 'Optional links to other man pages'
  \examples: '## Optional simple examples of the most important functions ...'
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(treenomial)
  > 
  > test_check("treenomial")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 46 ]
  > 
  > proc.time()
     user  system elapsed 
     2.54    0.17    2.65
Running 'cv.tree.R' [0s]
  Running 'deparse.R' [157s]
  Running 'no_obs.R' [0s]
Running the tests in 'tests/deparse.R' failed.
Complete output:
  > ## PR#15696
  > 
  > ir.tr <- tree::tree(Species ~., iris)
  > head(model.frame(ir.tr))
    Species Sepal.Length Sepal.Width Petal.Length Petal.Width
  1  setosa          5.1         3.5          1.4         0.2
  2  setosa          4.9         3.0          1.4         0.2
  3  setosa          4.7         3.2          1.3         0.2
  4  setosa          4.6         3.1          1.5         0.2
  5  setosa          5.0         3.6          1.4         0.2
  6  setosa          5.4         3.9          1.7         0.4
  > ## infinite-looped in 1.0-34
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.03    0.21
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.0Mb
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("treespace")
  Loading required package: treespace
  Loading required package: ape
  Loading required package: ade4
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
  > 
  > proc.time()
     user  system elapsed 
     7.00    1.18    8.15
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trekcolors)
  > 
  > test_check("trekcolors")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 47 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 47 ]
  > 
  > proc.time()
     user  system elapsed 
     1.42    0.25    1.64
Running 'testthat.R' [182s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("TrenchR")
  Loading required package: TrenchR
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 277 ]
  > 
  > proc.time()
     user  system elapsed 
     4.23    0.43    4.67
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trending)
  > 
  > test_check("trending")
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 46 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-brm.R:4:3', 'test-glm.R:19:3', 'test-glm_nb.R:16:3',
    'test-lm.R:16:3', 'test-printing.R:6:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 46 ]
  > 
  > proc.time()
     user  system elapsed 
     9.29    0.75   10.03
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TRES)
  Loading required package: ManifoldOptim
  Loading required package: Rcpp
  > 
  > test_check("TRES")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • skip (3): 'test-TRR_TPR.R:3:1', 'test-auxiliary.R:3:1', 'test-examples.R:3:1'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.82    0.23    1.25
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.5Mb
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(triangulr)
  > 
  > test_check("triangulr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 255 ]
  > 
  > proc.time()
     user  system elapsed 
     2.78    0.53    3.26
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(triebeard)
  > 
  > test_check("triebeard")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
  > 
  > proc.time()
     user  system elapsed 
     1.04    0.32    1.35
Running 'testthat.R' [183s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(triplot)
  > 
  > test_check("triplot")
  Welcome to DALEX (version: 2.4.3).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 84 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 84 ]
  > 
  > proc.time()
     user  system elapsed 
    12.15    0.95   13.09
Running 'spelling.R' [151s]
  Running 'testthat.R' [186s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.04    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trip)
  > 
  > test_check("trip")
  
  Longitudes contain values greater than 180, 
  
  
  
  
   Data fully validated: returning object of class  trip 
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 112 ]
  > 
  > proc.time()
     user  system elapsed 
    18.46    0.82   19.31
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(triptych)
  > 
  > test_check("triptych")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.18    0.34    1.51
Running 'spelling.R' [158s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.06    0.25
Running 'testthat.R' [214s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > testthat::test_check("TruncExpFam")
  Loading required package: TruncExpFam
  Welcome to TruncExpFam 1.1.1.
  Please read the documentation on ?TruncExpFam to learn more about the package.
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 572 ]
  > 
  > proc.time()
     user  system elapsed 
    36.20    9.92   46.15
Running 'testthat.R' [150s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_binary.R:4:3', 'test_rosenbrock.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.68    0.25    1.87
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tryCatchLog)
  Using futile.logger for logging...
  > 
  > 
  > 
  > # Set to something like [1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/de_DE.UTF-8"
  > # to ensure english error messages
  > # DISABLED - DOES NOT WORK (AT LEAST NOT ON OSX)!
  > # Sys.setlocale("LC_ALL", "en_US.UTF-8")
  > # Sys.getlocale()
  > 
  > # https://stackoverflow.com/questions/47977951/how-to-ensure-english-error-messages-in-testthat-unit-tests
  > Sys.setenv("LANGUAGE" = "EN")  # work-around to always create english R (error) messages
  > 
  > 
  > 
  > test_check("tryCatchLog")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 446 ]
  > 
  > proc.time()
     user  system elapsed 
     5.18    0.70    5.86
Running 'spelling.R' [150s]
  Running 'testthat.R' [181s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE, error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.03    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tsbox)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("tsbox")
  Starting 2 test processes
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 652 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-error_handling.R:237:3',
    'test-nonstandard_cnames.R:20:3', 'test-nonstandard_cnames.R:58:3',
    'test-readme.R:2:3', 'test-object_conversion.R:6:3',
    'test-object_conversion.R:47:3', 'test-object_conversion.R:83:3',
    'test-object_conversion.R:114:3', 'test-object_conversion.R:151:3',
    'test-ts_.R:19:3', 'test-ts_first_of_period.R:1:1', 'test-ts_index.R:2:1',
    'test-ts_frequency.R:28:3', 'test-ts_plot.R:2:3', 'test-ts_summary.R:7:3',
    'test-tsibble.R:44:3', 'test-tzone.R:8:3'
  
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 652 ]
  > 
  > proc.time()
     user  system elapsed 
     4.37    0.50   29.65
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library("TSdist") 
  Loading required package: proxy
  
  Attaching package: 'proxy'
  
  The following objects are masked from 'package:stats':
  
      as.dist, dist
  
  The following object is masked from 'package:base':
  
      as.matrix
  
  Loaded TSdist v3.7.1. See ?TSdist for help, citation("TSdist") for use in publication.
  
  > test_package("TSdist")
  No installed testthat tests found for TSdist
  > 
  > 
  > proc.time()
     user  system elapsed 
     1.59    0.45    2.06
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running 'testthat.R' [183s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tsdistributions)
  Loading required package: tsmethods
  > 
  > test_check("tsdistributions")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
  > 
  > proc.time()
     user  system elapsed 
    27.84    0.50   28.34
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tsensembler)
  > 
  > test_check("tsensembler")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     2.53    0.42    2.89
Running 'bar.R' [171s]
  Running 'foo.R' [175s]
  Running 'rats.R' [0s]
  Comparing 'rats.Rout' to 'rats.Rout.save' ... OK
Running the tests in 'tests/bar.R' failed.
Complete output:
  > 
  >  library(TSHRC)
  > 
  >  options(digits=4) # avoid rounding differences
  > 
  >  data(rats)
  >  attach(rats)
  > 
  >  set.seed(42)
  > 
  >  twostage(time, delta, group, nboot = 2500)
      LRPV     MTPV     TSPV 
  0.003372 0.060000 0.003372 
  > 
  >  twostage(time, delta, group, nboot = 2500)
      LRPV     MTPV     TSPV 
  0.003372 0.052800 0.003372 
  > 
  >  twostage(time, delta, group, nboot = 2500)
      LRPV     MTPV     TSPV 
  0.003372 0.049600 0.003372 
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.48    0.09    0.57 
Running the tests in 'tests/foo.R' failed.
Complete output:
  > 
  >  library(TSHRC)
  > 
  >  options(digits=4) # avoid rounding differences
  > 
  >  n <- 200
  > 
  >  set.seed(42)
  > 
  >  x1 <- rexp(n)
  >  y1 <- rexp(n, rate = 1 / 2)
  >  t1 <- pmin(x1, y1)
  >  d1 <- as.numeric(t1 == x1)
  >  g1 <- rep(0, n)
  > 
  >  a <- 1.25
  >  b <- 1 / gamma(1 + 1 / a)
  >  x2 <- rweibull(n, shape = a, scale = b)
  >  y2 <- rexp(n, rate = 1 / 2)
  >  t2 <- pmin(x2, y2)
  >  d2 <- as.numeric(t2 == x2)
  >  g2 <- rep(1, n)
  > 
  >  twostage(c(t1, t2), c(d1, d2), c(g1, g2), nboot = 2500)
     LRPV    MTPV    TSPV 
  0.31888 0.01520 0.04014 
  > 
  >  twostage(c(t1, t2), c(d1, d2), c(g1, g2), nboot = 2500)
    LRPV   MTPV   TSPV 
  0.3189 0.0168 0.0417 
  >  
  >  twostage(c(t1, t2), c(d1, d2), c(g1, g2), nboot = 2500)
     LRPV    MTPV    TSPV 
  0.31888 0.02560 0.05027 
  > 
  > 
  > proc.time()
     user  system elapsed 
     4.21    0.04    4.25
Running 'testthat.R' [148s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tsmethods)
  > library(xts)
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > test_check("tsmethods")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     0.71    0.20    0.90
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > library("TSP")
  > test_check("TSP")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 37 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • skipped test for concorde/linkern. Not installed. (2):
    'test-concorde.R:18:1', 'test-insert_cut_etc.R:73:1'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 37 ]
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.92    0.25    1.15
Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ttcg)
  > 
  > test_check("ttcg")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
     1.95    0.84    2.78
Running 'testthat.R' [151s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tubern)
  > 
  > test_check("tubern")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-get-report.R:5:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.78    0.15    0.87
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tuber)
  > 
  > test_check("tuber")
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 0 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-captions.R:5:3', 'test-get-details.R:5:3',
    'test-get-related-videos.R:5:3', 'test-list-channel-activities.R:5:3',
    'test-list-channel-sections.R:3:1', 'test-pkg-style.R:5:5'
  
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.42    0.31    1.68
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tufte)
  > 
  > test_check("tufte")
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 0 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-html.R:2:3', 'test-html.R:36:3', 'test-html.R:43:3',
    'test-html.R:51:3'
  
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.96    0.20    1.39
Running 'spelling.R' [153s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE, error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.06    0.23
Package vignette with \VignetteEngine{} not specifying an engine package:
  'turner_introduction.Rnw'
Engines should be specified as \VignetteEngine{PKG::ENG}.
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tvgeom)
  > 
  > test_check("tvgeom")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
  > 
  > proc.time()
     user  system elapsed 
     6.23    1.65    7.87
Running 'test-all.R' [169s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("tvm")
  Loading required package: tvm
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
  > 
  > proc.time()
     user  system elapsed 
     1.17    0.12    1.26
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tvthemes)
  > library(ggplot2)
  > 
  > test_check("tvthemes")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 619 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-fonts.R:2:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 619 ]
  > 
  > proc.time()
     user  system elapsed 
     5.34    0.84    5.56
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tweenr)
  > 
  > test_check("tweenr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 78 ]
  > 
  > proc.time()
     user  system elapsed 
     1.07    0.20    1.28
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(twilio)
  > 
  > test_check("twilio")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 4 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test_tw_get_message_media.R:4:3',
    'test_tw_get_messages_list.R:4:3', 'test_tw_send_message.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     1.21    0.18    1.37
Package which this enhances but not available for checking: 'sl3'
Running 'testthat.R' [186s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(txshift)
  txshift v0.3.8: Efficient Estimation of the Causal Effects of Stochastic
  Interventions
  > 
  > test_check("txshift")
  [ FAIL 0 | WARN 5 | SKIP 0 | PASS 10 ]
  
  [ FAIL 0 | WARN 5 | SKIP 0 | PASS 10 ]
  > 
  > proc.time()
     user  system elapsed 
    27.92    1.00   28.89
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(typed)
  
  Attaching package: 'typed'
  
  The following object is masked from 'package:utils':
  
      ?
  
  The following object is masked from 'package:base':
  
      declare
  
  > 
  > test_check("typed")
  # typed function
  function () 
  {
  }
  <environment: 0x000002553fcace68>
  # typed function
  function (x) 
  {
      check_output(check_arg(x, Double()), Double())
  }
  <environment: 0x000002553fcace68>
  # Return type: Double()
  # Arg types:
  # x: Double()
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 188 ]
  > 
  > proc.time()
     user  system elapsed 
     3.37    0.31    3.70
Running 'test.R' [173s]
Running the tests in 'tests/test.R' failed.
Complete output:
  > library(types)
  
  Attaching package: 'types'
  
  The following object is masked from 'package:utils':
  
      ?
  
  > add <- function(x = ? numeric, y = 1) {
  +   x + y
  + } ? numeric
  > 
  > add2 <- function(x = 1, y = ? numeric) {
  +   sum(x, y) ? numeric
  + }
  > 
  > label <- function(x) paste(as.call(list(x[[1]], quote(...))), collapse = "\n")
  > 
  > expect_error <- function(x, regexp) {
  +   error <- tryCatch({
  +     x
  +     NULL
  +   }, error = function(e) e)
  + 
  +   if (is.null(error)) {
  +     stop(label(x), " did not throw an error.")
  +   }
  +   if (!grepl(regexp, error$message)) {
  +     stop(error$message, " did not match ", regexp)
  +   }
  +   invisible(TRUE)
  + }
  > 
  > expect_error(add(), "argument is missing, with no default")
  > expect_error(add2(), "argument is missing, with no default")
  > 
  > stopifnot(add(1, 2) == 3)
  > stopifnot(add2(1, 2) == 3)
  > 
  > add_untyped <- remove_types(add)
  > stopifnot(identical(formals(add_untyped), as.pairlist(alist(x=, y = 1))))
  > stopifnot(all.equal(body(add_untyped), quote({ x + y })))
  > 
  > add2_untyped <- remove_types(add2)
  > stopifnot(identical(formals(add2_untyped), as.pairlist(alist(x = 1, y = ))))
  > stopifnot(all.equal(body(add2_untyped), quote({ sum(x, y) })))
  > 
  > stopifnot(identical(remove_types(quote(a ? b)), quote(a)))
  > stopifnot(identical(remove_types(quote(a + 1 ? b)), quote(a + 1)))
  > 
  > stopifnot(identical(remove_types(expression(a ? b, a + 1 ? b)), expression(a, a + 1)))
  > 
  > stopifnot(identical(remove_types(list(quote(a ? b), quote(a + 1 ? b))), list(quote(a), quote(a + 1))))
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.07    0.26
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library (testthat)
  > library (typetracer)
  > 
  > test_check ("typetracer")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 30 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-trace-fns.R:10:9'
  • On Windows (2): 'test-trace-package.R:17:1', 'test-utils.R:45:1'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 30 ]
  > 
  > proc.time()
     user  system elapsed 
     1.31    0.25    1.54
Running 'tinytest.R' [176s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("uaparserjs")
  + }
  
  test_uaparserjs.R.............    0 tests    
  test_uaparserjs.R.............    0 tests    
  test_uaparserjs.R.............    1 tests [0;32mOK[0m 
  test_uaparserjs.R.............    2 tests [0;32mOK[0m 
  test_uaparserjs.R.............    3 tests [0;32mOK[0m [0;34m0.1s[0m
  All ok, 3 results (0.1s)
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.68    0.20    0.87
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.5Mb
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ubms)
  Loading required package: unmarked
  
  Attaching package: 'ubms'
  
  The following objects are masked from 'package:unmarked':
  
      fitList, projected
  
  The following object is masked from 'package:base':
  
      gamma
  
  > test_check("ubms")
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 301 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test_colext.R:3:1', 'test_distsamp.R:3:1', 'test_fit.R:3:1',
    'test_fitlist.R:3:1', 'test_linpred.R:3:1', 'test_multinomPois.R:3:1',
    'test_occu.R:3:1', 'test_occuRN.R:3:1', 'test_occuTTD.R:3:1',
    'test_pcount.R:3:1', 'test_plot_effects.R:3:1', 'test_plot_posteriors.R:3:1',
    'test_ranef.R:3:1', 'test_residuals.R:3:1', 'test_spatial.R:3:1',
    'test_ubmsFit_methods.R:3:1', 'test_utils.R:3:1'
  
  [ FAIL 0 | WARN 0 | SKIP 17 | PASS 301 ]
  > 
  > proc.time()
     user  system elapsed 
    11.12    0.60   11.75
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(uclust)
  Loading required package: dendextend
  
  ---------------------
  Welcome to dendextend version 1.17.1
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  You may ask questions at stackoverflow, use the r and dendextend tags: 
  	 https://stackoverflow.com/questions/tagged/dendextend
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  Loading required package: robcor
  > 
  > test_check("uclust")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     0.92    0.31    1.18
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   4.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.5Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
Running 'spelling.R' [153s]
  Running 'testthat.R' [150s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.23    0.01    0.23 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(uklr)
  > 
  > test_check("uklr")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-build-sparql.R:3:1', 'test-empty-return.R:1:1'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.84    0.12    0.95
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ukpolice)
  > 
  > test_check("ukpolice")
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 0 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-crime-at-location.R:4:3', 'test-empty-functions.R:4:3',
    'test-forces.R:4:3', 'test-neighbourhood-boundary.R:4:3',
    'test-neighbourhood.R:4:3', 'test-specific-crime-no-location-crime.R:4:3',
    'test-stop-and-search.R:4:3', 'test-street-crime.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.04    0.17    1.18
Running 'testthat.R' [207s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(umap)
  > 
  > test_check("umap")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 249 ]
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
    16.51    1.54   39.01
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.4Mb
Argument items with no description in Rd file 'HC.Rd':
  'X' 'K'
Argument items with no description in Rd file 'KA.Rd':
  'X' 'K' 'distancemetric'
Argument items with no description in Rd file 'SOMs.Rd':
  'X' 'K' 'topo' 'rlen' 'alpha' 'n.hood'
Argument items with no description in Rd file 'binarise.Rd':
  'U' 'K' 'technique' 'parameter'
Argument items with no description in Rd file 'closestToSquareFactors.Rd':
  'n'
Argument items with no description in Rd file 'clustDist.Rd':
  'U1' 'U2' 'X' 'criterion'
Argument items with no description in Rd file 'clustVec2partMat.Rd':
  'C'
Argument items with no description in Rd file 'clusterDataset.Rd':
  'X' 'K' 'D' 'methods'
Argument items with no description in Rd file 'factors.Rd':
  'n' 'primeonly'
Argument items with no description in Rd file 'fixnans.Rd':
  'X' 'type'
Argument items with no description in Rd file 'fuzzystretch.Rd':
  'X' 'x0'
Argument items with no description in Rd file 'generateCoPaM.Rd':
  'U' 'relabel_technique' 'w' 'X' 'distCriterion' 'K' 'GDM'
Argument items with no description in Rd file 'isValidBPM.Rd':
  'U'
Argument items with no description in Rd file 'isempty.Rd':
  'X'
Argument items with no description in Rd file 'isnullorempty.Rd':
  'X'
Argument items with no description in Rd file 'kmeansKA.Rd':
  'X' 'K' 'distancemetric' 'iter.max' 'nstart' 'algorithm' 'trace'
Argument items with no description in Rd file 'mnplots.Rd':
  'Vmse' 'mseCache' 'subplotdim' 'subplotind' 'minimiseDistance'
Argument items with no description in Rd file 'mseclusters.Rd':
  'X' 'B' 'normalise'
Argument items with no description in Rd file 'normaliseMatrix.Rd':
  'X' 'type'
Argument items with no description in Rd file 'partMat2clustVec.rd':
  'U' 'skipValidity'
Argument items with no description in Rd file 'permutations.Rd':
  'n'
Argument items with no description in Rd file 'relabelClusts.Rd':
  'ref' 'input' 'technique' 'X' 'distCriterion'
Running 'testthat.R' [146s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(uncmbb)
  > 
  > test_check("uncmbb")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     0.96    0.23    1.18
Running 'spelling.R' [0s]
  Running 'testthat.R' [152s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(uncorbets)
  > 
  > test_check("uncorbets")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
  > 
  > proc.time()
     user  system elapsed 
     0.82    0.31    1.14
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(understandBPMN)
  > 
  > test_check("understandBPMN")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 304 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 304 ]
  > 
  > proc.time()
     user  system elapsed 
     6.18    0.45    6.62
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unheadr)
  > 
  > test_check("unheadr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
  > 
  > proc.time()
     user  system elapsed 
     2.67    0.37    3.01
Running 'spelling.R' [165s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.04    0.20
Running 'testthat.R' [148s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unifed)
  > 
  > test_check("unifed")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
  > 
  > proc.time()
     user  system elapsed 
     0.64    0.21    0.84
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/unigd.Rcheck/00install.out' for details.
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unine)
  > 
  > test_check("unine")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
  > 
  > proc.time()
     user  system elapsed 
     0.85    0.21    1.07
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unisensR)
  > 
  > test_check("unisensR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 121 ]
  > 
  > proc.time()
     user  system elapsed 
     6.78    1.53    8.17
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unitedR)
  Loading required package: plyr
  > 
  > test_check("unitedR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.17    0.95
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(units)
  udunits database from D:/RCompile/CRANpkg/lib/4.4/units/share/udunits/udunits2.xml
  > 
  > test_check("units")
  [ FAIL 0 | WARN 13 | SKIP 6 | PASS 454 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test_misc.R:88:3', 'test_misc.R:131:3', 'test_plot.R:11:3',
    'test_plot.R:59:3', 'test_plot.R:76:3', 'test_tidyverse.R:11:3'
  
  [ FAIL 0 | WARN 13 | SKIP 6 | PASS 454 ]
  Deleting unused snapshots:
  • plot/ggplot2-lab.svg
  • plot/ggplot2-manual.svg
  • plot/ggplot2-nolab.svg
  • plot/ggplot2-trans-unit.svg
  • plot/ggplot2-transformed.svg
  • plot/plot-boxplot.svg
  • plot/plot-degree-c.svg
  • plot/plot-division.svg
  • plot/plot-hist.svg
  • plot/plot-inverse.svg
  • plot/plot-lab.svg
  • plot/plot-line.svg
  • plot/plot-nothing.svg
  • plot/plot-npower.svg
  • plot/plot-parentheses.svg
  > do.call(units_options, units:::.default_options)
  > 
  > proc.time()
     user  system elapsed 
     8.21    0.90    9.10
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(univariateML)
  > 
  > test_check("univariateML")
  Maximum likelihood estimates for the Weibull model 
  shape  scale  
  2.544  2.899  
  
  Maximum likelihood for the Weibull model 
   
  Call:  mlweibull(x = x) 
  
  Estimates: 
     shape     scale  
  2.544195  2.899315  
  
  Data:            x (10 obs.)
  Support:         (0, Inf)
  Density:         stats::dweibull
  Log-likelihood:  -14.54088
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 501 ]
  > 
  > proc.time()
     user  system elapsed 
     7.56    0.60    8.17
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    libs  14.6Mb
Running 'testthat.R' [152s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unmarked)
  > test_check("unmarked")
  [ FAIL 0 | WARN 0 | SKIP 34 | PASS 106 ]
  
  ══ Skipped tests (34) ══════════════════════════════════════════════════════════
  • On CRAN (34): 'test_colext.R:2:1', 'test_crossVal.R:2:1',
    'test_distsamp.R:2:1', 'test_distsampOpen.R:2:1', 'test_fitList.R:3:1',
    'test_gdistremoval.R:2:1', 'test_gdistsamp.R:2:1', 'test_gmultmix.R:2:1',
    'test_goccu.R:2:1', 'test_gpcount.R:2:1', 'test_linearComb.R:3:1',
    'test_modSel.R:3:1', 'test_multinomPois.R:2:1', 'test_multmixOpen.R:2:1',
    'test_nmixTTD.R:2:1', 'test_nonparboot.R:2:1', 'test_occu.R:3:1',
    'test_occuCOP.R:2:1', 'test_occuFP.R:2:1', 'test_occuMS.R:2:1',
    'test_occuMulti.R:2:1', 'test_occuPEN.R:2:1', 'test_occuRN.R:2:1',
    'test_occuTTD.R:2:1', 'test_parboot.R:2:1', 'test_pcount.R:2:1',
    'test_pcount.spHDS.R:2:1', 'test_pcountOpen.R:2:1', 'test_plotEffects.R:3:1',
    'test_powerAnalysis.R:2:1', 'test_predict.R:3:1', 'test_ranef_predict.R:2:1',
    'test_simulate.R:2:1', 'test_vif.R:2:1'
  
  [ FAIL 0 | WARN 0 | SKIP 34 | PASS 106 ]
  > 
  > proc.time()
     user  system elapsed 
     2.53    0.35    2.87
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(unpivotr)
  > 
  > test_check("unpivotr")
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
  
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
  > 
  > proc.time()
     user  system elapsed 
     8.06    0.62    8.70
Running 'spelling.R' [0s]
  Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(updater)
  > 
  > test_check("updater")
  x Could not determine the last R version installed.
  x Could not determine the last R version installed.
  x Couldn't locate previous R version's package library.
  [1] "a"
  [1] "b"
  [1] "c"
  [1] "d"
  [1] "e"
  [1] "f"
  [1] "g"
  [1] "h"
  [1] "i"
  [1] "j"
  [1] "k"
  [1] "l"
  [1] "m"
  [1] "n"
  [1] "o"
  [1] "p"
  [1] "q"
  [1] "r"
  [1] "s"
  [1] "t"
  [1] "u"
  [1] "v"
  [1] "w"
  [1] "x"
  [1] "y"
  [1] "z"
  > CRAN: R6, Rcpp, askpass, brio, callr, cli, commonmark, covr, crayon, curl, desc, diffobj, digest, evaluate, fansi, fs, glue, highr, ..., spatial, and survival
  > Unknown: MASS and translations
  i Packages in repositories CRAN and Unknown will be installed from CRAN (<@CRAN@>)
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
     0.87    0.25    1.06
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(upstartr)
  > 
  > test_check("upstartr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ]
  > 
  > proc.time()
     user  system elapsed 
     2.25    0.45    2.70
Running 'testthat.R' [152s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(urlshorteneR)
  In order to use bitly functions, you first need to authenticate.
                          For that execute 'bitly_auth()' in R console.
  > # bitly_token <- bitly_auth(key = "be03aead58f23bc1aee6e1d7b7a1d99d62f0ede8", secret = "f9c6a3b18968e991e35f466e90c7d883cc176073")
  > # saveRDS(bitly_token, file = "tests/bitly_local_token.rds")
  > #
  > # if (interactive()) {
  > #   setwd("~/Documents/R-package-urlshortener")
  > #   bitly_token <- readRDS("tests/bitly_local_token.rds")
  > # } else {
  > #   setwd("~/main/")
  > #   bitly_token <- readRDS("tests/bitly_local_token.rds")
  > # }
  > #
  > # test_check("urlshorteneR")
  > 
  > proc.time()
     user  system elapsed 
     0.67    0.17    0.81
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usa)
  
  Attaching package: 'usa'
  
  The following objects are masked from 'package:datasets':
  
      state.abb, state.area, state.center, state.division, state.name,
      state.region
  
  > 
  > test_check("usa")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
  > 
  > proc.time()
     user  system elapsed 
     0.90    0.18    1.07
Package suggested but not available for checking: 'USA.state.boundaries.data'
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usdata)
  > 
  > test_check("usdata")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     1.03    0.23    1.25
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usedist)
  > 
  > test_check("usedist")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 30 ]
  > 
  > proc.time()
     user  system elapsed 
     1.23    0.21    1.40
Running 'spelling.R' [168s]
  Running 'testthat.R' [9s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.04    0.21
Running 'spelling.R' [167s]
  Running 'testthat.R' [172s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.06    0.20 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usemodels)
  > 
  > 
  > if (identical(Sys.getenv("NOT_CRAN"), "true")) { # emulates `testthat:::on_cran()`
  +   if (utils::packageVersion("testthat") >= "2.99.0.9000") {
  +     test_check("usemodels")
  +   }
  + }
  > 
  > 
  > proc.time()
     user  system elapsed 
     2.96    0.46    3.37
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usincometaxes)
  > 
  > test_check("usincometaxes")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.31    1.48
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(usmapdata)
  > 
  > test_check("usmapdata")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 37 ]
  > 
  > proc.time()
     user  system elapsed 
     2.10    0.34    2.46
Running 'spelling.R' [165s]
  Running 'testthat.R' [9s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE))
  +   spelling::spell_check_test(
  +     vignettes = TRUE,
  +     error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.07    0.21
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(utilsIPEA)
  > 
  > test_check("utilsIPEA")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
     1.10    0.25    1.34
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.4/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  21.9Mb
Running 'engine.R' [164s]
  Running 'testthat.R' [157s]
Running the tests in 'tests/engine.R' failed.
Complete output:
  > library(V8)
  Using V8 engine 11.8.172.13
  > 
  > proc.time()
     user  system elapsed 
     0.32    0.09    0.40 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(V8)
  Using V8 engine 11.8.172.13
  > 
  > test_check("V8")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 69 ]
  > 
  > proc.time()
     user  system elapsed 
     1.20    0.21    1.40
Running 'testthat.R' [278s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vaccine)
  vaccine (version 1.2.1).
  Type ?vaccine to get started.
  > 
  > test_check("vaccine")
  Loading required package: nnls
  Loading required package: gam
  Loading required package: splines
  Loading required package: foreach
  Loaded gam 1.22-3
  
  Super Learner
  Version: 2.0-29
  Package created on 2024-02-06
  
  Loading required namespace: ranger
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 140 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 140 ]
  > 
  > proc.time()
     user  system elapsed 
   110.67    6.71  116.51
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vacuum)
  > 
  > test_check("vacuum")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     0.82    0.10    0.92
Running 'testthat.R' [185s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(valaddin)
  > 
  > test_check("valaddin")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4149 ]
  > 
  > proc.time()
     user  system elapsed 
    22.59    1.82   24.45
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat);
  > library(valection);
  
  
  ##########################
  #### valection v1.0.0 ####
  ##########################
  
  checking C library availability...FAIL
  > 
  > test_check("valection");
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.57    0.15    0.67
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Running 'testthat.R' [161s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(validateIt)
  > if (!requireNamespace("here", quietly = TRUE)) {
  +   install.packages("here")
  + }
  > 
  > library(here)
  here() starts at D:/RCompile
  > test_check("validateIt")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
  > 
  > proc.time()
     user  system elapsed 
     1.59    0.37    1.95
Running 'testthat.R' [190s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(vdiffr)
  > library(valr)
  > 
  > test_check("valr")
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 460 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_glyph.r:8:3', 'test_glyph.r:28:3'
  • On Windows (1): 'test_read_bed.r:48:3'
  • run db tests manually. (2): 'test-db.r:6:3', 'test-db.r:21:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 460 ]
  > 
  > proc.time()
     user  system elapsed 
    28.12    4.10   30.64
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/vapour.Rcheck/00install.out' for details.
Running 'testthat.R' [234s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("varclust")
  Loading required package: varclust
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     1.59    0.21   60.50
Running 'doRUnit.R' [160s]
Running the tests in 'tests/doRUnit.R' failed.
Complete output:
  > #### doRUnit.R --- Run RUnit tests
  > ####------------------------------------------------------------------------
  > 
  > ### Originally follows Gregor Gojanc's example in CRAN package  'gdata'
  > ### and the corresponding section in the R Wiki:
  > ###  http://wiki.r-project.org/rwiki/doku.php?id=developers:runit
  > 
  > ### MM: Vastly changed:  This should also be "runnable" for *installed*
  > ##              package which has no ./tests/
  > ## ----> put the bulk of the code e.g. in  ../inst/unitTests/runTests.R :
  > 
  > ### DJS: Added the possibility of different testing levels
  > ### environment variable LEVEL set by make
  > ### default value of 1 is level used in check and install
  > 
  > if(require("RUnit", quietly=TRUE)) {
  + 
  +   ## --- Setup ---
  + 
  +   wd <- getwd()
  +   pkg <- sub("\\.Rcheck$", '', basename(dirname(wd)))
  +   level <- Sys.getenv("LEVEL")
  + 
  +   library(package=pkg, character.only=TRUE)
  + 
  +   path <- system.file("unitTests", package = pkg)
  + 
  +   stopifnot(file.exists(path), file.info(path.expand(path))$isdir)
  + 
  +   source(file.path(path, "runTests.R"), echo = TRUE)
  + }
  
  > if (require("RUnit", quietly = TRUE)) {
  +     if (Sys.getenv("RCMDCHECK") == "FALSE") {
  +         level <- Sys.getenv("LEVEL")
  +         pkg <- Sys. .... [TRUNCATED] 
  [1] "D:/RCompile/CRANpkg/lib/4.4/VarianceGamma/unitTests/report"
  RUNIT TEST PROTOCOL -- Sat Mar 23 10:30:28 2024 
  *********************************************** 
  Number of test functions: 0 
  Number of errors: 0 
  Number of failures: 0 
  
   
  1 Test Suite : 
  VarianceGamma unit testing - 0 test functions, 0 errors, 0 failures
  > 
  > proc.time()
     user  system elapsed 
     0.26    0.10    0.36
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VarRedOpt)
  > 
  > test_check("VarRedOpt")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     0.57    0.10    0.68
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vasicekreg)
  > 
  > test_check("vasicekreg")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.62    0.28    1.84
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > test_check("vatcheckapi")
  Loading required package: vatcheckapi
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-status.R:3:3', 'test-vat.R:3:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     0.75    0.15    0.89
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vaxpmx)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(MASS)
  
  Attaching package: 'MASS'
  
  The following object is masked from 'package:dplyr':
  
      select
  
  > 
  > # test_dir("tests/testthat")
  > test_check("vaxpmx")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     2.85    0.17    2.96
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VC2copula)
  Loading required package: copula
  > 
  > test_check("VC2copula")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 563 ]
  > 
  > proc.time()
     user  system elapsed 
     5.90    0.57    6.54
Running 'test_check.R' [160s]
Running the tests in 'tests/test_check.R' failed.
Complete output:
  > library(testthat)
  > library(vcmeta)
  > 
  > test_check("vcmeta")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 300 ]
  > 
  > proc.time()
     user  system elapsed 
     3.14    0.96    4.10
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(veccompare)
  > 
  > test_check("veccompare")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
  > 
  > proc.time()
     user  system elapsed 
     0.90    0.39    1.23
Running 'spelling.R' [158s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.10    0.14    0.20
Documented arguments not in \usage in Rd file 'vein-deprecated.Rd':
  'object'

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.
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vembedr)
  > 
  > test_check("vembedr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 67 ]
  > 
  > proc.time()
     user  system elapsed 
     1.25    0.20    1.39
Running 'spelling.R' [166s]
  Running 'testthat.R' [193s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.07    0.25 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(vermeulen)
  > 
  > test_check("vermeulen")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
    26.37    1.95   29.64
Running 'spelling.R' [166s]
  Running 'testthat.R' [167s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.07    0.21 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(versionsort)
  > 
  > test_check("versionsort")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
     0.81    0.31    1.09
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.06    0.18
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   3.2Mb
Argument items with no description in Rd file 'learnPartitionWithLLR.Rd':
  'type' 'procedure' 'ql' 'qq' 'BinaryLearningProcedure'
Argument items with no description in Rd file 'plotClassifRule.Rd':
  'object'
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(viafr)
  > 
  > test_check("viafr")
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 0 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test_get.R:3:1', 'test_search.R:3:1', 'test_suggest.R:3:1',
    'test_utils.R:3:1'
  
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.12    0.21    1.28
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vici)
  > 
  > test_check("vici")
  function (input, output, session)  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-serv.R:10:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     1.75    0.32    2.07
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VicmapR)
  
  Attaching package: 'VicmapR'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("VicmapR")
  Reading layer `melbourne' from data source 
    `D:\RCompile\CRANpkg\lib\4.4\VicmapR\shapes\melbourne.geojson' 
    using driver `GeoJSON'
  Simple feature collection with 1 feature and 8 fields
  Geometry type: MULTIPOLYGON
  Dimension:     XY
  Bounding box:  xmin: 144.897 ymin: -37.85066 xmax: 144.9913 ymax: -37.77545
  Geodetic CRS:  WGS 84
  [ FAIL 0 | WARN 0 | SKIP 18 | PASS 34 ]
  
  ══ Skipped tests (18) ══════════════════════════════════════════════════════════
  • On CRAN (18): 'test-build-query.R:16:3', 'test-build-query.R:42:3',
    'test-build-query.R:50:3', 'test-build-query.R:62:3',
    'test-build-query.R:82:3', 'test-check_geoserver.R:16:3',
    'test-citation.R:16:3', 'test-citation.R:34:3', 'test-citation.R:44:3',
    'test-convert-layer-names.R:17:3', 'test-convert-layer-names.R:37:3',
    'test-convert-layer-names.R:55:3', 'test-cql-predicates.R:92:3',
    'test-filter.R:16:3', 'test-filter.R:26:3', 'test-filter.R:35:3',
    'test-listLayers.R:16:3', 'test-utils-metadata.R:16:3'
  
  [ FAIL 0 | WARN 0 | SKIP 18 | PASS 34 ]
  > 
  > proc.time()
     user  system elapsed 
     6.53    0.54   10.75
Running 'test-all.R' [163s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("vietnameseConverter")
  Loading required package: vietnameseConverter
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
  > 
  > proc.time()
     user  system elapsed 
     2.00    0.34    2.26
Documented arguments not in \usage in Rd file 'draw_map_shiny.Rd':
  'rigth.lim'

Documented arguments not in \usage in Rd file 'map_summary.Rd':
  'rigth.lim'

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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.1Mb
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(vinereg)
  > 
  > if (require(testthat)) test_check("vinereg")
  Loading required package: testthat
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 62 ]
  > 
  > proc.time()
     user  system elapsed 
     9.56    0.25    9.67
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(viraldomain)
  > 
  > test_check("viraldomain")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-knn_domain_score.R:12:3', 'test-mars_domain_score.R:80:3',
    'test-nn_domain_score.R:80:3', 'test-normalized_domain_plot.R:18:3',
    'test-simple_domain_plot.R:18:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     4.92    0.84    5.71
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(viralmodels)
  > 
  > test_check("viralmodels")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-viralmodel.R:40:3', 'test-viraltab.R:39:3',
    'test-viralvis.R:39:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
    25.31    0.92   26.25
Running 'spelling.R' [158s]
  Running 'testthat.R' [258s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE,
  +     error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.07    0.25 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(virtuoso)
  > 
  > Sys.setenv(INTERACTIVE = FALSE) # Overrides detected interactive behavior
  > test_check("virtuoso")
  virtuoso isn't running.
  No active virtuoso process detected.
  [ FAIL 0 | WARN 0 | SKIP 9 | PASS 18 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-vos_configure.R:5:3', 'test-vos_install-errors.R:9:3',
    'test-vos_install-errors.R:18:3', 'test-vos_install-errors.R:30:3',
    'test-vos_install-errors.R:41:3', 'test-vos_odbc.R:4:3',
    'test-vos_query.R:16:3'
  • On Windows (1): 'test-vos_install.R:15:3'
  • has_virtuoso() is not TRUE (1): 'test-vos_install.R:5:3'
  
  [ FAIL 0 | WARN 0 | SKIP 9 | PASS 18 ]
  > 
  > proc.time()
     user  system elapsed 
     5.50  109.59  115.35
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(visa)
  > 
  > test_check("visa")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     2.20    0.43    2.62
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(viscomplexr)
  > 
  > test_check("viscomplexr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
  > 
  > proc.time()
     user  system elapsed 
     1.59    0.34    3.87
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VisitorCounts)
  > 
  > test_check("VisitorCounts")
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 7 ]
  
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 7 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     3.90    0.50    4.32
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(visOmopResults)
  > 
  > test_check("visOmopResults")
  Starting 2 test processes
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 324 ]
  > 
  > proc.time()
     user  system elapsed 
     1.92    0.45   19.17
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > # local_edition(3)
  > # devtools::test()
  > 
  > test_check("vistime")
  Loading required package: vistime
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 121 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     3.45    0.62    4.04
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vitae)
  
  Attaching package: 'vitae'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("vitae")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-template.R:3:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.40    2.37
Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(vivaldi)
  > 
  > test_check("vivaldi")
  >2 annotations: character(0)
  >2 annotations: character(0)
  >2 annotations: character(0)
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ]
  
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ]
  > 
  > proc.time()
     user  system elapsed 
     3.82    0.40    4.21
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VMDecomp)
  > 
  > test_check("VMDecomp")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     4.78    1.40    6.00
Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(VMDML)
  > 
  > test_check("VMDML")
  
  Call:
  svm(formula = yt ~ ., data = traindata, kernel = ker.funct, type = svm.type)
  
  
  Parameters:
     SVM-Type:  nu-regression 
   SVM-Kernel:  radial 
         cost:  1 
           nu:  0.5 
  
  Number of Support Vectors:  124
  
  
  Call:
  svm(formula = yt ~ ., data = traindata, kernel = ker.funct, type = svm.type)
  
  
  Parameters:
     SVM-Type:  nu-regression 
   SVM-Kernel:  radial 
         cost:  1 
           nu:  0.5 
  
  Number of Support Vectors:  123
  
  
  Call:
  svm(formula = yt ~ ., data = traindata, kernel = ker.funct, type = svm.type)
  
  
  Parameters:
     SVM-Type:  nu-regression 
   SVM-Kernel:  radial 
         cost:  1 
           nu:  0.5 
  
  Number of Support Vectors:  124
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.57    0.64    3.15
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > local_edition(3)
  > 
  > library(vmr)
  Package: vmr | Virtual Machines for R
  Author: Jean-François Rey <jf.rey.public@gmail.com>
  Version: 0.0.6
  License: GPLV3
  'vmr' package is under development
  Be comprehensible and feedback are welcome.
  Do not use virtual machine for production!
  Enjoy!
  Vagrant seems not to be installed.
  Please visit the page below and download and install vagrant: 
  https://www.vagrantup.com/downloads.html
  
  > 
  > test_check("vmr")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 2 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test_vagrantfile.R:23:3', 'test_vagrantfile.R:68:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 2 ]
  Deleting unused snapshots:
  • vagrantfile/Vagrantfile.default
  • vagrantfile/Vagrantfile.mount
  • vagrantfile/Vagrantfile.ssh
  • vagrantfile/Vagrantfile.virtualbox
  > 
  > proc.time()
     user  system elapsed 
     0.70    0.34    1.14
Running 'testthat.R' [182s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vntrs)
  > 
  > test_check("vntrs")
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-vntrs.R:13:3', 'test-vntrs.R:38:3', 'test-vntrs.R:58:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
    14.40    0.29   14.67
Running 'test_base.R' [252s]
Running the tests in 'tests/test_base.R' failed.
Complete output:
  > if (require("testthat")){
  +     test_check("voi")
  + }
  Loading required package: testthat
  Loading required package: voi
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 164 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test_evppi.R:42:5', 'test_evppi.R:59:5', 'test_evppi.R:69:3'
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 164 ]
  > 
  > proc.time()
     user  system elapsed 
    94.93    2.87   97.89
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/vol2birdR.Rcheck/00install.out' for details.
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(voronoiTreemap)
  > test_check("voronoiTreemap")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 3 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test_vt_d3.R:17:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     1.09    0.25    1.32
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
Running 'spelling.R' [155s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   spelling::spell_check_test(
  +     vignettes = TRUE, error = FALSE,
  +     skip_on_cran = TRUE
  +   )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.17    0.07    0.23
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vov)
  > 
  > test_check("vov")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 41 ]
  > 
  > proc.time()
     user  system elapsed 
     0.98    0.26    1.23
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
Running 'testthat.R' [152s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(vrnmf)
  > 
  > testthat::test_check("vrnmf")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
  > 
  > proc.time()
     user  system elapsed 
     1.57    0.28    1.84
Running 'spelling.R' [167s]
  Running 'testthat.R' [39s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.07    0.23
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(vstdct)
  > 
  > test_check("vstdct")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
  > 
  > proc.time()
     user  system elapsed 
     2.45    0.42    2.86
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(VulnToolkit)
  > 
  > test_check("VulnToolkit")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.32    1.76
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > testthat::test_check("vvshiny")
  Loading required package: vvshiny
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 61 ]
  
  [ FAIL 0 | WARN 2 | SKIP 0 | PASS 61 ]
  > 
  > proc.time()
     user  system elapsed 
     2.82    0.60    3.39
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(walkboutr)
  > 
  > test_check("walkboutr")
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  [ FAIL 0 | WARN 4 | SKIP 8 | PASS 31 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • empty test (8): 'test-process_accelerometry_counts_into_bouts.R:1:1',
    'test-process_accelerometry_counts_into_bouts.R:14:1',
    'test-process_accelerometry_counts_into_bouts.R:27:1',
    'test-process_accelerometry_counts_into_bouts.R:40:1',
    'test-process_bouts_and_gps_epochs_into_walkbouts.R:2:1',
    'test-process_bouts_and_gps_epochs_into_walkbouts.R:33:1',
    'test-process_bouts_and_gps_epochs_into_walkbouts.R:83:1',
    'test-process_gps_data_into_gps_epochs.R:145:1'
  
  [ FAIL 0 | WARN 4 | SKIP 8 | PASS 31 ]
  > 
  > proc.time()
     user  system elapsed 
     4.56    0.54    5.15
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running 'test_all.R' [181s]
Running the tests in 'tests/test_all.R' failed.
Complete output:
  > library("testthat")
  > test_check("walker")
  Loading required package: walker
  Loading required package: bayesplot
  This is bayesplot version 1.11.1
  - Online documentation and vignettes at mc-stan.org/bayesplot
  - bayesplot theme set to bayesplot::theme_default()
     * Does _not_ affect other ggplot2 plots
     * See ?bayesplot_theme_set for details on theme setting
  Loading required package: Rcpp
  Loading required package: rstan
  Loading required package: StanHeaders
  
  rstan version 2.32.6 (Stan version 2.32.2)
  
  For execution on a local, multicore CPU with excess RAM we recommend calling
  options(mc.cores = parallel::detectCores()).
  To avoid recompilation of unchanged Stan programs, we recommend calling
  rstan_options(auto_write = TRUE)
  For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
  change `threads_per_chain` option:
  rstan_options(threads_per_chain = 1)
  
  Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
  Note: Since walker version 1.0.0, the prior distribution for the
  standard deviation parameters is Gamma(shape, rate).
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 9 ]
  
  [ FAIL 0 | WARN 4 | SKIP 0 | PASS 9 ]
  > 
  > proc.time()
     user  system elapsed 
     8.28    0.67    8.93
Running 'helper-functions.R' [147s]
  Running 'testthat.R' [15s]
Running the tests in 'tests/helper-functions.R' failed.
Complete output:
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.04    0.21
Running 'tinytest.R' [174s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("wand")
  + }
  
  test_wand.R...................    0 tests    
  test_wand.R...................    0 tests    
  test_wand.R...................    0 tests    
  test_wand.R...................    0 tests    
  test_wand.R...................    0 tests    
  test_wand.R...................   52 tests [0;32mOK[0m [0;34m0.1s[0m
  All ok, 52 results (0.1s)
  > 
  > 
  > proc.time()
     user  system elapsed 
     0.31    0.10    0.40
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.3Mb
Running 'spelling.R' [147s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.15    0.07    0.21
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(washi)
  > 
  > test_check("washi")
  Couldn't find 'sans'. Defaulting to 'sans'.
  Couldn't find 'sans'. Defaulting to 'sans'.
  a flextable object.
  col_keys: `a`, `b` 
  header has 1 row(s) 
  body has 5 row(s) 
  original dataset sample: 
    a  b
  1 1  6
  2 2  7
  3 3  8
  4 4  9
  5 5 10
  NULL
  Couldn't find 'sans'. Defaulting to 'sans'.
  Couldn't find 'sans'. Defaulting to 'sans'.
  Couldn't find 'sans'. Defaulting to 'sans'.
  Couldn't find 'sans'. Defaulting to 'sans'.
  [ FAIL 0 | WARN 4 | SKIP 5 | PASS 15 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-flextable.R:9:3', 'test-fonts.R:3:3',
    'test-palettes.R:48:3', 'test-scales.R:42:3', 'test-theme.R:34:3'
  
  [ FAIL 0 | WARN 4 | SKIP 5 | PASS 15 ]
  > 
  > proc.time()
     user  system elapsed 
     3.07    0.73    3.79
Running 'spelling.R' [0s]
  Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(waspr)
  
  Attaching package: 'waspr'
  
  The following object is masked from 'package:base':
  
      summary
  
  > 
  > test_check("waspr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     0.85    0.15    1.00
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(waterquality)
  > library(terra)
  terra 1.7.71
  
  Attaching package: 'terra'
  
  The following objects are masked from 'package:testthat':
  
      compare, describe
  
  > 
  > test_check("waterquality")
  Am092Bsub calculated!
  Am092Bsub calculated!
  TurbChip09NIROverGreen calculated!
  Al10SABI calculated!
  Am092Bsub calculated!
  Al10SABI calculated!
  Am092Bsub calculated!
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
  > 
  > proc.time()
     user  system elapsed 
     8.37    0.62    8.95
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wdm)
  > 
  > test_check("wdm")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 77 ]
  > 
  > proc.time()
     user  system elapsed 
     10.6     0.5    11.1
Running 'testthat.R' [158s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wdnr.gis)
  Loading required package: arcpullr
  Loading required package: sf
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  > 
  > test_check("wdnr.gis")
  [ FAIL 0 | WARN 3 | SKIP 1 | PASS 33 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-get-functions.R:1:1'
  
  [ FAIL 0 | WARN 3 | SKIP 1 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
     2.03    0.53    2.50
Package suggested but not available for checking: 'prepr'
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # load packages
  > library(testthat)
  > library(wdpar)
  Loading required package: sf
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  > 
  > # enable parallel testing
  > Sys.unsetenv("R_TESTS")
  > 
  > # run tests
  > test_check("wdpar")
  [ FAIL 0 | WARN 0 | SKIP 30 | PASS 20 ]
  
  ══ Skipped tests (30) ══════════════════════════════════════════════════════════
  • On CRAN (30): 'test_000_setup.R:5:3', 'test_internal.R:75:3',
    'test_internal.R:99:3', 'test_st_erase_overlaps.R:33:3',
    'test_st_repair_geometry.R:4:3', 'test_st_repair_geometry.R:21:3',
    'test_st_repair_geometry.R:39:3', 'test_wdpa_clean.R:16:3',
    'test_wdpa_clean.R:41:3', 'test_wdpa_clean.R:63:3', 'test_wdpa_clean.R:85:3',
    'test_wdpa_clean.R:107:3', 'test_wdpa_clean.R:123:3',
    'test_wdpa_clean.R:141:3', 'test_wdpa_clean.R:153:3',
    'test_wdpa_clean.R:169:3', 'test_wdpa_clean.R:193:3',
    'test_wdpa_clean.R:216:3', 'test_wdpa_clean.R:232:3',
    'test_wdpa_clean.R:254:3', 'test_wdpa_clean.R:277:3',
    'test_wdpa_clean.R:298:3', 'test_wdpa_fetch.R:4:3', 'test_wdpa_fetch.R:15:3',
    'test_wdpa_fetch.R:26:3', 'test_wdpa_fetch.R:38:3', 'test_wdpa_fetch.R:55:3',
    'test_wdpa_read.R:4:3', 'test_wdpa_read.R:25:3', 'test_wdpa_read.R:50:3'
  
  [ FAIL 0 | WARN 0 | SKIP 30 | PASS 20 ]
  > 
  > proc.time()
     user  system elapsed 
     2.92    0.43    3.35
Running 'testthat.R' [152s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(webdriver)
  > 
  > if (Sys.getenv("NOT_CRAN", "") != "" || Sys.getenv("CI", "") != "") {
  +   if (! requireNamespace("servr", quietly = TRUE)) {
  +     message("Need the 'servr' package to run the tests")
  +   }
  +   if (is.null(webdriver:::find_phantom())) install_phantomjs()
  +   message("Using phantom.js from", webdriver:::find_phantom(), "\n")
  + 
  +   test_check("webdriver")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.48    0.17    0.65
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(webexercises)
  > 
  > test_check("webexercises")
  [ FAIL 0 | WARN 0 | SKIP 7 | PASS 54 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-add_to_bookdown.R:2:3', 'test-add_to_bookdown.R:38:3',
    'test-add_to_bookdown.R:87:3', 'test-add_to_bookdown.R:143:3',
    'test-compilation.R:2:3', 'test-create_quarto_doc.R:18:3'
  • requires pandoc and human inspection (1): 'test-create_quarto_doc.R:38:3'
  
  [ FAIL 0 | WARN 0 | SKIP 7 | PASS 54 ]
  > 
  > proc.time()
     user  system elapsed 
     1.23    0.21    1.43
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Documented arguments not in \usage in Rd file 'read_img.Rd':
  'imgfile'

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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(websocket)
  > 
  > test_check("websocket")
  [2024-03-23 23:42:49] [error] consume error: websocketpp.processor:4 (A message was too large)
  [2024-03-23 23:42:50] [error] Server handshake response error: websocketpp.processor:20 (Invalid HTTP status.)
  [2024-03-23 23:42:52] [error] Server handshake response error: websocketpp.processor:20 (Invalid HTTP status.)
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
  > 
  > proc.time()
     user  system elapsed 
     1.26    0.23    8.34
Argument items with no description in Rd file 'zdifference_ordinal.Rd':
  'na.rm'
Running 'testthat.R' [222s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > test_check("weyl")
  Loading required package: weyl
  Checking test 1 ...
  Test  1  passed
  Checking test 2 ...
  Test  2  passed
  Checking test 3 ...
  Test  3  passed
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 153 ]
  > 
  > proc.time()
     user  system elapsed 
    58.35    1.26   59.65
S3 methods shown with full name in Rd file 'QIC.gee.Rd':
  'QIC.gee'

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.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(whereport)
  > 
  > test_check("whereport")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
  > 
  > proc.time()
     user  system elapsed 
     0.90    0.31    1.18
Running 'testthat.R' [155s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(whitebox)
  > # whitebox:::wbt_rust_backtrace('1')
  > test_check("whitebox")
  [ FAIL 0 | WARN 0 | SKIP 41 | PASS 19 ]
  
  ══ Skipped tests (41) ══════════════════════════════════════════════════════════
  • On CRAN (41): 'test-toolchains.R:23:3', 'test-wbt.R:13:3', 'test-wbt.R:71:3',
    'test-wbt.R:120:3', 'test-wbt.R:149:3', 'test-wbt.R:196:3',
    'test-wbt_absolute_value.R:5:3', 'test-wbt_arc_cos.R:5:3',
    'test-wbt_arc_sin.R:5:3', 'test-wbt_arc_tan.R:5:3', 'test-wbt_arcosh.R:5:3',
    'test-wbt_arsinh.R:5:3', 'test-wbt_artanh.R:5:3', 'test-wbt_ceil.R:5:3',
    'test-wbt_cos.R:5:3', 'test-wbt_cosh.R:5:3',
    'test-wbt_cumulative_distribution.R:5:3', 'test-wbt_decrement.R:5:3',
    'test-wbt_exp.R:5:3', 'test-wbt_exp2.R:5:3', 'test-wbt_floor.R:5:3',
    'test-wbt_increment.R:5:3', 'test-wbt_is_no_data.R:5:3', 'test-wbt_ln.R:5:3',
    'test-wbt_log10.R:5:3', 'test-wbt_log2.R:5:3', 'test-wbt_negate.R:5:3',
    'test-wbt_quantiles.R:5:3', 'test-wbt_reciprocal.R:5:3',
    'test-wbt_round.R:5:3', 'test-wbt_sin.R:5:3', 'test-wbt_sinh.R:5:3',
    'test-wbt_square.R:5:3', 'test-wbt_square_root.R:5:3', 'test-wbt_tan.R:5:3',
    'test-wbt_tanh.R:5:3', 'test-wbt_to_degrees.R:5:3',
    'test-wbt_to_radians.R:5:3', 'test-wbt_truncate.R:5:3',
    'test-wbt_z_scores.R:5:3', 'test-whitebox-package.R:17:3'
  
  [ FAIL 0 | WARN 0 | SKIP 41 | PASS 19 ]
  > 
  > proc.time()
     user  system elapsed 
     1.93    0.34    2.26
Running 'testthat.R' [176s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(whitechapelR)
  > 
  > test_check("whitechapelR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
  > 
  > proc.time()
     user  system elapsed 
     1.35    0.29    1.64
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(whomds)
  Loading required package: psych
  
  Attaching package: 'psych'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  Thank you for using whomds. To learn more about the WHO Model Disability Survey (MDS) and for contact information, go to https://www.who.int/health-topics/disability
  > 
  > test_check("whomds")
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 4 ]
  
  [ FAIL 0 | WARN 1 | SKIP 0 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     5.45    0.67    6.14
Running 'testthat.R' [181s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(WH)
  > 
  > test_check("WH")
  Computing y as log(d / ec)
  Using d as weights
  Using d as weights
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Using outer iteration / Brent method
  Computing y as y = log(d / ec)
  Using d as weights
  Using d as weights
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  Using performance iteration / Nelder-Mead method
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 172 ]
  > 
  > proc.time()
     user  system elapsed 
    17.60    3.53   21.18
Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(WikidataR)
  > 
  > test_check("WikidataR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
  > 
  > proc.time()
     user  system elapsed 
     2.40    0.40    7.57
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(wikkitidy)
  > 
  > test_check("wikkitidy")
  [ FAIL 0 | WARN 0 | SKIP 27 | PASS 89 ]
  
  ══ Skipped tests (27) ══════════════════════════════════════════════════════════
  • On CRAN (27): 'test-get-diff.R:2:3', 'test-get-diff.R:10:3',
    'test-get-diff.R:21:3', 'test-get-history-count.R:8:3',
    'test-get-page-data.R:2:3', 'test-get-page-data.R:29:3',
    'test-get-query-results.R:2:3', 'test-get-query-results.R:11:3',
    'test-get-query-results.R:21:3', 'test-get-rest-resource.R:2:3',
    'test-get-rest-resource.R:9:3', 'test-get-rest-resource.R:17:3',
    'test-get-rest-resource.R:24:3', 'test-get-rest-resource.R:30:3',
    'test-prop-query-type.R:60:3', 'test-query-category-members.R:2:3',
    'test-query-category-members.R:15:3', 'test-rest-request.R:2:3',
    'test-rest-request.R:9:3', 'test-rest-request.R:16:3',
    'test-rest-request.R:26:3', 'test-rest-request.R:36:3', 'test-utils.R:8:3',
    'test-wiki-action-request.R:15:3', 'test-wiki-action-request.R:22:3',
    'test-xtools-page-api.R:2:3', 'test-xtools-page-api.R:18:3'
  
  [ FAIL 0 | WARN 0 | SKIP 27 | PASS 89 ]
  > 
  > proc.time()
     user  system elapsed 
     3.81    0.53    6.14
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wildcard)
  > 
  > test_check("wildcard")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
  > 
  > proc.time()
     user  system elapsed 
     1.03    0.15    1.18
Running 'testthat.R' [343s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wildmeta)
  > 
  > test_check("wildmeta")
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 449 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-parallelization.R:125:3', 'test-parallelization.R:188:3',
    'test-parallelization.R:277:3', 'test-rma-mv-methods.R:235:3',
    'test-rma-uni-methods.R:183:3'
  • empty test (1): 'test-parallelization.R:317:1'
  
  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 449 ]
  > 
  > proc.time()
     user  system elapsed 
   156.75    7.09  164.03
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wilson)
  
  Attaching package: 'wilson'
  
  The following object is masked from 'package:stats':
  
      heatmap
  
  > 
  > test_check("wilson")
  [ FAIL 0 | WARN 11 | SKIP 1 | PASS 77 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-download.R:16:3'
  
  [ FAIL 0 | WARN 11 | SKIP 1 | PASS 77 ]
  > 
  > proc.time()
     user  system elapsed 
    11.64    0.87   12.56
Running 'testthat.R' [185s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wk)
  > 
  > test_check("wk")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1669 ]
  > 
  > proc.time()
     user  system elapsed 
    19.45    2.67   22.17
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(WoodburyMatrix)
  > 
  > test_check("WoodburyMatrix")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-lintr.R:5:5'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
  > 
  > proc.time()
     user  system elapsed 
     2.98    0.42    3.39
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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.
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wordpiece.data)
  > 
  > test_check("wordpiece.data")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 4 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-loaders.R:26:3', 'test-loaders.R:40:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 4 ]
  > 
  > proc.time()
     user  system elapsed 
     0.85    0.17    1.01
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(WordR)
  > 
  > test_check("WordR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
     7.21    1.18    8.37
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wordsalad)
  > 
  > test_check("wordsalad")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
  > 
  > proc.time()
     user  system elapsed 
     5.65    1.14    6.76
Running 'testthat.R' [211s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(worldfootballR)
  > 
  > test_check("worldfootballR")
  [ FAIL 0 | WARN 0 | SKIP 56 | PASS 0 ]
  
  ══ Skipped tests (56) ══════════════════════════════════════════════════════════
  • On CRAN (56): 'test-fbref.R:22:3', 'test-fbref.R:29:3', 'test-fbref.R:38:3',
    'test-fbref.R:47:3', 'test-fbref.R:56:3', 'test-fbref.R:95:3',
    'test-fbref.R:111:3', 'test-fbref.R:131:3', 'test-fbref.R:144:3',
    'test-fbref.R:160:3', 'test-fbref.R:180:3', 'test-fbref.R:215:3',
    'test-fbref.R:228:3', 'test-fbref.R:239:3', 'test-fbref.R:265:3',
    'test-fbref.R:276:3', 'test-fbref.R:285:3', 'test-fbref.R:300:3',
    'test-fbref.R:316:3', 'test-fbref.R:324:3', 'test-fbref.R:335:3',
    'test-fotmob.R:5:3', 'test-fotmob.R:21:3', 'test-fotmob.R:123:3',
    'test-fotmob.R:185:3', 'test-fotmob.R:351:3', 'test-fotmob.R:366:3',
    'test-fotmob.R:381:3', 'test-fotmob.R:396:3', 'test-load.R:5:3',
    'test-load.R:23:3', 'test-load.R:42:3', 'test-load.R:61:3',
    'test-load.R:74:3', 'test-load.R:93:3', 'test-transfermarkt.R:4:3',
    'test-transfermarkt.R:17:3', 'test-transfermarkt.R:32:3',
    'test-transfermarkt.R:49:3', 'test-transfermarkt.R:56:3',
    'test-transfermarkt.R:64:3', 'test-transfermarkt.R:71:3',
    'test-transfermarkt.R:78:3', 'test-transfermarkt.R:90:3',
    'test-transfermarkt.R:111:3', 'test-transfermarkt.R:124:3',
    'test-transfermarkt.R:142:3', 'test-transfermarkt.R:159:3',
    'test-transfermarkt.R:178:3', 'test-transfermarkt.R:196:3',
    'test-understat.R:5:3', 'test-understat.R:12:3', 'test-understat.R:20:3',
    'test-understat.R:28:3', 'test-understat.R:35:3', 'test-understat.R:43:3'
  
  [ FAIL 0 | WARN 0 | SKIP 56 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     2.62    0.42   61.76
Documented arguments not in \usage in Rd file 'new_givens_path.Rd':
  'generate'

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.
Running 'testthat.R' [149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(woylier)
  > 
  > test_check("woylier")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
  > 
  > proc.time()
     user  system elapsed 
     0.56    0.15    0.67
Running 'testthat.R' [225s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(wpa)
  
   Thank you for using the {wpa} R package!
   
   Our analysts have taken every care to ensure that this package runs smoothly and bug-free.
   
   However, if you do happen to encounter any, please report any issues at
   https://github.com/microsoft/wpa/issues/
   
   Happy coding!
  > 
  > test_check("wpa")
  [ FAIL 0 | WARN 300 | SKIP 0 | PASS 12 ]
  
  [ FAIL 0 | WARN 300 | SKIP 0 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
    57.00    1.64   58.76
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Running 'testthat.R' [189s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wrappedtools)
  Package wrappedtools is still experimental, be warned that there might be dragons
  > 
  > test_check("wrappedtools")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
  > 
  > proc.time()
     user  system elapsed 
    18.70    0.92   19.64
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wrappr)
  > 
  > test_check("wrappr")
  [1] 1
  [1] ""
  [1] ""
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 41 ]
  > 
  > proc.time()
     user  system elapsed 
     0.89    0.29    1.17
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("wrassp")
  Loading required package: wrassp
  Loading required package: tibble
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 1336 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_libasspVSwrassp.R:11:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 1336 ]
  > 
  > proc.time()
     user  system elapsed 
    20.78    0.81   21.60
Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(WRI)
  > 
  > test_check("WRI")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
  > 
  > proc.time()
     user  system elapsed 
     2.15    0.35    2.50
Running 'spelling.R' [177s]
  Running 'testthat.R' [26s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.09    0.23
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wrswoR)
  > 
  > set.seed(20150812L)
  > 
  > test_check("wrswoR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 337 ]
  > 
  > proc.time()
     user  system elapsed 
     1.75    0.40    2.14
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wsjplot)
  > 
  > test_check("wsjplot")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     0.93    0.26    1.18
Documented arguments not in \usage in Rd file 'Cut.off.Rd':
  'main'

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.
Running 'testthat.R' [149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(httr)
  > library(jsonlite)
  > library(WufooR)
  > 
  > # test_check("WufooR")
  > 
  > proc.time()
     user  system elapsed 
     0.81    0.10    0.92
Running 'tinytest.R' [167s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if (requireNamespace("tinytest", quietly=TRUE) ) {
  +   if (requireNamespace('data.table', quietly = TRUE)) {
  +     # don't multi-thread during CRAN checks
  +     data.table::setDTthreads(1)
  +   }
  +   tinytest::test_package("WVPlots")
  + }
  Loading required package: wrapr
  
  test_All.R....................    0 tests    
  test_All.R....................    0 tests    
  test_All.R....................    0 tests    
  test_All.R....................    0 tests    TableGrob (3 x 2) "arrange": 5 grobs
    z     cells    name                grob
  1 1 (2-2,1-1) arrange      gtable[layout]
  2 2 (2-2,2-2) arrange      gtable[layout]
  3 3 (3-3,1-1) arrange      gtable[layout]
  4 4 (3-3,2-2) arrange      gtable[layout]
  5 5 (1-1,1-2) arrange text[GRID.text.224]
  
  test_All.R....................    1 tests [0;32mOK[0m [0;34m2.0s[0m
  All ok, 1 results (2.0s)
  > 
  > 
  > proc.time()
     user  system elapsed 
     3.78    0.40    4.12
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.5Mb
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xaringanExtra)
  > 
  > test_check("xaringanExtra")
  [ FAIL 0 | WARN 0 | SKIP 7 | PASS 154 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-banner.R:28:5', 'test-banner.R:43:5',
    'test-banner.R:77:5', 'test-freezeframe.R:35:5', 'test-scribble.R:35:5',
    'test-search.R:31:5', 'test-search.R:46:5'
  
  [ FAIL 0 | WARN 0 | SKIP 7 | PASS 154 ]
  > 
  > proc.time()
     user  system elapsed 
     2.04    0.64    6.51
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xegaGpGene)
  > 
  > test_check("xegaGpGene")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
     1.10    0.17    1.26
Running 'testthat.R' [186s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xega)
  Loading required package: parallelly
  > 
  > test_check("xega")
  .....................
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 44 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-xega.R:40:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 44 ]
  > 
  > 
  > proc.time()
     user  system elapsed 
    15.50    0.87   16.37
Running 'spelling.R' [168s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.06    0.23
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    java  25.4Mb
Running 'testthat.R' [144s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(xlcutter) # nolint
  > 
  > test_check("xlcutter")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 23 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-xlsx_cutter.R:16:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 23 ]
  > 
  > proc.time()
     user  system elapsed 
     1.26    0.28    1.53
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/xLLiM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/xml2.Rcheck/00install.out' for details.
Found the following significant warnings:
  DocParse.c:1334:5: warning: 'xmlKeepBlanksDefault' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.4/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.1Mb
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xmpdf)
  > 
  > test_check("xmpdf")
  [ FAIL 0 | WARN 0 | SKIP 16 | PASS 42 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-docinfo.R:187:5', 'test-messages.R:9:9',
    'test-messages.R:38:9'
  • On Windows (1): 'test-n_pages.R:26:5'
  • supports_exiftool() is not TRUE (3): 'test-docinfo.R:131:5',
    'test-n_pages.R:30:5', 'test-xmp.R:88:5'
  • supports_get_bookmarks() && supports_set_bookmarks() is not TRUE (1):
    'test-bookmarks.R:153:5'
  • supports_get_bookmarks() is not TRUE (3): 'test-bookmarks.R:13:5',
    'test-bookmarks.R:18:5', 'test-bookmarks.R:39:5'
  • supports_get_xmp() && supports_set_xmp() is not TRUE (1): 'test-xmp.R:5:5'
  • supports_pdftk() is not TRUE (4): 'test-bookmarks.R:95:5',
    'test-cat_pages.R:39:5', 'test-docinfo.R:21:5', 'test-n_pages.R:21:5'
  
  [ FAIL 0 | WARN 0 | SKIP 16 | PASS 42 ]
  > 
  > proc.time()
     user  system elapsed 
     2.79    2.04    6.92
Running 'testthat.R' [164s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xpectr)
  > 
  > test_check("xpectr")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 842 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • skipping due to breaking changes in R 4.0.0 (2):
    'test_gxs_selection.R:1382:5', 'test_gxs_selection.R:1810:5'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 842 ]
  > 
  > proc.time()
     user  system elapsed 
     5.20    0.35    5.59
Running 'testthat.R' [165s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xportr)
  > 
  > test_check("xportr")
  Variable type mismatches found.
  2 variables coerced
  
   Metadata successfully imported
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 241 ]
  > 
  > proc.time()
     user  system elapsed 
     8.43    0.87    9.31
Running 'testthat.R' [190s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 518 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-model-summary.R:59:3', 'test-read_nm_files.R:54:3',
    'test-read_nm_tables.R:61:3', 'test-read_nm_tables.R:71:3',
    'test-vpc.R:50:3', 'test-xpose_data.R:31:3', 'test-xpose_data.R:47:3',
    'test-xpose_save.R:22:3'
  
  [ FAIL 0 | WARN 0 | SKIP 8 | PASS 518 ]
  > 
  > proc.time()
     user  system elapsed 
    38.09    3.42   40.53
Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xrf)
  > 
  > test_check("xrf")
  [ FAIL 0 | WARN 13 | SKIP 0 | PASS 35 ]
  
  [ FAIL 0 | WARN 13 | SKIP 0 | PASS 35 ]
  > 
  > proc.time()
     user  system elapsed 
     8.03    0.46    8.48
Invalid package aliases in Rd file 'XRjulia-package.Rd':
  'XRjulia-package'
Argument items with no description in Rd file 'getCondition.Rd':
  'object'
Argument items with no description in Rd file 'screen.Rd':
  'fac' 'condition' 'position'
Running 'testthat.R' [153s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xxhashlite)
  > 
  > test_check("xxhashlite")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 41 ]
  > 
  > proc.time()
     user  system elapsed 
     0.81    0.21    0.98
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(yahoofinancer)
  > 
  > test_check("yahoofinancer")
  Loading required namespace: httptest
  Failed with error:  'unused argument (quietyly = TRUE)'
  Loading required namespace: httptest
  Failed with error:  'unused argument (quietyly = TRUE)'
  Loading required namespace: httptest
  Failed with error:  'unused argument (quietyly = TRUE)'
  Loading required namespace: httptest
  Failed with error:  'unused argument (quietyly = TRUE)'
  Loading required namespace: httptest
  Failed with error:  'unused argument (quietyly = TRUE)'
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-index.R:19:3', 'test-ticker.R:22:3',
    'test-trending.R:13:3', 'test-utils.R:2:3', 'test-utils.R:7:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     1.23    0.18    1.40
Running 'testthat.R' [193s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(yamlet)
  
  Attaching package: 'yamlet'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("yamlet")
  tibble [4 × 1] (S3: tbl_df/tbl/data.frame)
   $ RACE: 'dvec' chr [1:4] "WHITE" "WHITE" "WHITE" "WHITE"
    ..- attr(*, "label")= chr "Race"
   'dvec' int [1:4] 0 1 0 1
   - attr(*, "label")= chr "sex"
   - attr(*, "guide")=List of 2
    ..$ female: int 0
    ..$ male  : int 1
   'dvec' int [1:4] 0 1 0 1
   - attr(*, "label")= chr "sex"
   - attr(*, "guide")=List of 2
    ..$ female: int 0
    ..$ male  : int 1
   'dvec' num(0) 
  List of 2
   $ : 'dvec' num 1
   $ : 'dvec' num 1
  blq: [ LOQ Y/N, [ 'No': 0, 'Yes': 1 ]]
  letters: [ Letters, [ a, b, c, NA ]]
  letters: [ Letters, [ a, b, c, 'NA' ]]
  [ FAIL 0 | WARN 1 | SKIP 2 | PASS 511 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): 'test-yamlet.R:1340:1', 'test-yamlet.R:1345:1'
  
  [ FAIL 0 | WARN 1 | SKIP 2 | PASS 511 ]
  > 
  > proc.time()
     user  system elapsed 
    20.46    1.37   21.84
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(yarr)
  > 
  > test_check("yarr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
  Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 9 (D:\temp\RtmpyYWzsf\filebd2c5d9b13fa)
  2: In for (i in seq_len(n)) { :
    closing unused connection 8 (D:\temp\RtmpyYWzsf\filebd2c1553fdb)
  3: In for (i in seq_len(n)) { :
    closing unused connection 7 (D:\temp\RtmpyYWzsf\filebd2c16783508)
  4: In for (i in seq_len(n)) { :
    closing unused connection 6 (D:\temp\RtmpyYWzsf\filebd2c5503408c)
  5: In for (i in seq_len(n)) { :
    closing unused connection 5 (D:\temp\RtmpyYWzsf\filebd2c491d5711)
  6: In for (i in seq_len(n)) { :
    closing unused connection 4 (D:\temp\RtmpyYWzsf\filebd2c491d5711)
  > 
  > proc.time()
     user  system elapsed 
     0.79    0.32    1.10
Running 'spelling.R' [0s]
  Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(yatah)
  > 
  > test_check("yatah")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 113 ]
  > 
  > proc.time()
     user  system elapsed 
     2.12    0.40    2.50
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ycevo)
  > 
  > test_check("ycevo")
  [ FAIL 0 | WARN 28 | SKIP 0 | PASS 13 ]
  
  [ FAIL 0 | WARN 28 | SKIP 0 | PASS 13 ]
  > 
  > proc.time()
     user  system elapsed 
     5.54    0.62    6.17
Running 'spelling.R' [0s]
  Running 'testthat.R' [160s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(yfR)
  > 
  > test_check("yfR")
  v Using fallback SP500 composition from 2022-12-28
  v Using fallback IBOV composition from 2022-12-28
  v Using fallback FTSE composition from 2022-12-28
  v Using fallback DOW composition from 2022-12-28
  v Using fallback testthat-collection composition from 2022-12-28
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 24 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-yf_collection.R:20:5', 'test-yf_collection.R:55:5',
    'test-yf_convert_to_wide.R:7:5', 'test-yf_get.R:25:5', 'test-yf_get.R:135:5',
    'test-yf_get.R:173:5', 'test-yf_get.R:191:5', 'test-yf_get_dividends.R:18:5',
    'test-yf_live_prices.R:18:5'
  • Skipping since parallel is not supported due to YF api limits (1):
    'test-yf_get.R:98:3'
  • Skipping since parallel is not supported due to YF api limits, and
    collections are large datasets for single session download. (1):
    'test-yf_collection.R:75:3'
  
  [ FAIL 0 | WARN 0 | SKIP 11 | PASS 24 ]
  > 
  > proc.time()
     user  system elapsed 
     1.78    0.26    2.01
Running 'testthat.R' [170s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ymd)
  > 
  > test_check("ymd")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
  > 
  > proc.time()
     user  system elapsed 
     0.98    0.26    1.18
Running 'testthat.R' [154s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Ymisc)
  > 
  > test_check("Ymisc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
  > 
  > proc.time()
     user  system elapsed 
     0.68    0.17    0.84
Running 'spelling.R' [151s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('spelling', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.18    0.04    0.21
Running 'testthat.R' [144s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(yyjsonr)
  > 
  > # fromJSON <- fromJSON
  > # toJSON   <- toJSON
  > # validate <- jsonlite::validate
  > # prettify <- jsonlite::prettify
  > test_check("yyjsonr")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 214 ]
  > 
  > proc.time()
     user  system elapsed 
     1.90    0.50    2.43
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
Running 'testthat.R' [171s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zeallot)
  > 
  > test_check("zeallot")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 151 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • must wrap piped expressions in parentheses or use right operator (1):
    'test-pipe.R:4:3'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 151 ]
  > 
  > proc.time()
     user  system elapsed 
     1.56    0.23    1.78
Running 'testthat.R' [147s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zebu)
  > 
  > test_check("zebu")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 9 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_permtest.R:1:1'
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 9 ]
  > 
  > proc.time()
     user  system elapsed 
     2.04    0.29    2.32
Running 'testthat.R' [217s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zeitgebr)
  Loading required package: behavr
  Loading required package: data.table
  > 
  > test_check("zeitgebr")
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 7 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • empty test (4): 'test-chi_sq_periodogram.R:3:1',
    'test-cwt_periodogram.R:3:1', 'test-ls_periodogram.R:3:1',
    'test-periodogram.R:3:1'
  
  [ FAIL 0 | WARN 0 | SKIP 4 | PASS 7 ]
  > 
  > proc.time()
     user  system elapsed 
    62.64    6.90   68.98
Auto-generated content requiring editing in Rd file 'ZIBseq-package.Rd':
  \seealso: '~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...'
Running 'spelling.R' [152s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > 
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +     spelling::spell_check_test(
  +         vignettes = TRUE,
  +         error = TRUE,
  +         skip_on_cran = TRUE
  +     )
  + }
  NULL
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.04    0.20
Running 'testthat.R' [177s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zipangu)
  > 
  > test_check("zipangu")
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 145 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-jholiday.R:75:3', 'test-zipcode.R:90:3'
  
  [ FAIL 0 | WARN 0 | SKIP 2 | PASS 145 ]
  > 
  > proc.time()
     user  system elapsed 
    10.18    0.29   10.46
Running 'testthat.R' [174s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zipfextR)
  > 
  > test_check("zipfextR")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
  > 
  > proc.time()
     user  system elapsed 
     4.48    0.31    4.81
Running 'testthat.R' [169s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("zlog")
  > 
  > test_check("zlog")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 101 ]
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.17    1.65
Running 'testthat.R' [148s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zmisc)
  > 
  > test_check("zmisc")
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 141 ]
  > 
  > proc.time()
     user  system elapsed 
     1.42    0.26    1.68
Running 'testthat.R' [188s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(zoomerjoin)
  _R_CHECK_LIMIT_CORES_ is set to TRUE. Running on 2 cores
  > 
  > test_check("zoomerjoin")
  Loading required package: babynames
  Loading required package: stringdist
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  Joining by 'name'
  
  [ FAIL 0 | WARN 60 | SKIP 0 | PASS 183 ]
  
  [ FAIL 0 | WARN 60 | SKIP 0 | PASS 183 ]
  > 
  > proc.time()
     user  system elapsed 
    60.50    3.01   46.59
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ztpln)
  > 
  > test_check("ztpln")
  number of iterations= 10 
  number of iterations= 9 
  One of the variances is going to zero;  trying new starting values.
  WARNING! NOT CONVERGENT! 
  number of iterations= 1000 
  number of iterations= 39 
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
  > 
  > proc.time()
     user  system elapsed 
     7.46    0.50    7.95
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
Running examples in ‘Andromeda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: groupApply
> ### Title: Apply a function to groups of data in an Andromeda table
> ### Aliases: groupApply
> 
> ### ** Examples
> 
> andr <- andromeda(cars = cars)
> 
> fun <- function(x) {
+   return(tibble::tibble(speed = x$speed[1], meanDist = mean(x$dist)))
+ }
> 
> result <- groupApply(andr$cars, "speed", fun)
Error in `rlang::sym()`:
! No known SQL translation
Backtrace:
     ▆
  1. ├─Andromeda::groupApply(andr$cars, "speed", fun)
  2. │ └─Andromeda::batchApply(...)
  3. │   └─dbplyr::sql_render(tbl, connection)
  4. │     ├─dbplyr::sql_render(...)
  5. │     └─dbplyr:::sql_render.tbl_lazy(...)
  6. │       ├─dbplyr::sql_render(...)
  7. │       └─dbplyr:::sql_render.lazy_query(...)
  8. │         ├─dbplyr::sql_build(query, con = con, sql_options = sql_options)
  9. │         └─dbplyr:::sql_build.lazy_select_query(query, con = con, sql_options = sql_options)
 10. │           ├─dbplyr::select_query(...)
 11. │           │ └─dbplyr:::check_character(order_by)
 12. │           │   └─rlang::is_character(x)
 13. │           └─dbplyr::translate_sql_(op$order_by, con = con)
 14. │             └─base::lapply(...)
 15. │               └─dbplyr (local) FUN(X[[i]], ...)
 16. │                 ├─dbplyr::escape(eval_tidy(x, mask), con = con)
 17. │                 └─rlang::eval_tidy(x, mask)
 18. └─rlang::sym
 19.   └─cli::cli_abort(...)
 20.     └─rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingAndromeda.Rmd’ using rmarkdown

Quitting from lines 175-184 [unnamed-chunk-17] (UsingAndromeda.Rmd)
Error: processing vignette 'UsingAndromeda.Rmd' failed with diagnostics:
No known SQL translation
--- failed re-building ‘UsingAndromeda.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘thurstonianIRT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/baggr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bakR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/baldur.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayes4psy.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesbr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BayesGmed.Rcheck/00install.out’ for details.
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
S3 methods shown with full name in documentation object 'export.bce':
  ‘export.bce’

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.
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'select.cfs':
  ‘select.cfs’

S3 methods shown with full name in documentation object 'select.fast.filter':
  ‘select.fast.filter’

S3 methods shown with full name in documentation object 'select.forward.Corr':
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object 'select.forward.wrapper':
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object 'select.inf.chi2':
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object 'select.inf.gain':
  ‘select.inf.gain’

S3 methods shown with full name in documentation object 'select.inf.symm':
  ‘select.inf.symm’

S3 methods shown with full name in documentation object 'select.process':
  ‘select.process’

S3 methods shown with full name in documentation object 'select.relief':
  ‘select.relief’

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.
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(chronicler)
  > 
  > test_check("chronicler")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 15 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-test_chronicler.R:72:3'): first and only error message is ok ──
  grepl("Can't subset columns that don't exist", result_pipe$log_df$message) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-test_chronicler.R:89:3'): if multiple error messages, next ones are 'pipe failed' ──
  grepl("Can't subset columns that don't exist", result_pipe$log_df$message[1]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 15 ]
  Error: Test failures
  Execution halted
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Package required but not available: ‘ctsem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [6s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(cryptotrackr)
  > 
  > test_check("cryptotrackr")
  No encoding supplied: defaulting to UTF-8.
  [1] " {\"jsonrpc\":\"2.0\",\"error\":{\"code\":429,\"message\":\"Too many requests for a specific RPC call, contact your app developer or support@rpcpool.com.\"}, \"id\": null } \r\n"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-solana.R:4:3'): the "solana_get_signature_for_address" function returns a list ──
  Error in `solana_api_call(url, request_body)`: Request failed with status code: 429
  Backtrace:
      ▆
   1. └─cryptotrackr::solana_get_signature_for_address(url, address) at test-solana.R:4:3
   2.   └─cryptotrackr::solana_api_call(url, request_body)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘datagovsgR-vignette.Rmd’ using rmarkdown

Quitting from lines 32-33 [unnamed-chunk-2] (datagovsgR-vignette.Rmd)
Error: processing vignette 'datagovsgR-vignette.Rmd' failed with diagnostics:
Server Error has occured.
--- failed re-building ‘datagovsgR-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘datagovsgR-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DCPO.Rcheck/00install.out’ for details.
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'add.joint.mean.many':
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

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.
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EcoEnsemble.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/eggCounts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
checkRd: (5) ePCR.Rd:0-17: Must have a \description
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EpiNow2.Rcheck/00install.out’ for details.
S3 methods shown with full name in documentation object 'addDrug.Lexis':
  ‘addDrug.Lexis’

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.
Found the following significant warnings:
  Rd warning: no hsearch.rds meta data for package ergm
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ergm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
S3 methods shown with full name in documentation object 'summary.error_interval':
  ‘summary.error_interval’

S3 methods shown with full name in documentation object 'summary.measure':
  ‘summary.measure’

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.
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
Running ‘testthat.R’ [3s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(fishRman)
  > 
  > test_check("fishRman")
  The resource you requested cannot be served. Error message:
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fish.R:16:3'): the right dataframe is returned from the API ────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Failed to connect to fishrman.ddnsfree.com port 443 after 3228 ms: Couldn't connect to server
  Backtrace:
      ▆
   1. └─fishRman::fish(bait) at test-fish.R:16:3
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       ├─base (local) tryCatchOne(...)
   5.       │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   6.       └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
   7.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FlexReg.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Running examples in ‘ggprism-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotation_ticks
> ### Title: Add ticks as ggplot annotation
> ### Aliases: annotation_ticks
> 
> ### ** Examples
> 
> ## Generally it is better to use the guide_prism_minor function.
> ## However annotation_ticks is useful in a few specific situations.
> library(ggplot2)
> 
> ## easily put ticks without labels around a plot with a border
> ggplot(mtcars, aes(x = mpg, y = disp)) +
+   geom_point() +
+   theme_prism(border = TRUE) +
+   coord_cartesian(clip = "off") +
+   annotation_ticks(sides = "tr", type = "major", outside = TRUE) +
+   theme(plot.margin = unit(c(4, 4, 4, 4), "mm"))
Error in `plot_theme()`:
! The `legend.text.align` theme element is not defined in the element
  hierarchy.
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. └─ggplot2:::print.ggplot(x)
  3.   ├─ggplot2::ggplot_gtable(data)
  4.   └─ggplot2:::ggplot_gtable.ggplot_built(data)
  5.     └─ggplot2:::plot_theme(plot)
  6.       └─ggplot2:::validate_theme(theme)
  7.         └─base::mapply(...)
  8.           └─ggplot2 (local) `<fn>`(...)
  9.             └─cli::cli_abort(...)
 10.               └─rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘axes.Rmd’ using rmarkdown

Quitting from lines 38-48 [unnamed-chunk-2] (axes.Rmd)
Error: processing vignette 'axes.Rmd' failed with diagnostics:
<Guide> classes have been rewritten as <ggproto> classes.
The old S3 guide methods have been superseded.
--- failed re-building ‘axes.Rmd’

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

Quitting from lines 44-51 [unnamed-chunk-2] (colours.Rmd)
Error: processing vignette 'colours.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building ‘colours.Rmd’

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

Quitting from lines 45-59 [unnamed-chunk-2] (ggprism.Rmd)
Error: processing vignette 'ggprism.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building ‘ggprism.Rmd’

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

Quitting from lines 66-74 [unnamed-chunk-3] (pvalues.Rmd)
Error: processing vignette 'pvalues.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building ‘pvalues.Rmd’

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

Quitting from lines 53-63 [unnamed-chunk-3] (themes.Rmd)
Error: processing vignette 'themes.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building ‘themes.Rmd’

SUMMARY: processing the following files failed:
  ‘axes.Rmd’ ‘colours.Rmd’ ‘ggprism.Rmd’ ‘pvalues.Rmd’ ‘themes.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘metaBMA’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glancedata)
  > 
  > test_check("glancedata")
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_numerical_vars.R:7:3'): histogram mode is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:14:3'): density is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:22:3'): boxplot is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:30:3'): violin is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:37:3'): qqplot is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/glmmrBase.Rcheck/00install.out’ for details.
Package required but not available: ‘glmmrBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Dependence on R version ‘4.1.2’ not with patchlevel 0
S3 methods shown with full name in documentation object 'bw.abram.temp':
  ‘bw.abram.temp’

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.
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lgpr.Rcheck/00install.out’ for details.
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
Found the following significant warnings:
  Warning: replacing previous import ‘ggmulti::coord_radial’ by ‘ggplot2::coord_radial’ when loading ‘loon.ggplot’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/loon.ggplot.Rcheck/00install.out’ for details.
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/metaBMA.Rcheck/00install.out’ for details.
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mrbayes.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/multinma.Rcheck/00install.out’ for details.
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/networkscaleup.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OncoBayes2.Rcheck/00install.out’ for details.
S3 methods shown with full name in documentation object 'pamr-internal':
  ‘print.nsc’ ‘print.nsccv’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/pcFactorStan.Rcheck/00install.out’ for details.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
  ...
--- re-building ‘PhyloTree_vignette_1.Rmd’ using rmarkdown
--- finished re-building ‘PhyloTree_vignette_1.Rmd’

--- re-building ‘PhyloTree_vignette_2.Rmd’ using rmarkdown

Quitting from lines 149-159 [unnamed-chunk-10] (PhyloTree_vignette_2.Rmd)
Error: processing vignette 'PhyloTree_vignette_2.Rmd' failed with diagnostics:
DNA sequences in list not of the same length.
--- failed re-building ‘PhyloTree_vignette_2.Rmd’

SUMMARY: processing the following file failed:
  ‘PhyloTree_vignette_2.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
  ...
--- re-building ‘prWarp-homo-example.Rmd’ using rmarkdown

Quitting from lines 70-76 [plot non aff] (prWarp-homo-example.Rmd)
Error: processing vignette 'prWarp-homo-example.Rmd' failed with diagnostics:
unused argument (plot.param = list(pt.cex = 0.3, mean.cex = 0.8, mean.col = "red"))
--- failed re-building ‘prWarp-homo-example.Rmd’

--- re-building ‘prWarp-papionin-example.Rmd’ using rmarkdown

Quitting from lines 80-87 [plot total shape] (prWarp-papionin-example.Rmd)
Error: processing vignette 'prWarp-papionin-example.Rmd' failed with diagnostics:
unused argument (plot.param = list(pt.cex = 0.5))
--- failed re-building ‘prWarp-papionin-example.Rmd’

SUMMARY: processing the following files failed:
  ‘prWarp-homo-example.Rmd’ ‘prWarp-papionin-example.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rcbayes.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(receptiviti)
  > 
  > test_check("receptiviti")
  Status: ERROR
  Message: URL is unreachable
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 16 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • no API key (2): 'test-receptiviti.R:31:1', 'test-receptiviti_status.R:17:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-receptiviti_status.R:6:3'): failures works ───────────────────
  ...[] (`actual`) not identical to "Message: 404" (`expected`).
  
  `actual`:   "Message: 500"
  `expected`: "Message: 404"
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 16 ]
  Error: Test failures
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rPBK.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘glmmrBase’

Package suggested but not available for checking: ‘cmdstanr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
S3 methods shown with full name in documentation object 'matmult':
  ‘%*%.rv’

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.
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
‘sandwich-CL.Rnw’... [14s/16s] NOTE
differences from ‘sandwich-CL.Rout.save’
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  ‘sandwich-OOP.Rnw’... [3s/3s] OK
  ‘sandwich.Rnw’... [1s/2s] OK
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
Running examples in ‘SCDB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_schema
> ### Title: Get the current schema of a database-related objects
> ### Aliases: get_schema
> 
> ### ** Examples
> 
> conn <- get_connection(drv = RSQLite::SQLite())
> 
> dplyr::copy_to(conn, mtcars, name = "mtcars")
> 
> get_schema(conn)
[1] "temp"
> get_schema(get_table(conn, id("mtcars", conn = conn)))
Error in unclass(dbplyr::remote_table(.x))$schema : 
  $ operator is invalid for atomic vectors
Calls: get_schema -> get_schema.tbl_dbi
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-principles.Rmd’ using rmarkdown

Quitting from lines 76-82 [example_1] (basic-principles.Rmd)
Error: processing vignette 'basic-principles.Rmd' failed with diagnostics:
error in evaluating the argument 'name' in selecting a method for function 'dbRemoveTable': invalid 'envir' argument of type 'character'
--- failed re-building ‘basic-principles.Rmd’

Error in `purrr::map_chr()`:
ℹ In index: 2.
Caused by error:
! invalid 'envir' argument of type 'character'
Backtrace:
     ▆
  1. ├─`<fn>`(`<Logger>`)
  2. │ └─.subset2(e, "finalize")()
  3. │   ├─dbplyr::build_sql(...)
  4. │   │ └─purrr::map_chr(enexprs(...), escape_expr, con = con)
  5. │   │   └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
  6. │   │     ├─purrr:::with_indexed_errors(...)
  7. │   │     │ └─base::withCallingHandlers(...)
  8. │   │     ├─purrr:::call_with_cleanup(...)
  9. │   │     └─dbplyr (local) .f(.x[[i]], ...)
 10. │   │       └─rlang::eval_bare(x, .env)
 11. │   ├─dbplyr::as.sql(id(self$log_tbl, conn = private$log_conn), con = private$log_conn)
 12. │   ├─SCDB::id(self$log_tbl, conn = private$log_conn)
 13. │   └─SCDB:::id.tbl_dbi(self$log_tbl, conn = private$log_conn)
 14. │     ├─base::with(...)
 15. │     └─base::with.default(...)
 16. │       └─base::eval(substitute(expr), data, enclos = parent.frame())
 17. └─base::.handleSimpleError(...)
 18.   └─purrr (local) h(simpleError(msg, call))
 19.     └─cli::cli_abort(...)
 20.       └─rlang::abort(...)
--- re-building ‘slowly-changing-dimension.Rmd’ using rmarkdown
--- finished re-building ‘slowly-changing-dimension.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-principles.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ctsemOMX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:

  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
interpolate_aw 6.213  0.070   7.057
st_as_sf       5.582  0.214   7.392
S3 methods shown with full name in documentation object 'plot.predictions':
  ‘plot.predictions’

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.
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object 'size.penalize':
  ‘size.penalize’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/thurstonianIRT.Rcheck/00install.out’ for details.
Running examples in ‘uniswappeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: liquidity_range_all_v3
> ### Title: Forecast Price for liquidity range for a pair's tokens UniswapV3
> ### Aliases: liquidity_range_all_v3
> 
> ### ** Examples
> 
> liquidity_range_all_v3(pair_address = "0x1d42064fc4beb5f8aaf85f4617ae8b3b5b8bd801",
+                        days = 30, cap = 10, sims = 1000)
Warning: tz(): Don't know how to compute timezone for object of class NULL; returning "UTC".
Error in `[.data.frame`(data, , c("Date", "token0Price", "token1Price")) : 
  undefined columns selected
Calls: liquidity_range_all_v3 -> [ -> [.data.frame
Execution halted
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
Found the following significant warnings:

  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
vlda_plot 6.169  0.057   7.227
vlda      3.594  0.185   5.064
S3 methods shown with full name in documentation object 'QIC.gee':
  ‘QIC.gee’

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.
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Package required but not available: ‘prophet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/baggr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/baldur.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayes4psy.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesbr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesdfa.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(canadianmaps)
  > 
  > test_check("canadianmaps")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-functions.R:14:3'): check-functions: scale_fill_map() returns a ggplot manual fill object ──
  output$scale_name (`actual`) not equal to "manual" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('manual')
  ── Failure ('test-functions.R:23:3'): check-functions: scale_color_map() returns a ggplot manual fill object ──
  output$scale_name (`actual`) not equal to "manual" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('manual')
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cbq.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/conStruct.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(cryptotrackr)
  > 
  > test_check("cryptotrackr")
  No encoding supplied: defaulting to UTF-8.
  [1] " {\"jsonrpc\":\"2.0\",\"error\":{\"code\":429,\"message\":\"Too many requests for a specific RPC call, contact your app developer or support@rpcpool.com.\"}, \"id\": null } \r\n"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-solana.R:4:3'): the "solana_get_signature_for_address" function returns a list ──
  Error in `solana_api_call(url, request_body)`: Request failed with status code: 429
  Backtrace:
      ▆
   1. └─cryptotrackr::solana_get_signature_for_address(url, address) at test-solana.R:4:3
   2.   └─cryptotrackr::solana_api_call(url, request_body)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DCPO.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘tmbstan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dsfa.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EcoEnsemble.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/eggCounts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EpiNow2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/fdaPDE.Rcheck/00install.out’ for details.
Package required but not available: ‘modeltime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [4s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(fishRman)
  > 
  > test_check("fishRman")
  The resource you requested cannot be served. Error message:
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fish.R:16:3'): the right dataframe is returned from the API ────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Failed to connect to fishrman.ddnsfree.com port 443 after 3235 ms: Couldn't connect to server
  Backtrace:
      ▆
   1. └─fishRman::fish(bait) at test-fish.R:16:3
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       ├─base (local) tryCatchOne(...)
   5.       │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   6.       └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
   7.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FlexReg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gastempt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
Missing link or links in documentation object 'gisco_countrycode.Rd':
  ‘[countrycode:countrycode-package]{countrycode::countrycode-package}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glancedata)
  > 
  > test_check("glancedata")
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_numerical_vars.R:7:3'): histogram mode is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:14:3'): density is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:22:3'): boxplot is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:30:3'): violin is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:37:3'): qqplot is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/glmmrBase.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/greencrab.toolkit.Rcheck/00install.out’ for details.
Package required but not available: ‘modeltime’

Package suggested but not available for checking: ‘healthyR.ai’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'healthyR.ts', 'healthyR.ai'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/historicalborrowlong.Rcheck/00install.out’ for details.
Package required but not available: ‘tmbstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: replacing previous import ‘ggmulti::coord_radial’ by ‘ggplot2::coord_radial’ when loading ‘loon.ggplot’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/loon.ggplot.Rcheck/00install.out’ for details.
Packages required but not available: 'modeltime', 'modeltime.resample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/multilevelcoda.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/networkscaleup.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/pema.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/prophet.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rlgt.Rcheck/00install.out’ for details.
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createH5LigerDataset
> ### Title: Create on-disk ligerDataset Object
> ### Aliases: createH5LigerDataset
> 
> ### ** Examples
> 
> h5Path <- system.file("extdata/ctrl.h5", package = "rliger")
> ld <- createH5LigerDataset(h5Path)
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: ../../../src/H5F.c in H5Fopen(): line 412: unable to open file
        class: HDF5
        major: File accessibility
        minor: Unable to open file

    error #001: ../../../src/H5Fint.c in H5F_open(): line 1655: unable to open file: time = Sun Mar 24 15:48:34 2024
, name = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', tent_flags = 1
        class: HDF5
        major: File accessibility
        minor: Unable to open file

    error #002: ../../../src/H5FD.c in H5FD_open(): line 722: open failed
        class: HDF5
        major: Virtual File Layer
        minor: Unable to initialize object

    error #003: ../../../src/H5FDsec2.c in H5FD__sec2_open(): line 351: unable to open file: name = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', errno = 30, error message = 'Read-only file system', flags = 1, o_flag        class: HDF5
        major: File accessibility
        
Calls: createH5LigerDataset -> <Anonymous> -> initialize -> H5File.open
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rmBayes.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RoBTT.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘tmbstan’
‘sandwich-CL.Rnw’... [14s/17s] NOTE
differences from ‘sandwich-CL.Rout.save’
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  ‘sandwich-OOP.Rnw’... [3s/4s] OK
  ‘sandwich.Rnw’... [1s/2s] OK
Running ‘testthat.R’ [176s/252s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("testthat")
  > library("sentopics")
  > 
  > if (Sys.getenv("R_COVR") != "true") {
  +   test_check("sentopics")
  + } else {
  +   test_check("sentopics", reporter = default_reporter())
  +   # test_check("sentopics", reporter = LocationReporter)
  + }
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 326 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-parallel_chains.R:97:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-others.R:2:3'): get_ECB_conferences works ──────────────────────
  Error in ``[.data.table`(res, , c({
      tmp <- data.table::rbindlist(sections)
      tmp[, `:=`(paragraph_id, paste0(doc_id, "_", .I))]
      tmp
  }), by = c("date", "doc_id", "title"))`: j doesn't evaluate to the same number of columns for each group
  Backtrace:
      ▆
   1. └─sentopics:::get_ECB_press_conferences(years = 1998) at test-others.R:2:3
   2.   ├─...[]
   3.   └─data.table::`[.data.table`(...)
  
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 326 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:

  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
interpolate_aw 6.806  0.098   8.762
st_as_sf       5.862  0.256   7.694
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ssMousetrack.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/thurstonianIRT.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘modeltime’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tmbstan.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tsnet.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
vlda_plot 6.231  0.074    7.34
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
installed size is 88.8Mb
  sub-directories of 1Mb or more:
    libs  87.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      8.0Mb
Running ‘testthat.R’ [322s/324s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3. ├─base::suppressWarnings(...) at test-simulateabn.R:799:7
   4. │ └─base::withCallingHandlers(...)
   5. └─abn::buildScoreCache(...) at test-simulateabn.R:800:9
   6.   └─abn::buildScoreCache.bayes(...)
   7.     └─... %do% ...
   8.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
   9.         └─base::library(p, character.only = TRUE)
  
  [ FAIL 30 | WARN 0 | SKIP 35 | PASS 485 ]
  Deleting unused snapshots:
  • tographviz/graph.dot
  • tographviz/graph1.dot
  • tographviz/graph_group.dot
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘data_simulation.Rmd’ using rmarkdown
File fit_model-1.png not found in resource path
Error: processing vignette 'data_simulation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘data_simulation.Rmd’

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

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

--- re-building ‘multiprocessing.Rmd’ using rmarkdown
File benchmarkBoxPlot-1.png not found in resource path
Error: processing vignette 'multiprocessing.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘multiprocessing.Rmd’

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

--- re-building ‘parameter_learning.Rmd’ using rmarkdown
File unnamed-chunk-3-1.png not found in resource path
Error: processing vignette 'parameter_learning.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘parameter_learning.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘data_simulation.Rmd’ ‘multiprocessing.Rmd’ ‘parameter_learning.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.4Mb
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    include  13.4Mb
installed size is  7.8Mb
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    doc    1.7Mb
    libs   5.8Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DeconRNASeq', 'WGCNA'
installed size is  8.5Mb
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    libs   8.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.0Mb
    libs   2.6Mb
installed size is  5.8Mb
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    R       2.0Mb
    data    1.3Mb
    files   1.7Mb
installed size is  5.3Mb
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    R     2.0Mb
    doc   2.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
Packages suggested but not available for checking: 'HiTC', 'snpStats'
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  6.4Mb
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    libs   6.2Mb
installed size is  6.0Mb
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    libs   5.9Mb
installed size is  5.7Mb
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    libs   5.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.7Mb
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    extdata   3.4Mb
    libs      2.1Mb
installed size is  9.3Mb
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    libs   8.8Mb
installed size is  5.3Mb
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    libs   4.1Mb
installed size is 19.1Mb
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    libs  17.8Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   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(...)
  ── Error ('test-update.R:111:5'): render_docs also transform new/modified vignettes if specified: docsify ──
  Error in `render_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
installed size is  6.0Mb
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    doc    1.4Mb
    libs   3.9Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    31.4Mb
Bad \usage lines found in documentation object 'annmatrix':
  <unescaped bksl>method{@}{annmatrix}(object, name)
  <unescaped bksl>method{@}{annmatrix}(object, name) <- value

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.
Package suggested but not available for checking: ‘GEOquery’
installed size is 36.1Mb
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    R  36.1Mb
Package suggested but not available for checking: ‘rhdf5’
installed size is 10.4Mb
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    libs   9.0Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs   1.7Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          5.5Mb
    screenshots   1.6Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   1.6Mb
    doc    1.7Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Packages suggested but not available for checking:
  'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder',
  'AffymetrixDataTestFiles'
installed size is  6.1Mb
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    R             3.1Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
installed size is 360.0Mb
  sub-directories of 1Mb or more:
    R       5.1Mb
    libs  354.4Mb
installed size is  5.8Mb
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    libs   5.3Mb
installed size is  6.4Mb
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    include   6.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   9.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
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installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
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Packages required but not available: 'siggenes', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.7Mb
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    libs  22.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.1Mb
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    data   6.0Mb
installed size is 114.9Mb
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    libs  113.2Mb
installed size is 95.7Mb
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    libs  93.9Mb
installed size is 63.5Mb
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installed size is  6.6Mb
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.7Mb
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Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.1Mb
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installed size is 13.6Mb
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Package suggested but not available for checking: ‘reactome.db’
installed size is 12.9Mb
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Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 70.7Mb
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installed size is 42.2Mb
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installed size is 118.1Mb
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    doc     1.0Mb
    libs  116.6Mb
installed size is  7.8Mb
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installed size is  5.4Mb
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installed size is 24.4Mb
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installed size is 11.2Mb
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installed size is 87.0Mb
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installed size is 98.4Mb
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installed size is 114.0Mb
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installed size is 45.9Mb
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    libs  44.4Mb
installed size is 58.8Mb
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    help   1.8Mb
    libs  54.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.5Mb
installed size is  8.7Mb
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    libs   8.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 12.8Mb
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installed size is 25.9Mb
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installed size is  5.3Mb
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installed size is 11.0Mb
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installed size is 12.9Mb
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    libs  12.6Mb
installed size is  8.1Mb
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    libs   8.0Mb
installed size is  8.4Mb
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    libs   7.9Mb
installed size is 87.5Mb
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    libs  87.2Mb
installed size is 18.1Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
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installed size is  7.1Mb
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installed size is 10.8Mb
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installed size is 32.0Mb
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installed size is  6.4Mb
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package suggested but not available for checking: ‘BRugs’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    libs  95.1Mb
Running ‘testthat.R’ [31s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:61:1
   2. │ └─... %>% xml2::read_xml()
   3. ├─xml2::read_xml(.)
   4. └─xml2:::read_xml.character(x = .)
   5.   └─xml2:::check_string(x)
   6.     └─xml2:::stop_input_type(...)
   7.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 238 ]
  Error: Test failures
  Execution halted
  Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
installed size is 48.8Mb
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    libs  45.5Mb
installed size is 14.4Mb
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    libs  13.4Mb
installed size is 47.4Mb
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    libs  47.0Mb
installed size is 36.5Mb
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    libs  35.9Mb
installed size is 52.3Mb
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    libs  51.7Mb
installed size is 25.4Mb
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    libs  24.4Mb
installed size is 60.6Mb
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    data   2.7Mb
    libs  57.4Mb
installed size is 12.8Mb
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    libs   7.7Mb
installed size is 10.3Mb
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    libs   6.0Mb
installed size is 162.1Mb
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installed size is  5.4Mb
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    libs   4.8Mb
installed size is  9.6Mb
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    libs   7.7Mb
installed size is  5.6Mb
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installed size is  6.2Mb
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
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installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    libs      2.4Mb
installed size is  7.3Mb
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installed size is  9.2Mb
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    libs   9.0Mb
installed size is 27.8Mb
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    libs  27.7Mb
installed size is  9.4Mb
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    libs   8.0Mb
installed size is 12.0Mb
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    extdata   2.3Mb
    libs      9.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 19.7Mb
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    libs  18.1Mb
installed size is  5.7Mb
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installed size is 94.9Mb
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    libs  94.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
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installed size is  6.0Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
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installed size is  6.5Mb
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Package suggested but not available for checking: ‘IHW’
installed size is 45.1Mb
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installed size is 138.2Mb
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installed size is  8.6Mb
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installed size is 33.9Mb
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installed size is  7.4Mb
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installed size is 14.1Mb
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installed size is 167.8Mb
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installed size is 97.6Mb
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installed size is 50.4Mb
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installed size is 90.8Mb
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installed size is  6.7Mb
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installed size is  5.2Mb
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installed size is  7.4Mb
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installed size is 13.1Mb
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installed size is 396.6Mb
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    lib      385.9Mb
installed size is 93.4Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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    libs   4.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 44.0Mb
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    libs  43.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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installed size is  8.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is 12.0Mb
  sub-directories of 1Mb or more:
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installed size is 31.9Mb
  sub-directories of 1Mb or more:
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installed size is 110.8Mb
  sub-directories of 1Mb or more:
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installed size is 12.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘GENIE3’

Package suggested but not available for checking: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘bunching_examples.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_examples.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_examples.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_examples.log for more info.
--- failed re-building ‘bunching_examples.Rmd’

--- re-building ‘bunching_theory.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'bunching_theory.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/bunching.Rcheck/vign_test/bunching/vignettes/bunching_theory.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bunching_theory.log for more info.
--- failed re-building ‘bunching_theory.Rmd’

SUMMARY: processing the following files failed:
  ‘bunching_examples.Rmd’ ‘bunching_theory.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 21.5Mb
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    libs  19.9Mb
installed size is 116.6Mb
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    libs  114.3Mb
installed size is 20.0Mb
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    libs  19.8Mb
installed size is 128.2Mb
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installed size is 44.3Mb
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    libs  43.9Mb
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
Package required but not available: ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Package suggested but not available for checking: ‘batchelor’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.9Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is 38.3Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is  5.8Mb
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    libs   5.1Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  19.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   3.5Mb
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
installed size is  6.6Mb
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    data      1.6Mb
    extdata   1.1Mb
    libs      3.4Mb
installed size is 163.3Mb
  sub-directories of 1Mb or more:
    libs  162.9Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   9.5Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
Package suggested but not available for checking: ‘pbdMPI’
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Packages suggested but not available for checking: 'entab', 'mzR'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   4.3Mb
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.0Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.2Mb
installed size is 17.6Mb
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    libs  16.9Mb
Package suggested but not available for checking: ‘moe430a.db’
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Package required but not available: ‘GenomicInteractions’

Packages suggested but not available for checking:
  'InteractionSet', 'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.6Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  10.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    libs  49.7Mb
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  28.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Packages suggested but not available for checking:
  'conosPanel', 'p2data', 'rhdf5'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Running examples in ‘conos-Ex.R’ failed
The error most likely occurred in:

> ### Name: Conos
> ### Title: Conos R6 class
> ### Aliases: Conos
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$new`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$buildGraph`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> con$buildGraph(k=10, k.self=5, space='PCA', ncomps=10, n.odgenes=20, matching.method='mNN',
+     metric='angular', score.component.variance=TRUE, verbose=TRUE)
found 0 out of 1 cached PCA space pairs ... 
running 1 additional PCA space pairs 
Error in irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE,  : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: <Anonymous> ... FUN -> quickPlainPCA -> lapply -> FUN -> <Anonymous>
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─base::suppressWarnings(con$buildGraph(ncomps = 25)) at test_functions.R:15:1
    2. │ └─base::withCallingHandlers(...)
    3. └─con$buildGraph(ncomps = 25)
    4.   └─private$updatePairs(...)
    5.     └─sccore::plapply(...)
    6.       └─base::lapply(...)
    7.         └─conos (local) FUN(X[[i]], ...)
    8.           └─conos:::quickPlainPCA(...)
    9.             └─base::lapply(...)
   10.               └─conos (local) FUN(X[[i]], ...)
   11.                 └─irlba::irlba(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
installed size is 20.1Mb
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installed size is 68.5Mb
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    libs  67.3Mb
installed size is  6.1Mb
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    data   3.5Mb
    libs   2.1Mb
installed size is  5.9Mb
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    help   2.6Mb
    libs   3.2Mb
installed size is  8.1Mb
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    R     2.4Mb
    doc   3.5Mb
installed size is  5.6Mb
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    libs          2.8Mb
    sample_data   2.6Mb
Package suggested but not available for checking: ‘phyloseq’
installed size is  5.1Mb
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    extdata   3.8Mb
Package suggested but not available for checking: ‘ProData’
fishp: no visible binding for global variable ‘markname’
fishp: no visible binding for global variable ‘sum_chisq’
fishp: no visible binding for global variable ‘sum_z’
pvalues_to_zscores: no visible binding for global variable ‘markname’
tetracorr: no visible binding for global variable ‘PLCORR’
Undefined global functions or variables:
  PLCORR markname sum_chisq sum_z
installed size is  8.2Mb
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    doc    1.9Mb
    libs   5.3Mb
installed size is  5.1Mb
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    doc       1.6Mb
    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.5Mb
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    libs   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
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    libs   6.9Mb
installed size is  5.3Mb
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    doc    1.6Mb
    libs   2.9Mb
installed size is  7.3Mb
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    libs   7.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   5.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 41.5Mb
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    libs  41.4Mb
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
installed size is 199.5Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    1.7Mb
    libs  194.4Mb
Package required and available but unsuitable version: ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdMPI’
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    doc    1.2Mb
    libs   4.6Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.1Mb
    libs   3.0Mb
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Package suggested but not available for checking: ‘snpStats’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.9Mb
Packages required and available but unsuitable versions: 'utils', 'methods'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.4Mb
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘WGCNA’
Package unavailable to check Rd xrefs: ‘WGCNA’
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.8Mb
installed size is  5.1Mb
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    libs   4.1Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.3Mb
Packages required but not available:
  'signatureSearch', 'signatureSearchData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.0Mb
Packages suggested but not available for checking: 'GOstats', 'MEGENA'
Packages suggested but not available for checking:
  'IHW', 'RNASeqPower', 'zFPKM'
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Packages suggested but not available for checking: 'rhdf5', 'HDF5Array'
Package unavailable to check Rd xrefs: ‘HDF5Array’
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
installed size is 69.9Mb
  sub-directories of 1Mb or more:
    libs  69.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Package unavailable to check Rd xrefs: ‘airway’
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Packages suggested but not available for checking: 'GENIE3', 'reactome.db'
Package unavailable to check Rd xrefs: ‘GENIE3’
Package required but not available: ‘GOstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   2.4Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  12.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      2.0Mb
    extdata   2.3Mb
Package unavailable to check Rd xrefs: ‘doMPI’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   7.7Mb
installed size is 53.8Mb
  sub-directories of 1Mb or more:
    libs  53.4Mb
Warning in checkDepPackageVersion(dep_pkg = "Matrix", this_pkg = "TMB") :
  Package version inconsistency detected.
TMB was built with Matrix version 1.6.4
Current Matrix version is 1.6.5
Please re-install TMB from source or restore original ‘Matrix’ package (see '?reinstalling' for more information)

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.
installed size is 65.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  64.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.5Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.7Mb
installed size is 366.1Mb
  sub-directories of 1Mb or more:
    libs  365.3Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   9.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
    libs   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   8.4Mb
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.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.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs        9.4Mb
    shiny_app   1.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  10.7Mb
Packages required but not available: 'HDF5Array', 'rhdf5'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  11.7Mb
installed size is 127.1Mb
  sub-directories of 1Mb or more:
    libs  126.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 94.4Mb
  sub-directories of 1Mb or more:
    libs  93.7Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
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Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm6): Font bbm6 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

--- finished re-building ‘residuetheorem.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 61.7Mb
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Packages required but not available:
  'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.4Mb
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Package suggested but not available for checking: ‘Rmpi’
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Packages suggested but not available for checking: 'mzR', 'gcspikelite'
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Package required but not available: ‘PSCBS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
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Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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.
installed size is 20.0Mb
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installed size is 11.2Mb
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installed size is 14.5Mb
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installed size is  7.6Mb
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installed size is 10.9Mb
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Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    2. │ └─base::withVisible(...elt(i))
    3. └─fastTopics::umap_plot(fit1, fill = "loading", verbose = FALSE)
    4.   └─fastTopics::umap_from_topics(fit, dims = 2, ...)
    5.     └─uwot::umap(...)
    6.       └─uwot:::uwot(...)
    7.         └─uwot:::spectral_init(V, ndim = n_components, verbose = verbose)
    8.           └─uwot:::irlba_tsvd_normalized_laplacian_init(A, ndim, verbose = FALSE)
    9.             └─uwot:::irlba_spectral_tsvd(L, ndim + 1)
   10.               ├─base::suppressWarnings(...)
   11.               │ └─base::withCallingHandlers(...)
   12.               └─irlba::irlba(L, nv = n, nu = 0, maxit = iters)
  
  [ FAIL 1 | WARN 3 | SKIP 7 | PASS 234 ]
  Error: Test failures
  Execution halted
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installed size is 11.0Mb
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installed size is 14.3Mb
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installed size is  7.6Mb
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installed size is 40.4Mb
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installed size is 11.9Mb
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installed size is 17.0Mb
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installed size is 24.8Mb
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installed size is  7.3Mb
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Packages suggested but not available for checking: 'MicrobeDS', 'phyloseq'
installed size is 39.9Mb
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Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  attr(,"class")
  [1] "gg"     "ggplot"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(phyloseq)`: there is no package called 'phyloseq'
  Backtrace:
      ▆
   1. └─base::library(phyloseq) at test-ilr.R:11:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  Error: Test failures
  Execution halted
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Package required but not available: ‘rhdf5’

Package suggested but not available for checking: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.2Mb
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installed size is 31.9Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
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Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
installed size is 11.7Mb
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    R      2.0Mb
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installed size is  7.9Mb
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    libs   3.3Mb
installed size is  7.8Mb
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installed size is 300.5Mb
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installed size is 10.6Mb
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installed size is  5.3Mb
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installed size is  9.0Mb
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installed size is  5.4Mb
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installed size is  9.1Mb
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installed size is  6.7Mb
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installed size is 82.6Mb
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installed size is 36.0Mb
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Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.6Mb
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installed size is 14.9Mb
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Package suggested but not available for checking: ‘WGCNA’
installed size is  5.5Mb
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installed size is  6.0Mb
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Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.5Mb
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installed size is 36.1Mb
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installed size is 12.2Mb
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installed size is  9.4Mb
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    R      2.1Mb
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installed size is 17.9Mb
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    doc    1.1Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/gdalBindings.Rcheck/00install.out’ for details.
installed size is 274.2Mb
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installed size is 12.9Mb
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Running examples in ‘GEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: eep_optim
> ### Title: The Wrapper Function that Returns the Final Estimates from
> ###   Maximum Likelihood Estimation for EEP.
> ### Aliases: eep_optim
> 
> ### ** Examples
> 
> eep_optim(seq(1:100))
Error in stats::optim(init, lower = lower_bound, eep_nll, method = "L-BFGS-B",  : 
  L-BFGS-B needs finite values of 'fn'
Calls: eep_optim -> raw_est_eep -> <Anonymous>
Execution halted
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installed size is  6.7Mb
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    libs      1.4Mb
Package required but not available: ‘GEOquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.1Mb
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    doc    1.5Mb
    libs   9.7Mb
Package which this enhances but not available for checking: ‘simplifyEnrichment’
Package required but not available: ‘biocViews’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
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    libs   4.2Mb
Package required but not available: ‘reactome.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.3Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘geoAr_geofacet.Rmd’ using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_geofacet.Rmd’

--- re-building ‘geoAr_leaflet.Rmd’ using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_leaflet.Rmd’

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

SUMMARY: processing the following files failed:
  ‘geoAr_geofacet.Rmd’ ‘geoAr_leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
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installed size is  6.7Mb
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installed size is 15.3Mb
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installed size is 103.2Mb
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installed size is 34.1Mb
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installed size is 35.0Mb
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    libs  34.5Mb
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.4Mb
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    doc       3.0Mb
    extdata   1.6Mb
    libs      3.1Mb
installed size is  5.6Mb
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    libs   5.2Mb
Running examples in ‘ggESDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 19.2Mb
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installed size is  7.0Mb
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installed size is  9.6Mb
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Package required but not available: ‘MicrobiomeStat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
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installed size is  8.9Mb
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    testdata   4.8Mb
installed size is  7.7Mb
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installed size is 17.9Mb
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installed size is  5.8Mb
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installed size is  5.9Mb
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installed size is  7.1Mb
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Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
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installed size is 33.8Mb
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installed size is 12.1Mb
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installed size is  9.7Mb
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installed size is 30.2Mb
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installed size is 176.9Mb
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installed size is  7.9Mb
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installed size is 11.7Mb
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installed size is 11.9Mb
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installed size is 19.6Mb
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installed size is  5.7Mb
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installed size is  8.6Mb
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installed size is  5.0Mb
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Package required but not available: ‘DOSE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  8.1Mb
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installed size is  5.9Mb
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installed size is  5.3Mb
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installed size is  6.9Mb
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installed size is  5.3Mb
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installed size is  5.9Mb
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installed size is  8.2Mb
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installed size is  5.7Mb
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installed size is 11.8Mb
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installed size is 11.9Mb
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installed size is 157.0Mb
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installed size is  5.5Mb
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Running examples in ‘HCD-Ex.R’ failed
The error most likely occurred in:

> ### Name: HCD
> ### Title: hierarchical community detection with recursive spectral methods
> ### Aliases: HCD
> ### Keywords: HCD BTSBM
> 
> ### ** Examples
> 
> dt <- BTSBM(n=1600,d=4,a.seq=0.2^seq(0,4),lambda=50)
> A <- dt$A.list[[1]]
> # you can try various versions of the algorithm as below: the Fix is fastest and ECV is slowest.
> system.time(HCD.result <- HCD(A,method="SC",stopping="Fix",D=4))
Begin clustering....
Error in irlba(f, nu = 2, nv = 2) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: system.time -> HCD -> break.cl.sp -> irlba
Timing stopped at: 0.005 0 0.005
Execution halted
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installed size is  6.1Mb
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installed size is 10.9Mb
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installed size is  9.5Mb
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installed size is  7.4Mb
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installed size is 21.7Mb
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    libs  21.5Mb
installed size is  5.5Mb
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    doc    3.7Mb
Package required but not available: ‘Heatplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
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    libs   6.2Mb
installed size is  5.2Mb
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installed size is 22.9Mb
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    libs  18.9Mb
installed size is  5.2Mb
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installed size is  5.2Mb
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installed size is 10.9Mb
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installed size is  6.9Mb
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installed size is  9.6Mb
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installed size is 48.5Mb
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installed size is  6.9Mb
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installed size is 48.0Mb
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installed size is  6.1Mb
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installed size is  8.1Mb
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installed size is 12.0Mb
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installed size is 60.9Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/hoardeR.Rcheck/00install.out’ for details.
installed size is 10.0Mb
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installed size is 15.1Mb
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installed size is  8.5Mb
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    data   8.0Mb
installed size is 68.3Mb
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installed size is  6.0Mb
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Package suggested but not available for checking: ‘HTSFilter’
installed size is 10.0Mb
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installed size is  9.1Mb
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installed size is  9.9Mb
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installed size is  7.8Mb
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installed size is  7.9Mb
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    dict   1.5Mb
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installed size is 44.0Mb
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    libs  43.4Mb
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘microViz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
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installed size is  7.4Mb
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installed size is  5.8Mb
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installed size is  5.0Mb
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Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is 15.3Mb
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Package suggested but not available for checking: ‘mixAK’
installed size is  5.6Mb
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installed size is 31.1Mb
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installed size is  6.5Mb
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Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [19s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_equal(...) at test-center-graph.R:61:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::nrow(...)
    5. ├─iGraphMatch::pad(...)
    6. │ └─methods::is(m, "splrMatrix")
    7. └─iGraphMatch::center_graph(A, scheme = 2, use_splr = TRUE)
    8.   ├─iGraphMatch::splr(x = A[], a = -A[], rank = r, factorize = TRUE)
    9.   └─iGraphMatch::splr(x = A[], a = -A[], rank = r, factorize = TRUE)
   10.     └─irlba::irlba(a, rank)
  
  [ FAIL 2 | WARN 108 | SKIP 25 | PASS 147 ]
  Error: Test failures
  Execution halted
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installed size is  7.1Mb
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installed size is 14.3Mb
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installed size is 31.3Mb
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installed size is 21.7Mb
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installed size is  7.4Mb
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installed size is  5.2Mb
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installed size is  5.0Mb
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Packages required but not available: 'siggenes', 'RankProd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
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installed size is 11.7Mb
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Package unavailable to check Rd xrefs: ‘minfi’
installed size is 11.4Mb
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installed size is 30.2Mb
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installed size is  8.8Mb
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installed size is 12.0Mb
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installed size is  5.1Mb
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    shiny-server   1.0Mb
installed size is  9.1Mb
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Running ‘edge.R’ [1s/1s]
  Running ‘prcomp.r’ [1s/1s]
  Running ‘ssvd.R’ [1s/1s]
  Running ‘svdr.R’ [1s/1s]
  Running ‘test.R’ [1s/1s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  + 
  +   # test for https://github.com/bwlewis/irlba/issues/42
  +   set.seed(1234)
  +   a <- matrix(rnorm(10000), ncol=20)
  +   center <- runif(ncol(a))
  +   scale <- runif(ncol(a))
  +   L <- irlba(a, 5, scale=scale, center=center, fastpath=FAST)
  +   S <- svd(scale(a, center=center, scale=scale))
  +   if (isTRUE(max(abs(S$d[1:5] - L$d)) > 1e-3))
  +   {
  +     stop("Failed scale + center test fastpath=", FAST)
  +   }
  + }
  Error: Failed tprolate test fastpath=FALSE
  Execution halted
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installed size is 62.8Mb
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installed size is 13.7Mb
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installed size is  6.3Mb
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installed size is 19.3Mb
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File ‘JavaGD/libs/JavaGD.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.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.
installed size is 90.5Mb
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installed size is  7.4Mb
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installed size is  7.4Mb
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installed size is  9.7Mb
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installed size is 32.8Mb
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installed size is  7.0Mb
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installed size is 10.7Mb
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installed size is  6.6Mb
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Package suggested but not available for checking: ‘PSCBS’
Package unavailable to check Rd xrefs: ‘PSCBS’
installed size is 34.2Mb
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installed size is 16.9Mb
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installed size is  6.7Mb
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    htmlwidgets   1.1Mb
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Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.3Mb
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    help   6.9Mb
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
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installed size is 17.2Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’ using Sweave
Error: processing vignette 'Instruction_of_functions_of_R_package_KINSIMU.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Instruction_of_functions_of_R_package_KINSIMU.tex' failed.
LaTeX errors:
! LaTeX Error: Command \gather already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1560 }
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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installed size is  5.4Mb
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installed size is  8.4Mb
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installed size is  6.9Mb
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installed size is  8.4Mb
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installed size is  5.2Mb
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installed size is  9.7Mb
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    libs   5.7Mb
installed size is  5.4Mb
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Package unavailable to check Rd xrefs: ‘mixAK’
Package suggested but not available for checking: ‘VariantAnnotation’
installed size is  6.0Mb
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installed size is  7.1Mb
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installed size is 62.0Mb
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Package suggested but not available for checking: ‘org.Mm.eg.db’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.3Mb
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    testdata   1.3Mb
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installed size is  5.9Mb
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    doc-software   2.4Mb
installed size is  6.8Mb
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installed size is 64.9Mb
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installed size is 34.7Mb
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Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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installed size is  6.3Mb
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Package suggested but not available for checking: ‘RDRToolbox’
installed size is  5.6Mb
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    libs      1.0Mb
installed size is 52.8Mb
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installed size is 16.4Mb
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installed size is 50.0Mb
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Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘ggformula’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  6.2Mb
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    data   2.1Mb
    libs   3.9Mb
installed size is  6.1Mb
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    R      2.0Mb
    libs   1.9Mb
installed size is  6.0Mb
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    R   5.0Mb
installed size is 24.4Mb
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    libs  24.2Mb
installed size is 32.2Mb
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    libs  31.8Mb
Package suggested but not available for checking: ‘quitte’
installed size is  6.7Mb
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    libs   5.0Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  48.5Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Package suggested but not available for checking: ‘dittoSeq’
Packages suggested but not available for checking:
  'ssize', 'GEOquery', 'GEOmetadb', 'WGCNA', 'pdInfoBuilder', 'lumi',
  'oligo', 'GOstats'
installed size is  9.7Mb
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installed size is 10.5Mb
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    libs   9.5Mb
installed size is 11.1Mb
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    libs  10.8Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs         15.3Mb
installed size is 11.8Mb
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    R      2.7Mb
    data   2.4Mb
    libs   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.1Mb
installed size is 15.3Mb
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installed size is  5.3Mb
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    libs   3.4Mb
installed size is 10.0Mb
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    libs   8.3Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'clusterProfiler', 'org.Mm.eg.db',
  'wiggleplotr'
installed size is  8.6Mb
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    libs   8.3Mb
installed size is  8.3Mb
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    libs   7.4Mb
installed size is 42.0Mb
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    libs  41.8Mb
installed size is 13.2Mb
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    java   3.3Mb
    libs   8.8Mb
installed size is  5.8Mb
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    doc    1.4Mb
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installed size is 14.1Mb
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    libs  13.2Mb
installed size is 11.3Mb
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    R      2.1Mb
    libs   9.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.9Mb
installed size is 17.8Mb
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    doc    3.8Mb
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installed size is  5.6Mb
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    doc   2.9Mb
installed size is 34.3Mb
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    libs  33.2Mb
installed size is 17.5Mb
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    R      1.1Mb
    libs  15.9Mb
installed size is 11.3Mb
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    libs  10.9Mb
installed size is 64.1Mb
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    libs  62.7Mb
Package suggested but not available for checking: ‘file2meco’
installed size is 35.6Mb
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    libs  34.5Mb
installed size is 19.3Mb
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    libs  18.3Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
installed size is 155.4Mb
  sub-directories of 1Mb or more:
    libs  153.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is  8.5Mb
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    extdata   3.4Mb
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installed size is 22.2Mb
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    libs  21.1Mb
installed size is  8.6Mb
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    data   2.7Mb
    libs   5.5Mb
installed size is 107.1Mb
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    libs  106.3Mb
Packages suggested but not available for checking: 'phyloseq', 'biomformat'
installed size is  6.1Mb
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    R      3.0Mb
    help   2.2Mb
Packages suggested but not available for checking:
  'GEOquery', 'annaffy', 'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'
installed size is 21.4Mb
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    libs  21.0Mb
installed size is 60.3Mb
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installed size is  7.4Mb
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    libs   2.7Mb
installed size is 12.8Mb
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    libs  11.5Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    libs  20.6Mb
installed size is  9.5Mb
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    data   1.1Mb
    libs   6.5Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘dada2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.3Mb
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installed size is  6.5Mb
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    libs   6.2Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 119.3Mb
  sub-directories of 1Mb or more:
    libs  118.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.3Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Packages required but not available: 'phyloseq', 'dada2'

Packages suggested but not available for checking:
  'ANCOMBC', 'mia', 'phyloseqGraphTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  8.0Mb
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    data   2.0Mb
    libs   4.4Mb
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
installed size is 239.9Mb
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    include    9.6Mb
    libs     229.8Mb
installed size is  5.6Mb
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    R      2.1Mb
    data   2.3Mb
installed size is  6.0Mb
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    libs   5.7Mb
installed size is 35.9Mb
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    libs  35.4Mb
installed size is 22.1Mb
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installed size is 17.6Mb
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    doc    1.3Mb
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installed size is 20.7Mb
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    libs  20.5Mb
installed size is 110.1Mb
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installed size is 15.6Mb
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    libs  15.4Mb
installed size is 10.6Mb
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    libs  10.4Mb
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
Running ‘testthat.R’ [45s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ──
  Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
    You first need to install it, which you can do with:
        library(BiocManager)
        install("BSgenome.Hsapiens.UCSC.hg19")
  Backtrace:
      ▆
   1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 2 | WARN 14 | SKIP 23 | PASS 21 ]
  Error: Test failures
  Execution halted
installed size is  5.4Mb
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installed size is  5.3Mb
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    data   5.0Mb
installed size is  9.8Mb
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    libs   8.2Mb
installed size is  9.0Mb
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    R      2.0Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  7.4Mb
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    libs   6.9Mb
installed size is 14.8Mb
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    htmlwidgets  14.7Mb
installed size is 10.8Mb
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    data   2.0Mb
    libs   7.1Mb
installed size is  6.2Mb
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    libs     3.0Mb
    raster   2.2Mb
installed size is  5.8Mb
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    data   2.3Mb
    libs   2.6Mb
installed size is  5.4Mb
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    R   2.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/MPCR.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 85.9Mb
  sub-directories of 1Mb or more:
    libs  85.5Mb
installed size is 14.8Mb
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    data   1.6Mb
    libs  12.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.0Mb
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    libs   6.4Mb
installed size is 10.9Mb
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    R      2.1Mb
    data   4.5Mb
    libs   3.5Mb
installed size is 49.3Mb
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    libs  48.9Mb
installed size is  6.2Mb
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    R   6.1Mb
installed size is  5.7Mb
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    data   5.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘multe.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'multe.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/multe.Rcheck/vign_test/multe/vignettes/multe.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See multe.log for more info.
--- failed re-building ‘multe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
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    libs   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.2Mb
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 107.8Mb
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    libs  107.6Mb
installed size is 271.1Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.4Mb
    libs  264.0Mb
installed size is  6.1Mb
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    libs   4.7Mb
installed size is 35.8Mb
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    libs  35.5Mb
Error(s) in re-building vignettes:
--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

The following object is masked from ‘package:stats’:

    deriv

The following object is masked from ‘package:base’:

    single

Loading required package: polynom
Error: processing vignette 'multipol.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘multipol.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
Error(s) in re-building vignettes:
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

The following objects are masked from ‘package:base’:

    levels, rbind

--- finished re-building ‘cias.Rnw’

--- re-building ‘multivator.Rnw’ using Sweave

Attaching package: 'multivator'

The following objects are masked from 'package:base':

    levels, rbind

Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'multivator.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
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    libs   5.5Mb
installed size is 13.2Mb
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    libs  11.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.5Mb
installed size is  5.7Mb
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    libs   5.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 26.4Mb
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    data     1.9Mb
    libs    23.3Mb
    models   1.1Mb
installed size is  6.6Mb
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    libs   4.3Mb
installed size is 11.1Mb
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    libs  10.5Mb
installed size is  6.4Mb
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    data   4.6Mb
    doc    1.7Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   5.1Mb
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
installed size is  6.0Mb
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    libs   5.6Mb
installed size is  6.6Mb
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    data   1.5Mb
    libs   4.3Mb
installed size is 24.8Mb
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    libs  23.1Mb
installed size is 13.0Mb
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    libs  12.7Mb
installed size is  9.9Mb
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    doc    2.5Mb
    libs   5.5Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
installed size is  6.7Mb
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    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
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    doc    1.7Mb
    libs   5.5Mb
installed size is 243.5Mb
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    libs  242.8Mb
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              8.1Mb
    classic-bugs   1.5Mb
    include       11.5Mb
    libs          17.9Mb
installed size is  6.8Mb
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    doc       4.0Mb
    extdata   1.8Mb
installed size is 20.3Mb
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    libs  18.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running examples in ‘NMRphasing-Ex.R’ failed
The error most likely occurred in:

> ### Name: MPC_AAM
> ### Title: MPC_AAM
> ### Aliases: MPC_AAM
> 
> ### ** Examples
> 
> data("fdat")
> mpc_aam_phased1 <- MPC_AAM(fdat$frequency_domain)
Error in localMaximumSlidingWindow(x, winSize) : 
  DLL requires the use of native symbols
Calls: MPC_AAM ... getLocalMaximumCWT -> localMaximum -> localMaximumSlidingWindow
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown

Quitting from lines 82-92 [unnamed-chunk-5] (NMRphasing_vignette.rmd)
Error: processing vignette 'NMRphasing_vignette.rmd' failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘NMRphasing_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘NMRphasing_vignette.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.1Mb
    mods   3.3Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [12s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6. └─npi::npi_search(city = "Atlanta", limit = 1)
    7.   └─npi:::npi_process_results(...)
    8.     └─npi:::npi_control_requests(params, user_n)
    9.       └─npi:::npi_get_results(results = results, query = query)
   10.         └─npi:::npi_get(npi_url(), query = ...)
   11.           └─npi:::npi_api("GET", url, ...)
   12.             └─httr (local) FUN(url, ..., config = c(npi_config(), config))
   13.               └─httr:::request_perform(req, hu$handle$handle)
   14.                 ├─httr:::request_fetch(req$output, req$url, handle)
   15.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   16.                   └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced-use.Rmd’ using rmarkdown
Quitting from lines 39-46 (advanced-use.Rmd) 
Error: processing vignette 'advanced-use.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Could not resolve host: npiregistry.cms.hhs.gov
--- failed re-building ‘advanced-use.Rmd’

--- re-building ‘npi.Rmd’ using rmarkdown
Quitting from lines 34-36 (npi.Rmd) 
Error: processing vignette 'npi.Rmd' failed with diagnostics:
Could not resolve host: npiregistry.cms.hhs.gov
--- failed re-building ‘npi.Rmd’

SUMMARY: processing the following files failed:
  ‘advanced-use.Rmd’ ‘npi.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  15.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.0Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
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installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.1Mb
Packages required but not available: 'rhdf5', 'Rhdf5lib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.4Mb
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installed size is 31.2Mb
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installed size is 10.5Mb
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installed size is  5.9Mb
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installed size is 200.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
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installed size is 11.9Mb
  sub-directories of 1Mb or more:
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
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    libs      4.9Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking: 'gurobi', 'lpsymphony'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.5Mb
  sub-directories of 1Mb or more:
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installed size is 11.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
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installed size is 10.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘scde’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/PAMhm.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 14.2Mb
  sub-directories of 1Mb or more:
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    libs  12.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
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    libs   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘anomalize’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is 10.9Mb
  sub-directories of 1Mb or more:
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installed size is  6.6Mb
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installed size is  5.1Mb
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installed size is  6.2Mb
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installed size is  6.7Mb
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    libs      2.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
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installed size is 24.6Mb
  sub-directories of 1Mb or more:
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installed size is 133.1Mb
  sub-directories of 1Mb or more:
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installed size is 36.1Mb
  sub-directories of 1Mb or more:
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installed size is 34.1Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.3/pcSteiner.Rcheck/vign_test/pcSteiner/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.1Mb
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installed size is  7.5Mb
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installed size is 18.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘georob’
installed size is 136.3Mb
  sub-directories of 1Mb or more:
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installed size is  6.4Mb
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installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is  9.2Mb
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installed size is 59.7Mb
  sub-directories of 1Mb or more:
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installed size is 11.9Mb
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Package suggested but not available for checking: ‘seqLogo’
installed size is  7.8Mb
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installed size is  5.1Mb
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installed size is 45.7Mb
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installed size is  5.0Mb
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installed size is 47.3Mb
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installed size is 12.8Mb
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installed size is 12.4Mb
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installed size is  5.1Mb
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installed size is 23.4Mb
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installed size is  5.2Mb
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installed size is 22.8Mb
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Package required but not available: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘slingshot’
installed size is 17.3Mb
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installed size is  7.0Mb
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installed size is  7.5Mb
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installed size is  5.2Mb
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installed size is 12.8Mb
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installed size is  6.3Mb
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installed size is  7.2Mb
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Package unavailable to check Rd xrefs: ‘VariantAnnotation’
installed size is 19.5Mb
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installed size is 43.2Mb
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installed size is  6.4Mb
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installed size is 37.9Mb
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installed size is 13.0Mb
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installed size is  9.3Mb
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Packages required and available but unsuitable versions:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
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installed size is  5.9Mb
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installed size is 15.4Mb
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installed size is 10.1Mb
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installed size is  7.0Mb
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installed size is 10.5Mb
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installed size is 19.1Mb
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installed size is 21.8Mb
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installed size is 15.6Mb
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installed size is 14.7Mb
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installed size is 17.6Mb
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installed size is 17.8Mb
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installed size is 120.3Mb
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installed size is 36.4Mb
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installed size is  7.1Mb
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installed size is 21.4Mb
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Package suggested but not available for checking: ‘proDA’
installed size is  6.6Mb
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installed size is 26.4Mb
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installed size is  6.3Mb
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installed size is 127.4Mb
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installed size is  6.1Mb
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installed size is  5.2Mb
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installed size is  5.5Mb
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installed size is 12.3Mb
  sub-directories of 1Mb or more:
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installed size is 28.2Mb
  sub-directories of 1Mb or more:
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installed size is 51.3Mb
  sub-directories of 1Mb or more:
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installed size is 32.2Mb
  sub-directories of 1Mb or more:
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installed size is 16.6Mb
  sub-directories of 1Mb or more:
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Missing or unexported objects:
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  ‘async::when_all’
installed size is  5.9Mb
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installed size is  5.3Mb
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installed size is 80.9Mb
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installed size is 119.7Mb
  sub-directories of 1Mb or more:
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installed size is  6.0Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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installed size is 17.7Mb
  sub-directories of 1Mb or more:
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installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.7Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
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installed size is 38.0Mb
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    libs     33.4Mb
installed size is 11.5Mb
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installed size is 10.1Mb
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installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is 10.9Mb
  sub-directories of 1Mb or more:
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installed size is  9.8Mb
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installed size is 10.8Mb
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installed size is 11.3Mb
  sub-directories of 1Mb or more:
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installed size is  5.3Mb
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installed size is  7.5Mb
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installed size is 19.3Mb
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Package unavailable to check Rd xrefs: ‘BRugs’
Packages suggested but not available for checking: 'batchelor', 'slingshot'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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    doc    6.7Mb
    libs   1.2Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
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installed size is 43.1Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.7Mb
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installed size is 11.4Mb
  sub-directories of 1Mb or more:
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    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.1Mb
Package suggested but not available for checking: ‘Spectra’
Packages required and available but unsuitable versions:
  'GenomicRanges', 'IRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
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    extdata   4.1Mb
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installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
  sub-directories of 1Mb or more:
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installed size is 66.2Mb
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installed size is 13.1Mb
  sub-directories of 1Mb or more:
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installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    etc    1.9Mb
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installed size is 16.6Mb
  sub-directories of 1Mb or more:
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installed size is 21.5Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.8Mb
  sub-directories of 1Mb or more:
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installed size is  5.4Mb
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installed size is 57.1Mb
  sub-directories of 1Mb or more:
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installed size is 58.2Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rblpapi.Rcheck/00install.out’ for details.
installed size is 44.2Mb
  sub-directories of 1Mb or more:
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installed size is 14.0Mb
  sub-directories of 1Mb or more:
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installed size is 67.9Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.6Mb
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installed size is  6.8Mb
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installed size is  7.6Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
  'ROntoTools', 'hgu133plus2.db', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
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installed size is  9.4Mb
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installed size is  9.4Mb
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installed size is  8.3Mb
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installed size is 45.7Mb
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installed size is 34.0Mb
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installed size is  6.9Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
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installed size is  9.7Mb
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installed size is  6.4Mb
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installed size is 14.4Mb
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installed size is 17.8Mb
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installed size is  6.6Mb
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installed size is 20.3Mb
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  8.9Mb
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installed size is  5.4Mb
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Running examples in ‘realTimeloads-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_data
> ### Title: Returns x with gaps imputed using ARIMA and Decision Trees,
> ###   optional uncertainty estimation using Monte Carlo resampling
> ### Aliases: impute_data
> 
> ### ** Examples
> 
> # Impute non-tidal data
> time <- realTimeloads::ExampleData$Sediment_Samples$time
> xo <- realTimeloads::ExampleData$Sediment_Samples$SSCxs_mg_per_liter
> Q <- realTimeloads::ExampleData$Discharge$Discharge_m_cubed_per_s
> idata <- sample(1:length(xo),round(length(xo)*0.5),replace=FALSE)
> x <- rep(NA,length(xo))
> x[idata] <- xo[idata] # simulated samples
> flow_concentrtion_ratio <- imputeTS::na_interpolation(Q/x)
> Xreg <- cbind(Q,flow_concentrtion_ratio)
> Output <- impute_data(time,x,Xreg,MC = 10,ptrain = 0.8)
Error in optim(init[mask], getLike, method = "L-BFGS-B", lower = rep(0,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: impute_data -> <Anonymous> -> <Anonymous> -> optim
Execution halted
installed size is  5.6Mb
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installed size is  5.2Mb
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installed size is  7.0Mb
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installed size is  5.0Mb
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installed size is 18.4Mb
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installed size is 11.9Mb
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installed size is  7.3Mb
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installed size is 11.0Mb
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installed size is  6.2Mb
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installed size is  7.6Mb
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installed size is 18.0Mb
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installed size is  9.3Mb
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installed size is 10.3Mb
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installed size is  9.3Mb
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installed size is  6.5Mb
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installed size is 26.3Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RevGadgets’
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc     3.0Mb
    fonts   1.5Mb
    libs   22.1Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.2Mb
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.7Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs     19.0Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.1Mb
installed size is 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/rlibkriging.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package unavailable to check Rd xrefs: ‘EnhancedVolcano’
Running ‘testthat.R’ [25s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─testthat::expect_warning(...) at test_downstream.R:245:9
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─testthat::expect_is(...) at test_downstream.R:246:13
    7. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    8. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    9. └─rliger::runGSEA(pbmcPlot, genesets = "Immune System")
   10.   └─cli::cli_abort("Package {.pkg reactome.db} is needed for this function to work.\n            Please install it by command:\n            {.code BiocManager::install('reactome.db')}")
   11.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 1039 ]
  Error: Test failures
  Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    libs  131.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.2Mb
    minizinc   3.3Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 84.3Mb
  sub-directories of 1Mb or more:
    libs  83.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Package required but not available: ‘AnnotationHub’

Package suggested but not available for checking: ‘recount3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
installed size is 101.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     98.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   1.7Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is 86.5Mb
  sub-directories of 1Mb or more:
    libs  85.8Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/ROracle.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.4Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   7.7Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.3Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/RQuantLib.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  24.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is 296.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  289.2Mb
installed size is 67.1Mb
  sub-directories of 1Mb or more:
    libs  66.8Mb
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib   34.2Mb
    libs  11.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs    1.8Mb
    swipl  20.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.4Mb
    help   2.3Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.2Mb
Package suggested but not available for checking: ‘Gviz’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs       2.3Mb
    projects   2.9Mb
installed size is 100.0Mb
  sub-directories of 1Mb or more:
    libs  98.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.2Mb
installed size is 119.9Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  117.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   2.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  44.1Mb
matrixOps:
  function(e1, e2)
matrixOps.rvec:
  function(x, y)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 64.2Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     58.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Packages suggested but not available for checking:
  'BiocPkgTools', 'biocViews'
Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    8.4Mb
    yacas   1.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.1Mb
    yacas   1.3Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  44.5Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.0Mb
Packages suggested but not available for checking:
  'GOstats', 'networkTomography', 'org.Sc.sgd.db'
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
Package required and available but unsuitable version: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Package required but not available: ‘LoomExperiment’

Packages suggested but not available for checking:
  'scRNAseq', 'sceasy', 'SeuratDisk', 'SeuratWrappers',
  'zellkonverter', 'GEOfastq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘simplifyEnrichment’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
Package suggested but not available for checking: ‘oligoClasses’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 87.7Mb
  sub-directories of 1Mb or more:
    libs  85.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R   9.0Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  14.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   7.9Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SemiCompRisks.ltx’ using tex
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SemiCompRisks.ltx’

SUMMARY: processing the following file failed:
  ‘SemiCompRisks.ltx’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.4Mb
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.0Mb
    models   1.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.6Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘airway’
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.2Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Packages suggested but not available for checking: 'HDF5Array', 'BPCells'
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 261.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    libs    255.0Mb
    sqlite    1.5Mb
installed size is  7.0Mb
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    data   6.8Mb
installed size is  7.1Mb
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    R     2.0Mb
    doc   3.8Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: 40 90
  ── Failure ('test-getters.R:41:5'): days getters extracts correct days ─────────
  sh_wday(dt) (`actual`) not equal to c(4, 6) (`expected`).
  
    `actual`: 5 6
  `expected`: 4 6
  ── Failure ('test-getters.R:42:5'): days getters extracts correct days ─────────
  sh_wday(d) (`actual`) not equal to c(4, 6) (`expected`).
  
    `actual`: 5 6
  `expected`: 4 6
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
installed size is  8.0Mb
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installed size is 20.5Mb
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    www  19.7Mb
installed size is 12.6Mb
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    R     2.0Mb
    www   9.3Mb
installed size is  5.4Mb
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    libs   5.2Mb
installed size is 12.1Mb
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    libs  11.1Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.5Mb
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    extdata   1.0Mb
    help      1.7Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
installed size is  5.0Mb
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    R      2.0Mb
    libs   1.9Mb
Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      4.9Mb
installed size is  7.3Mb
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    data   2.9Mb
    libs   2.7Mb
installed size is 14.8Mb
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    doc    1.6Mb
    libs  12.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
installed size is  5.5Mb
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    data   2.0Mb
    libs   2.5Mb
installed size is 23.3Mb
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    doc    1.5Mb
    libs  20.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.7Mb
Packages required but not available: 'HTSSIP', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.0Mb
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    R      3.1Mb
    libs   6.8Mb
installed size is  7.8Mb
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    libs   7.5Mb
installed size is  9.4Mb
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    R         2.1Mb
    extdata   1.6Mb
    libs      5.0Mb
installed size is  7.4Mb
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    doc    1.1Mb
    libs   5.2Mb
installed size is 31.7Mb
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    libs  31.1Mb
installed size is  6.5Mb
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    data   6.1Mb
installed size is 20.7Mb
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    libs  20.3Mb
installed size is  9.4Mb
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    libs   8.9Mb
installed size is  7.2Mb
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    libs   7.0Mb
installed size is  7.7Mb
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    data   4.6Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.3Mb
    libs  10.1Mb
Package which this enhances but not available for checking: ‘Rmpi’
Packages suggested but not available for checking:
  'VariantAnnotation', 'TxDb.Hsapiens.UCSC.hg19.knownGene'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.9Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     4.1Mb
    doc   1.1Mb
installed size is 13.4Mb
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    data   1.3Mb
    doc    1.3Mb
    libs   9.6Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [17s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: "0427" "1946"
  ── Failure ('test-audioblastProcessors.R:103:3'): .calcTimesOfDay() works as expected ──
  as.character(o[2, ]) (`actual`) not equal to c("2248", "0124") (`expected`).
  
  `actual`:   "2254" "0119"
  `expected`: "2248" "0124"
  ── Failure ('test-audioblastProcessors.R:105:3'): .calcTimesOfDay() works as expected ──
  as.character(o[4, ]) (`actual`) not equal to c("1206", "2248") (`expected`).
  
  `actual`:   "1207" "2254"
  `expected`: "1206" "2248"
  
  [ FAIL 18 | WARN 0 | SKIP 7 | PASS 811 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
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    libs   7.2Mb
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.9Mb
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    data   4.0Mb
    doc    1.0Mb
installed size is  5.4Mb
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    data   4.8Mb
installed size is 17.8Mb
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    data   4.7Mb
    libs  13.0Mb
installed size is  5.1Mb
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    R      2.0Mb
    libs   2.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   4.8Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  33.7Mb
installed size is  7.2Mb
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    R      2.1Mb
    java   3.8Mb
installed size is 16.6Mb
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    libs  16.5Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
Package required but not available: ‘SpatialExperiment’

Packages suggested but not available for checking: 'rhdf5', 'HDF5Array'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 54.7Mb
  sub-directories of 1Mb or more:
    libs  53.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  11.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
installed size is 22.5Mb
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    libs  21.6Mb
installed size is 13.7Mb
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    data   3.1Mb
    libs  10.1Mb
installed size is  9.3Mb
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    libs   8.7Mb
installed size is  6.6Mb
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    shapes   3.2Mb
installed size is  5.9Mb
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Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Quitting from lines 111-120 (classic_speaq_vignette.Rmd) 
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Quitting from lines 71-83 (speaq2_illustrations.Rmd) 
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
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    data   4.8Mb
Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
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.
installed size is  7.4Mb
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    doc    3.1Mb
    libs   3.9Mb
installed size is 22.2Mb
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    libs  21.9Mb
installed size is 17.3Mb
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    libs  16.2Mb
installed size is  6.6Mb
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    libs   6.0Mb
installed size is  5.1Mb
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    doc    1.2Mb
    libs   3.3Mb
installed size is 16.4Mb
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    doc       1.1Mb
    extdata   2.6Mb
    libs     11.3Mb
installed size is  6.1Mb
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    R      2.0Mb
    libs   2.9Mb
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  50.5Mb
installed size is  5.7Mb
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    data   5.3Mb
installed size is 13.3Mb
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    data   1.1Mb
    help   1.1Mb
    libs  10.9Mb
installed size is  5.6Mb
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    shiny-squid   5.4Mb
installed size is 28.1Mb
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    doc    1.2Mb
    help   1.0Mb
    libs  25.6Mb
installed size is 104.3Mb
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    libs  103.8Mb
installed size is  5.1Mb
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    doc       1.6Mb
    lsndata   2.3Mb
installed size is 28.7Mb
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    libs  28.2Mb
installed size is 48.8Mb
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installed size is 17.0Mb
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    include  11.6Mb
    lib       3.3Mb
installed size is 90.0Mb
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installed size is  7.1Mb
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    libs   6.4Mb
installed size is  9.4Mb
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    data   3.0Mb
    libs   5.3Mb
installed size is  7.3Mb
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    extdata   2.4Mb
    libs      4.2Mb
installed size is  7.4Mb
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installed size is  6.2Mb
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installed size is  6.9Mb
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    libs   4.3Mb
installed size is 62.7Mb
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installed size is  6.0Mb
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installed size is  5.3Mb
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    libs   2.4Mb
installed size is  9.2Mb
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    doc    1.9Mb
    libs   6.4Mb
installed size is 28.3Mb
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    libs  26.7Mb
installed size is  9.4Mb
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    libs   7.1Mb
installed size is 10.4Mb
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installed size is 10.6Mb
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    libs   9.3Mb
installed size is 13.9Mb
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    doc    1.7Mb
    libs  10.9Mb
installed size is 34.7Mb
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    libs  33.9Mb
installed size is  9.8Mb
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    doc    7.1Mb
    libs   1.8Mb
installed size is  5.6Mb
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    libs   4.3Mb
installed size is 12.0Mb
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    libs  11.0Mb
installed size is  5.1Mb
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installed size is  6.0Mb
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installed size is  6.6Mb
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installed size is  8.4Mb
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installed size is 51.0Mb
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installed size is  6.8Mb
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    R      2.0Mb
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    libs   2.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  9.7Mb
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    R      2.0Mb
    data   2.3Mb
    doc    3.9Mb
installed size is 14.9Mb
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    doc    1.5Mb
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installed size is 63.6Mb
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    libs  63.0Mb
installed size is  9.0Mb
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    libs   7.2Mb
installed size is 44.4Mb
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    libs  43.9Mb
installed size is  5.7Mb
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    libs   5.0Mb
installed size is 45.7Mb
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    libs  44.8Mb
installed size is 19.8Mb
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installed size is  6.2Mb
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    R         2.3Mb
    extdata   3.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.5Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.3Mb
Packages required but not available: 'microbiome', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dearseq', 'GEOquery'
Package unavailable to check Rd xrefs: ‘dearseq’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
installed size is  5.1Mb
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    tklibs   4.7Mb
Package suggested but not available for checking: ‘igraph’
installed size is  9.7Mb
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    doc    7.5Mb
    libs   1.7Mb
installed size is 33.8Mb
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    libs  32.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.0Mb
installed size is 10.0Mb
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    libs   9.6Mb
installed size is 14.9Mb
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    libs  14.8Mb
installed size is  8.4Mb
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    doc    4.5Mb
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installed size is 293.7Mb
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installed size is 31.5Mb
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    libs       8.1Mb
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installed size is  9.0Mb
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installed size is  8.9Mb
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    libs   5.4Mb
installed size is  7.6Mb
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installed size is  5.4Mb
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installed size is 15.3Mb
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installed size is  7.2Mb
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installed size is 29.3Mb
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installed size is  5.2Mb
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Package suggested but not available for checking: ‘theftdlc’
installed size is  8.1Mb
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    R      5.0Mb
    data   3.0Mb
installed size is 52.9Mb
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Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is 47.1Mb
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installed size is  9.6Mb
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installed size is  5.1Mb
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installed size is 53.0Mb
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installed size is 11.3Mb
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Package suggested but not available for checking: ‘org.Rn.eg.db’
installed size is 60.5Mb
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installed size is  6.1Mb
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installed size is  7.3Mb
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installed size is 10.5Mb
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installed size is 16.4Mb
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installed size is 29.1Mb
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installed size is  6.1Mb
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    libs   5.1Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Package required but not available: ‘EnhancedVolcano’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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installed size is 211.8Mb
  sub-directories of 1Mb or more:
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    include    1.8Mb
    libs     201.6Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
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installed size is  6.3Mb
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installed size is 49.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  46.5Mb
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
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installed size is  5.9Mb
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installed size is  5.0Mb
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installed size is  5.3Mb
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installed size is 17.6Mb
  sub-directories of 1Mb or more:
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installed size is 123.5Mb
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    doc     3.9Mb
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installed size is 38.4Mb
  sub-directories of 1Mb or more:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/triptych.Rcheck/00install.out’ for details.
installed size is 33.6Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

SUMMARY: processing the following file failed:
  'tsglm.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
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    data   1.2Mb
    libs   9.3Mb
installed size is 43.8Mb
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    libs  43.2Mb
installed size is  8.6Mb
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    data   4.6Mb
    libs   2.6Mb
installed size is 96.8Mb
  sub-directories of 1Mb or more:
    libs  95.8Mb
installed size is 106.8Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     1.0Mb
    libs  103.5Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
installed size is 27.7Mb
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    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.4Mb
    libs  47.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 18.7Mb
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    libs  18.1Mb
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  36.2Mb
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 26.2Mb
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    doc    2.2Mb
    libs  23.8Mb
installed size is  9.4Mb
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    extdata   8.7Mb
installed size is  7.1Mb
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    libs   6.0Mb
installed size is 271.4Mb
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    extdata    2.8Mb
    libs     267.3Mb
installed size is  8.9Mb
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    libs   8.1Mb
installed size is  6.6Mb
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    libs   4.6Mb
Missing link or links in documentation object 'bigamma.mckay.Rd':
  ‘[VGAM]{gammaff.mm}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    help   3.2Mb
installed size is  5.2Mb
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    doc    2.7Mb
    libs   1.0Mb
installed size is 51.2Mb
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    doc    1.4Mb
    libs  49.5Mb
installed size is 10.8Mb
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    doc           2.0Mb
    htmlwidgets   6.9Mb
installed size is  6.4Mb
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    data   6.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     29.7Mb
installed size is 55.4Mb
  sub-directories of 1Mb or more:
    libs  55.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
Running ‘testthat.R’ [58s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  19: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  20: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  21: source_file(path, env = env(env), desc = desc, error_call = error_call)
  22: FUN(X[[i]], ...)
  23: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  28: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  29: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  30: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  31: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  32: test_check("wallace")
  An irrecoverable exception occurred. R is aborting now ...
installed size is  9.6Mb
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    R     2.1Mb
    doc   6.3Mb
installed size is 10.5Mb
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    client   9.4Mb
    doc      1.0Mb
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 40.7Mb
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    libs  39.8Mb
Package suggested but not available for checking: ‘ROTS’
installed size is  6.9Mb
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    data   3.4Mb
    help   1.9Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 54.1Mb
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    libs  53.2Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    java  28.5Mb
installed size is 25.8Mb
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    libs  25.4Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  42.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.6Mb
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  40.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.4Mb
installed size is 90.8Mb
  sub-directories of 1Mb or more:
    libs  89.8Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      9.5Mb
Running ‘testthat.R’ [583s/585s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3. ├─base::suppressWarnings(...) at test-simulateabn.R:799:7
   4. │ └─base::withCallingHandlers(...)
   5. └─abn::buildScoreCache(...) at test-simulateabn.R:800:9
   6.   └─abn::buildScoreCache.bayes(...)
   7.     └─... %do% ...
   8.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
   9.         └─base::library(p, character.only = TRUE)
  
  [ FAIL 30 | WARN 0 | SKIP 35 | PASS 485 ]
  Deleting unused snapshots:
  • tographviz/graph.dot
  • tographviz/graph1.dot
  • tographviz/graph_group.dot
  Error: Test failures
  Execution halted
installed size is  7.6Mb
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    doc    1.7Mb
    libs   5.6Mb
installed size is 15.0Mb
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Package suggested but not available for checking: ‘clinfun’
installed size is  9.2Mb
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    R      2.0Mb
    data   3.0Mb
    libs   2.7Mb
Packages suggested but not available for checking:
  'adespatial', 'hierfstat', 'spdep', 'poppr'
Package unavailable to check Rd xrefs: ‘spdep’
installed size is 10.4Mb
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    data  10.2Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  5.8Mb
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    libs   5.4Mb
Package unavailable to check Rd xrefs: ‘epiR’
installed size is  5.1Mb
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    libs   4.0Mb
Package which this enhances but not available for checking: ‘tripack’
Package unavailable to check Rd xrefs: ‘tripack’
installed size is 20.3Mb
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    libs  19.0Mb
Packages suggested but not available for checking: 'fBasics', 'Rmpfr'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [15s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   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(...)
  ── Error ('test-update.R:111:5'): render_docs also transform new/modified vignettes if specified: docsify ──
  Error in `render_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
Package suggested but not available for checking: ‘Biobase’
installed size is  5.7Mb
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    libs   3.7Mb
Package suggested but not available for checking: ‘AICcmodavg’
Package required but not available: ‘ctmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.0Mb
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    libs  23.5Mb
installed size is 29.0Mb
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    cereal   1.4Mb
    libs    27.5Mb
installed size is 35.6Mb
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    R  35.5Mb
Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
installed size is 10.6Mb
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    libs   9.1Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
installed size is  5.1Mb
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    libs   4.5Mb
installed size is  6.1Mb
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    R      2.0Mb
    doc    1.2Mb
    libs   1.8Mb
installed size is 30.4Mb
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    libs  30.1Mb
installed size is  5.8Mb
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    data   4.7Mb
installed size is 17.1Mb
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    libs  16.8Mb
Package unavailable to check Rd xrefs: ‘survey’
installed size is  6.2Mb
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    R             3.1Mb
    help          1.1Mb
    testScripts   1.1Mb
installed size is 356.7Mb
  sub-directories of 1Mb or more:
    R       5.0Mb
    libs  351.1Mb
Packages suggested but not available for checking: 'rJava', 'RWeka'
Package unavailable to check Rd xrefs: ‘RWeka’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
Package suggested but not available for checking: ‘AzureKeyVault’
installed size is  6.3Mb
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    data   6.2Mb
installed size is 117.3Mb
  sub-directories of 1Mb or more:
    libs  115.5Mb
Package suggested but not available for checking: ‘xgboost’
installed size is 97.8Mb
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    libs  96.0Mb
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  63.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   1.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is 71.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  68.3Mb
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is 133.2Mb
  sub-directories of 1Mb or more:
    doc     1.0Mb
    libs  131.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    doc   10.9Mb
    libs  12.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 67.1Mb
  sub-directories of 1Mb or more:
    libs  65.7Mb
installed size is 92.8Mb
  sub-directories of 1Mb or more:
    libs  91.8Mb
Package unavailable to check Rd xrefs: ‘fGarch’
installed size is 107.0Mb
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    libs  106.5Mb
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    libs  45.1Mb
installed size is 59.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs  55.6Mb
Package suggested but not available for checking: ‘sensitivity’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  10.4Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  20.4Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 70.0Mb
  sub-directories of 1Mb or more:
    libs  69.6Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs  14.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.7Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
Package unavailable to check Rd xrefs: ‘betareg’
Packages suggested but not available for checking: 'ssgraph', 'tmvtnorm'
Package unavailable to check Rd xrefs: ‘ssgraph’
installed size is 100.0Mb
  sub-directories of 1Mb or more:
    libs  98.5Mb
installed size is 49.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  46.5Mb
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
Package which this enhances but not available for checking: ‘caret’
installed size is 55.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  52.5Mb
Package suggested but not available for checking: ‘car’
Note: skipping ‘betareg.Rnw’ due to unavailable dependencies: 'car'
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   1.1Mb
    libs   7.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.1Mb
installed size is 167.4Mb
  sub-directories of 1Mb or more:
    include  167.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package suggested but not available for checking: ‘RODBC’
Package suggested but not available for checking: ‘RODBC’

Package which this enhances but not available for checking: ‘leaps’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  29.1Mb
Package suggested but not available for checking: ‘gaston’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.5Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  16.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.0Mb
installed size is 87.6Mb
  sub-directories of 1Mb or more:
    libs  87.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    help   2.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.8Mb
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: ‘Seurat’
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 140.9Mb
  sub-directories of 1Mb or more:
    R           2.0Mb
    libs      137.2Mb
    testdata    1.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.8Mb
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.1Mb
Package suggested but not available for checking: ‘reldist’
installed size is 177.5Mb
  sub-directories of 1Mb or more:
    libs  176.7Mb
installed size is 91.8Mb
  sub-directories of 1Mb or more:
    libs  91.2Mb
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
installed size is 93.3Mb
  sub-directories of 1Mb or more:
    libs  89.9Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BonEV.Rnw’ using Sweave
Error: processing vignette 'BonEV.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'BonEV.tex' failed.
LaTeX errors:
! LaTeX Error: File `underscore.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \parindent
               0in^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘BonEV.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 394.8Mb
  sub-directories of 1Mb or more:
    include   10.3Mb
    lib      384.1Mb
Package suggested but not available for checking: ‘sparsenet’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
Packages suggested but not available for checking:
  'RGtk2', 'cairoDevice', 'car', 'mediation'
Packages unavailable to check Rd xrefs: ‘car’, ‘mediation’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
Packages suggested but not available for checking:
  'BayesFactor', 'rstan', 'rstanarm', 'MCMCpack'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    doc   3.6Mb
Error(s) in re-building vignettes:
--- re-building ‘Brobdingnag.Rnw’ using Sweave
Loading required package: Brobdingnag
Loading required package: Matrix

Attaching package: ‘Brobdingnag’

The following objects are masked from ‘package:Matrix’:

    diag, t

The following objects are masked from ‘package:base’:

    diag, t

Error: processing vignette 'Brobdingnag.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Brobdingnag.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Brobdingnag.Rnw’

--- re-building ‘S4_brob.Rnw’ using Sweave
Creating a new generic function for ‘max’ in the global environment
Creating a new generic function for ‘min’ in the global environment
Creating a new generic function for ‘range’ in the global environment
Creating a new generic function for ‘prod’ in the global environment
Creating a new generic function for ‘sum’ in the global environment
Error: processing vignette 'S4_brob.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'S4_brob.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘S4_brob.Rnw’

SUMMARY: processing the following files failed:
  ‘Brobdingnag.Rnw’ ‘S4_brob.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 32.2Mb
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installed size is 110.2Mb
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installed size is 12.5Mb
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Package suggested but not available for checking: ‘gsl’
installed size is 23.1Mb
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installed size is 117.5Mb
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installed size is 18.8Mb
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installed size is 131.2Mb
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installed size is 41.2Mb
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installed size is 67.2Mb
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installed size is  9.8Mb
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Packages required but not available: 'org.Dr.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.6Mb
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installed size is  9.0Mb
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    R      2.0Mb
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installed size is 36.0Mb
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Package suggested but not available for checking: ‘alr4’
installed size is 22.6Mb
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installed size is  5.5Mb
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installed size is  5.5Mb
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installed size is  6.6Mb
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    R      2.4Mb
    libs   3.5Mb
installed size is 44.9Mb
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installed size is  6.4Mb
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installed size is 149.7Mb
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installed size is 17.9Mb
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installed size is 22.7Mb
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Package which this enhances but not available for checking: ‘mirt’
installed size is  6.1Mb
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Package unavailable to check Rd xrefs: ‘mirt’
installed size is 15.4Mb
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    libs   9.8Mb
Error(s) in re-building vignettes:
--- re-building ‘cem.Rnw’ using Sweave
Loading required package: cem
Loading required package: tcltk
Loading required package: lattice

How to use CEM? Type vignette("cem")

Loading required package: Amelia
Loading required package: Rcpp
## 
## Amelia II: Multiple Imputation
## (Version 1.8.1, built: 2022-11-18)
## Copyright (C) 2005-2023 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
## 
Error: processing vignette 'cem.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cem.tex' failed.
BibTeX errors:
The top-level auxiliary file: cem.aux
I couldn't open style file apsr.bst
---line 66 of file cem.aux
 : \bibstyle{apsr
 :               }
I'm skipping whatever remains of this command
I found no style file---while reading file cem.aux
--- failed re-building ‘cem.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘linkcomm’
installed size is  6.0Mb
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Packages suggested but not available for checking: 'drc', 'qpcR'
Package unavailable to check Rd xrefs: ‘qpcR’
Packages suggested but not available for checking: 'clustree', 'Seurat'
Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat'
installed size is  7.6Mb
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    R         2.8Mb
    extdata   4.3Mb
Packages required but not available:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
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installed size is  7.5Mb
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installed size is 13.5Mb
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installed size is  9.6Mb
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Package suggested but not available for checking: ‘seqHMM’
installed size is 17.3Mb
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installed size is 32.7Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘cloudUtil.Rnw’ using Sweave
Error: processing vignette 'cloudUtil.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cloudUtil.tex' failed.
LaTeX errors:
! LaTeX Error: File `pstricks.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cloudUtil.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
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installed size is 17.7Mb
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    libs  17.0Mb
installed size is  9.6Mb
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    libs   8.3Mb
Error(s) in re-building vignettes:
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’

Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘clValid.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.9Mb
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    libs  14.3Mb
installed size is  6.2Mb
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    data   6.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘weight_cause_cox.rnw’ using Sweave
Error: processing vignette 'weight_cause_cox.rnw' failed with diagnostics:
Running 'texi2dvi' on 'weight_cause_cox.tex' failed.
LaTeX errors:
! LaTeX Error: File `pgfplots.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \pgfplotsset
                 {compat=1.10}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘weight_cause_cox.rnw’

SUMMARY: processing the following file failed:
  ‘weight_cause_cox.rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cmvnorm.Rnw’ using Sweave

Attaching package: ‘cmvnorm’

The following objects are masked from ‘package:stats’:

    sd, var


Attaching package: ‘elliptic’

The following objects are masked from ‘package:cmvnorm’:

    Im<-, Re<-, sd

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'cmvnorm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cmvnorm.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cmvnorm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 33.3Mb
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    libs  33.1Mb
installed size is  6.2Mb
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    R      2.0Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘wTO’
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  11.5Mb
installed size is 51.8Mb
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    libs  51.0Mb
installed size is  6.6Mb
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    libs   5.4Mb
installed size is 16.4Mb
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    doc    1.8Mb
    libs  14.4Mb
Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'backShift', 'CAM', 'mboost',
  'huge', 'flare'
Package suggested but not available for checking: ‘rstan’
Running examples in ‘CompareMultipleModels-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_model_finder
> ### Title: Finding the Best Model Using Eight Metrics Values
> ### Aliases: best_model_finder
> 
> ### ** Examples
> 
> set.seed(123) # for reproducibility
> Y <- rnorm(100, 100, 10)
> model_1 <-CEEMDANML::carigaan(Y, ratio = 0.8, n_lag = 4)
Error in optim(init[mask], armafn, method = optim.method, hessian = TRUE,  : 
  non-finite finite-difference value [1]
Calls: <Anonymous> -> arima -> optim
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘compare-intro.Rnw’ using Sweave
Error: processing vignette 'compare-intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'compare-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref} % for \url^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘compare-intro.Rnw’

--- re-building ‘fundamentals.Rnw’ using Sweave

Attaching package: ‘compare’

The following object is masked from ‘package:base’:

    isTRUE

--- finished re-building ‘fundamentals.Rnw’

SUMMARY: processing the following file failed:
  ‘compare-intro.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 28.0Mb
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Packages suggested but not available for checking:
  'scagnostics', 'parsnip', 'C50', 'bartMachine', 'caret'
Packages suggested but not available for checking:
  'conosPanel', 'org.Mm.eg.db', 'p2data', 'rhdf5'
installed size is 11.3Mb
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installed size is 20.6Mb
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    libs  20.4Mb
installed size is 70.2Mb
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    libs  68.9Mb
Package required but not available: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.5Mb
Package suggested but not available for checking: ‘BiocParallel’
installed size is  5.4Mb
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    libs          2.7Mb
    sample_data   2.6Mb
installed size is  5.0Mb
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    extdata   3.8Mb
Package suggested but not available for checking: ‘rstanarm’
installed size is  6.0Mb
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Package suggested but not available for checking: ‘tidymodels’
installed size is  8.5Mb
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    doc    1.9Mb
    libs   5.5Mb
installed size is  7.0Mb
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    libs   6.9Mb
installed size is 41.6Mb
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installed size is  5.3Mb
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    data   4.1Mb
installed size is 26.8Mb
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Error(s) in re-building vignettes:
--- re-building ‘crs.Rnw’ using Sweave
Registered S3 method overwritten by 'crs':
  method         from
  predict.gsl.bs np  
Categorical Regression Splines (version 0.15-37)
[vignette("crs_faq") provides answers to frequently asked questions]
--- finished re-building ‘crs.Rnw’

--- re-building ‘crs_faq.Rnw’ using Sweave
--- finished re-building ‘crs_faq.Rnw’

--- re-building ‘spline_primer.Rnw’ using Sweave
Registered S3 method overwritten by 'crs':
  method         from
  predict.gsl.bs np  
Categorical Regression Splines (version 0.15-37)
[vignette("crs_faq") provides answers to frequently asked questions]
Error: processing vignette 'spline_primer.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'spline_primer.tex' failed.
LaTeX errors:
! LaTeX Error: File `harvard.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘spline_primer.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
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    data   4.1Mb
    doc    1.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is 180.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    2.0Mb
    libs  175.5Mb
Running ‘testthat.R’ [73s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Chain 1: Iteration: 290 / 300 [ 96%]  (Sampling)
  Chain 2: Iteration: 190 / 300 [ 63%]  (Sampling)
  Chain 1: Iteration: 300 / 300 [100%]  (Sampling)
  Chain 1: 
  Chain 1:  Elapsed Time: 22.012 seconds (Warm-up)
  Chain 1:                17.161 seconds (Sampling)
  Chain 1:                39.173 seconds (Total)
  Chain 1: 
  Chain 2: Iteration: 210 / 300 [ 70%]  (Sampling)
  Chain 2: Iteration: 230 / 300 [ 76%]  (Sampling)
  Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)
  Chain 2: Iteration: 270 / 300 [ 90%]  (Sampling)
  Chain 2: Iteration: 290 / 300 [ 96%]  (Sampling)
  
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    libs   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.1Mb
    libs   3.0Mb
Package suggested but not available for checking: ‘lme4’
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
Error(s) in re-building vignettes:
--- re-building ‘DBR.Rnw’ using Sweave
DBR 1.4.1
Bayesian Discretized Beta Regression for the Analysis of Ratings Data
Warning in cor.test.default(pain$severity, pain$interference, method = "spearman") :
  Cannot compute exact p-value with ties
Warning in cor.test.default(pain$age, pain$interference, method = "spearman") :
  Cannot compute exact p-value with ties
Warning in ks.test.default(pred_sample, pain$interference) :
  p-value will be approximate in the presence of ties
Error: processing vignette 'DBR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'DBR.tex' failed.
LaTeX errors:
! LaTeX Error: File `breqn.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 \usepackage
                {atbegshi}% http://ctan.org/pkg/atbegshi^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘DBR.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.3Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
Packages suggested but not available for checking: 'EMD', 'astrochron'
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tram', 'cotram'
Package unavailable to check Rd xrefs: ‘tram’
Package suggested but not available for checking: ‘missMDA’
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  33.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘desirability.Rnw’ using Sweave
Error: processing vignette 'desirability.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'desirability.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm2e.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘desirability.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Packages suggested but not available for checking: 'psych', 'sirt'
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.9Mb
Package suggested but not available for checking: ‘GOstats’
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.1Mb
Packages suggested but not available for checking: 'spaMM', 'glmmTMB'

Packages which this enhances but not available for checking:
  'rstan', 'BayesianTools'
Packages suggested but not available for checking: 'KrigInv', 'GPareto'
Package unavailable to check Rd xrefs: ‘KrigInv’
Package suggested but not available for checking: ‘parallelDist’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dirmcmc_vignette.Rnw’ using Sweave
Error: processing vignette 'dirmcmc_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'dirmcmc_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘dirmcmc_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is 87.5Mb
  sub-directories of 1Mb or more:
    libs  86.7Mb
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
Error(s) in re-building vignettes:
--- re-building ‘dlsem_vignette.Rnw’ using Sweave
Loading required package: dlsem
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
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    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Rgraphviz
Loading required package: grid
Error: processing vignette 'dlsem_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'dlsem_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘dlsem_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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installed size is  7.5Mb
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Package suggested but not available for checking: ‘PerformanceAnalytics’
installed size is  6.3Mb
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installed size is 12.9Mb
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Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.8Mb
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Package unavailable to check Rd xrefs: ‘warbleR’
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Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

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Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
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! LaTeX Error: File `dsfont.sty' not found.

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l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

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Error: processing vignette 'residuetheorem.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'residuetheorem.tex' failed.
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! LaTeX Error: File `dsfont.sty' not found.

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l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following files failed:
  ‘ellipticpaper.Rnw’ ‘residuetheorem.Rnw’

Error: Vignette re-building failed.
Execution halted
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Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
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Package suggested but not available for checking: ‘DESeq2’
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Package suggested but not available for checking: ‘fields’
installed size is 14.9Mb
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installed size is 14.1Mb
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installed size is 36.3Mb
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Running ‘testthat.R’ [14s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  attr(,"class")
  [1] "gg"     "ggplot"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(phyloseq)`: there is no package called 'phyloseq'
  Backtrace:
      ▆
   1. └─base::library(phyloseq) at test-ilr.R:11:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  Error: Test failures
  Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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installed size is 315.7Mb
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Packages suggested but not available for checking:
  'flexsurvcure', 'survminer'
Error(s) in re-building vignettes:
--- re-building ‘standsurv.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 85-90 (standsurv.Rmd) 
Error: processing vignette 'standsurv.Rmd' failed with diagnostics:
there is no package called 'flexsurvcure'
--- failed re-building ‘standsurv.Rmd’

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

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

--- re-building ‘distributions.Rnw’ using Sweave
--- finished re-building ‘distributions.Rnw’

--- re-building ‘flexsurv-examples.Rnw’ using Sweave
Loading required package: survival
Forming integrated rmst function...
Forming integrated mean function...
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser

--- finished re-building ‘flexsurv-examples.Rnw’

SUMMARY: processing the following file failed:
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Package suggested but not available for checking: ‘Mcomp’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/frailtypack.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘lala2015frbs.ltx’ using tex
--- finished re-building ‘lala2015frbs.ltx’

--- re-building ‘lala2015pmml.Rtex’ using Sweave
Warning in mean.default((real.val - res.test)^2) :
  argument is not numeric or logical: returning NA
Error: processing vignette 'lala2015pmml.Rtex' failed with diagnostics:
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LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

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! Emergency stop.
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l.4 \usepackage
               {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'lala2015pmml.Rtex'

SUMMARY: processing the following file failed:
  ‘lala2015pmml.Rtex’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘MARSS’
Packages suggested but not available for checking: 'fda', 'MARSS'
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installed size is 37.2Mb
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installed size is 14.0Mb
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Error(s) in re-building vignettes:
--- re-building ‘gamboostLSS_Tutorial.Rnw’ using Sweave
Loading required package: R2BayesX
Loading required package: BayesXsrc
Loading required package: colorspace
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-42. For overview type 'help("mgcv-package")'.
Loading required package: gamboostLSS
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs

Attaching package: 'gamboostLSS'

The following object is masked from 'package:stats':

    model.weights

Loading required namespace: BayesX
Error: processing vignette 'gamboostLSS_Tutorial.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gamboostLSS_Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'gamboostLSS_Tutorial.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘caret’
installed size is  9.6Mb
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installed size is 16.7Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/gdalBindings.Rcheck/00install.out’ for details.
installed size is 284.6Mb
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installed size is 11.4Mb
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--- re-building ‘geosphere.Rnw’ using Sweave
Loading required namespace: raster
Error: processing vignette 'geosphere.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'geosphere.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘geosphere.Rnw’

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Error: Vignette re-building failed.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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Packages suggested but not available for checking:
  'car', 'NetworkToolbox', 'NetworkComparisonTest'
installed size is  7.6Mb
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    doc    3.9Mb
    libs   2.1Mb
Packages suggested but not available for checking: 'psych', 'psychTools'
installed size is  8.7Mb
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    libs   8.6Mb
installed size is  5.6Mb
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    doc    1.7Mb
    libs   3.4Mb
installed size is  6.6Mb
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    libs   6.2Mb
installed size is 116.6Mb
  sub-directories of 1Mb or more:
    doc     1.4Mb
    libs  114.3Mb
installed size is 17.5Mb
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    libs  17.0Mb
Package suggested but not available for checking: ‘mlmRev’
installed size is 67.4Mb
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    libs  66.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 59.0Mb
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    libs  57.8Mb
installed size is 168.4Mb
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    libs  167.0Mb
installed size is 49.0Mb
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    libs  48.8Mb
installed size is 97.7Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs           92.3Mb
    test_data       2.3Mb
    vignette_data   1.1Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Package suggested but not available for checking: ‘AER’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.3Mb
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
Package unavailable to check Rd xrefs: ‘caret’
Package suggested but not available for checking: ‘SeqVarTools’
installed size is  7.9Mb
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    libs   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Package unavailable to check Rd xrefs: ‘repeated’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
installed size is 192.0Mb
  sub-directories of 1Mb or more:
    libs  191.1Mb
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Failure ('test_predict.GP.R:64:9'): check predict.GP ─────────────────────
  smse2 >= 0 & smse2 < 30 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Failure ('test_predict.GP.R:81:9'): check predict.GP ─────────────────────
  sum(gpp2$complete_data[, 5] - ms2 < 1e-05) >= 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
installed size is  8.0Mb
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    data   1.4Mb
    libs   6.1Mb
Error(s) in re-building vignettes:
--- re-building ‘gplm-examples.Rnw’ using Sweave
Loading required package: AER
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: survival
Error: processing vignette 'gplm-examples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gplm-examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.20 \usepackage
                {comment}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gplm-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘gplm-examples.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
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    libs  10.8Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  10.0Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Packages unavailable to check Rd xrefs: ‘repeated’, ‘gnlm’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    doc    1.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   3.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   2.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.7Mb
installed size is 275.7Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    help    1.0Mb
    java  272.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HAC.Rnw’ using Sweave
Loading required package: copula
Warning in hac2nacopula(hac) : NAs introduced by coercion
Error: processing vignette 'HAC.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'HAC.tex' failed.
LaTeX errors:
! LaTeX Error: File `german.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.47 \selectlanguage
                    {english}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'HAC.Rnw'

SUMMARY: processing the following file failed:
  'HAC.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building ‘HardyWeinberg.Rnw’ using Sweave
Loading required package: mice

Attaching package: 'mice'

The following object is masked from 'package:stats':

    filter

The following objects are masked from 'package:base':

    cbind, rbind

Loading required package: Rsolnp
Loading required package: nnet
Warning: Number of logged events: 1
Warning: Number of logged events: 1
Error: processing vignette 'HardyWeinberg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'HardyWeinberg.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'HardyWeinberg.Rnw'

SUMMARY: processing the following file failed:
  'HardyWeinberg.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.6Mb
    libs   6.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 161.5Mb
  sub-directories of 1Mb or more:
    libs  159.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   1.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
    libs   4.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.9Mb
    libs   1.4Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  19.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Packages suggested but not available for checking:
  'marray', 'affy', 'Biobase', 'limma'
Package unavailable to check Rd xrefs: ‘limma’
Note: skipping ‘hexagon_binning.Rnw’ due to unavailable dependencies:
  'marray'
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Package suggested but not available for checking: ‘geojsonio’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.6Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  58.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is 69.9Mb
  sub-directories of 1Mb or more:
    libs  69.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.4Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Package suggested but not available for checking: ‘jack’
Error(s) in re-building vignettes:
--- re-building ‘hypergeometric.Rnw’ using Sweave
Loading required package: hypergeo
Loading required package: elliptic

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Error: processing vignette 'hypergeometric.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'hypergeometric.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘hypergeometric.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
installed size is  5.8Mb
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    data   5.6Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.7Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  30.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.6Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    help   2.1Mb
    libs  18.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.2Mb
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     23.5Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs   12.3Mb
    share  10.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  29.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data           1.4Mb
    libs           1.9Mb
    shiny-server   1.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Note: skipping ‘tecator.Rmd’ due to unavailable dependencies: 'caret'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 64.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs  59.2Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  15.1Mb
Package unavailable to check Rd xrefs: ‘AER’
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          17.3Mb
installed size is 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
Packages which this enhances but not available for checking:
  'remMap', 'mcen', 'RMTL'
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   7.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   2.4Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.1Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  48.7Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    doc       1.5Mb
    extdata   1.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   9.6Mb
installed size is 95.4Mb
  sub-directories of 1Mb or more:
    libs  94.1Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  44.1Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      9.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    2.1Mb
    libs   1.5Mb
installed size is 64.2Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      20.3Mb
    testdata   1.3Mb
Package suggested but not available for checking: ‘pbkrtest’
Package unavailable to check Rd xrefs: ‘pbkrtest’
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  54.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Packages suggested but not available for checking: 'car', 'dynlm', 'AER'
Package unavailable to check Rd xrefs: ‘car’
installed size is 62.9Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  33.0Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘lorentz.Rnw’ using Sweave
Loading required package: magrittr
Error: processing vignette 'lorentz.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'lorentz.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘lorentz.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    libs  49.3Mb
Packages suggested but not available for checking:
  'sirt', 'kerdiest', 'car', 'mitml'
Package suggested but not available for checking: ‘LSDsensitivity’
Package unavailable to check Rd xrefs: ‘LSDsensitivity’
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  43.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.0Mb
    libs   1.9Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 71.7Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  64.7Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
Packages suggested but not available for checking:
  'ssize', 'WGCNA', 'KEGGgraph', 'pdInfoBuilder', 'lumi', 'oligo',
  'affy', 'genefilter', 'beadarray', 'GOstats', 'Category', 'impute'
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   3.1Mb
    libs   4.9Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Package suggested but not available for checking: ‘DescTools’
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs         15.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   3.0Mb
    libs   4.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.9Mb
Packages suggested but not available for checking: 'csampling', 'nlreg'
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      10.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'org.Mm.eg.db', 'wiggleplotr'
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.3Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   8.7Mb
Package suggested but not available for checking: ‘MBSP’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.9Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
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Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
* checking re-building of vignette outputs ...* using check arguments '--no-clean-on-error '
installed size is 38.8Mb
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    libs  37.6Mb
installed size is 16.3Mb
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    libs  15.8Mb
installed size is 18.6Mb
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    R      2.0Mb
    libs  16.0Mb
installed size is  6.5Mb
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    libs   5.9Mb
installed size is 64.7Mb
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    libs  63.3Mb
installed size is 33.2Mb
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    libs  32.0Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
installed size is 156.9Mb
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    libs  155.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
installed size is  8.6Mb
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    extdata   3.4Mb
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installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  8.7Mb
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    data   2.7Mb
    libs   5.5Mb
installed size is 109.1Mb
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    libs  108.3Mb
installed size is  6.2Mb
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    R      3.0Mb
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Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
installed size is 20.2Mb
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installed size is 56.8Mb
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    libs  56.3Mb
installed size is  7.3Mb
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    doc    2.3Mb
    help   2.0Mb
    libs   2.6Mb
installed size is 13.3Mb
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    libs  12.0Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    libs  21.9Mb
installed size is  9.8Mb
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    R      1.0Mb
    data   1.1Mb
    libs   6.8Mb
installed size is  5.3Mb
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    R      2.0Mb
    libs   2.1Mb
installed size is 19.9Mb
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    doc    1.7Mb
    libs  17.3Mb
installed size is  7.4Mb
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    libs   5.8Mb
installed size is  9.4Mb
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    libs   8.2Mb
installed size is  5.5Mb
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    data   2.9Mb
    doc    1.7Mb
installed size is 20.9Mb
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    libs  20.8Mb
installed size is 112.9Mb
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    libs  112.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.4Mb
Packages unavailable to check Rd xrefs: ‘lme4’, ‘mixAK’
Package unavailable to check Rd xrefs: ‘list’
Package suggested but not available for checking: ‘glmmTMB’
Packages suggested but not available for checking:
  'clustree', 'karyoploteR', 'regioneR'
installed size is 13.5Mb
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    libs  13.4Mb
installed size is  8.3Mb
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    data   2.3Mb
    libs   4.5Mb
Package unavailable to check Rd xrefs: ‘genefilter’
installed size is  5.2Mb
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    R      2.8Mb
    help   2.4Mb
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
installed size is 240.9Mb
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    include    9.6Mb
    libs     230.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
installed size is 34.5Mb
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    libs  34.0Mb
installed size is 20.5Mb
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    libs  19.7Mb
installed size is 16.6Mb
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    doc    1.3Mb
    libs  14.8Mb
installed size is 19.0Mb
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    libs  18.9Mb
installed size is 121.9Mb
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    libs  120.0Mb
installed size is 14.4Mb
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    libs  14.1Mb
Running ‘testthat.R’ [73s/138s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ──
  Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
    You first need to install it, which you can do with:
        library(BiocManager)
        install("BSgenome.Hsapiens.UCSC.hg19")
  Backtrace:
      ▆
   1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 2 | WARN 14 | SKIP 23 | PASS 21 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘survey’
installed size is 10.1Mb
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    libs   8.6Mb
installed size is  8.8Mb
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    R      2.0Mb
    doc    1.7Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘tmvtnorm’
Packages suggested but not available for checking: 'fftw', 'RODBC'
Packages unavailable to check Rd xrefs: ‘seewave’, ‘RODBC’
installed size is 11.0Mb
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    data   2.0Mb
    libs   7.3Mb
installed size is  6.3Mb
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    libs     3.0Mb
    raster   2.2Mb
Package suggested but not available for checking: ‘ergm’
installed size is  5.7Mb
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    data   2.3Mb
    libs   2.6Mb
Packages suggested but not available for checking: 'ctmm', 'amt'
Packages unavailable to check Rd xrefs: ‘ctmm’, ‘amt’
Packages suggested but not available for checking: 'mvoutlier', 'glmulti'
installed size is  9.7Mb
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    libs   8.5Mb
installed size is 65.4Mb
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    libs  65.1Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  13.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   4.5Mb
    libs   3.5Mb
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  45.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Package suggested but not available for checking: ‘ICAMS’
installed size is  6.1Mb
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    libs   4.5Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 86.0Mb
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    libs  85.8Mb
Package suggested but not available for checking: ‘statnet’
installed size is 278.2Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.4Mb
    libs  271.1Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  36.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Package unavailable to check Rd xrefs: ‘sampleSelection’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.6Mb
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    data     2.9Mb
    libs    24.0Mb
    models   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NBLAST-Clustering.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 21:31:32.757 R[43986:2287591920] XType: Using static font registry.

Quitting from lines 57-60 [unnamed-chunk-5] (NBLAST-Clustering.Rmd)
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
--- failed re-building ‘NBLAST-Clustering.Rmd’

SUMMARY: processing the following file failed:
  ‘NBLAST-Clustering.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
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    data   4.5Mb
    doc    1.7Mb
installed size is 13.9Mb
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    data   2.1Mb
    doc    6.5Mb
    libs   4.8Mb
installed size is  6.3Mb
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    data   1.5Mb
    libs   3.9Mb
installed size is 25.6Mb
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    libs  23.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.6Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
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    doc    1.7Mb
    libs   5.6Mb
installed size is 233.3Mb
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    libs  232.5Mb
installed size is 43.3Mb
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installed size is  8.0Mb
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installed size is 19.1Mb
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Package suggested but not available for checking: ‘csampling’
Package unavailable to check Rd xrefs: ‘csampling’
installed size is  9.7Mb
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installed size is 10.7Mb
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installed size is  6.3Mb
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    data   5.0Mb
installed size is 21.0Mb
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installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       5.7Mb
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installed size is  6.3Mb
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installed size is 12.9Mb
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
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    libs   1.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Running ‘testthat.R’ [27s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(odpc)
  > 
  > test_check("odpc")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_old_ver.R:75:3'): Equality with stored lambda for DFM model for single component sparse odpc ──
  sparse_fit[[1]]$lambda not equal to `old_lambda_sparse_dfm`.
  1/1 mismatches
  [1] 0.462 - 1.38 == -0.913
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
installed size is 92.1Mb
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installed size is 47.2Mb
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installed size is 39.6Mb
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installed size is  5.6Mb
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installed size is  6.3Mb
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installed size is 33.4Mb
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    share  10.2Mb
installed size is 10.7Mb
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    doc    2.4Mb
    libs   7.2Mb
installed size is 204.5Mb
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    R         3.1Mb
    data      1.4Mb
    libs    192.9Mb
    models    4.7Mb
installed size is  6.6Mb
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    doc    2.6Mb
    libs   3.6Mb
installed size is 11.2Mb
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    doc    1.5Mb
    libs   7.3Mb
installed size is  6.9Mb
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    extdata   1.1Mb
    libs      4.7Mb
installed size is 34.9Mb
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    extdata   2.1Mb
    libs     31.2Mb
installed size is  7.9Mb
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    libs   6.2Mb
installed size is 10.0Mb
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    libs   9.7Mb
installed size is 12.0Mb
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installed size is 16.2Mb
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installed size is  6.8Mb
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    doc    1.1Mb
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installed size is  5.8Mb
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    extdata   4.3Mb
Packages suggested but not available for checking:
  'org.Dr.eg.db', 'org.Mm.eg.db', 'scde'
installed size is  5.7Mb
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    data   5.1Mb
installed size is  8.6Mb
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installed size is 16.2Mb
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    libs  15.8Mb
installed size is  5.9Mb
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    libs   4.2Mb
installed size is 46.2Mb
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    doc    3.3Mb
    libs  42.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.9Mb
Error(s) in re-building vignettes:
--- re-building ‘partitionspaper.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'partitionspaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘partitionspaper.Rnw’

--- re-building ‘scrabble.Rnw’ using Sweave
Error: processing vignette 'scrabble.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'scrabble.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘scrabble.Rnw’

--- re-building ‘setpartitions.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'setpartitions.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'setpartitions.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘setpartitions.Rnw’

SUMMARY: processing the following files failed:
  ‘partitionspaper.Rnw’ ‘scrabble.Rnw’ ‘setpartitions.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
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    R      3.9Mb
    data   1.5Mb
installed size is 10.7Mb
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installed size is  6.8Mb
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    help   3.5Mb
installed size is  6.8Mb
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    R      3.1Mb
    help   3.5Mb
installed size is  6.9Mb
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    R      3.1Mb
    help   3.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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    doc    1.1Mb
    libs   1.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.6Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
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installed size is 140.0Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
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installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.1Mb
installed size is 21.3Mb
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    libs    8.5Mb
    share  12.8Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
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Packages suggested but not available for checking:
  'car', 'fields', 'georob', 'gstat'
Packages unavailable to check Rd xrefs: ‘fields’, ‘gstat’, ‘car’
installed size is 126.0Mb
  sub-directories of 1Mb or more:
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installed size is 10.2Mb
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installed size is 51.2Mb
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    libs  50.1Mb
installed size is 11.3Mb
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Package unavailable to check Rd xrefs: ‘lme4’
Packages suggested but not available for checking: 'Biostrings', 'seqLogo'
installed size is  7.7Mb
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    libs   3.7Mb
Package unavailable to check Rd xrefs: ‘phase1RMD’
Packages suggested but not available for checking:
  'randomForestSRC', 'xgboost'
installed size is  5.4Mb
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installed size is  5.7Mb
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installed size is  5.8Mb
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installed size is 46.5Mb
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installed size is  5.1Mb
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Packages suggested but not available for checking: 'INLA', 'DHARMa', 'rr2'
installed size is 12.4Mb
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    doc    2.0Mb
    libs   9.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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    data   2.1Mb
    doc    2.0Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
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installed size is  6.1Mb
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installed size is 23.5Mb
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Package suggested but not available for checking: ‘ellipse’
installed size is 18.8Mb
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installed size is  7.0Mb
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installed size is  7.6Mb
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installed size is 13.3Mb
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installed size is  6.4Mb
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installed size is  7.1Mb
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installed size is 40.3Mb
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installed size is  6.7Mb
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installed size is 39.4Mb
  sub-directories of 1Mb or more:
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installed size is 13.2Mb
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Package unavailable to check Rd xrefs: ‘rstan’
installed size is  7.3Mb
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installed size is  5.0Mb
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installed size is  8.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
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installed size is 11.7Mb
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installed size is  5.4Mb
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installed size is  5.0Mb
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    data   4.9Mb
Package suggested but not available for checking: ‘bipartite’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.8Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    4.7Mb
    libs  11.2Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  12.7Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.6Mb
installed size is 123.0Mb
  sub-directories of 1Mb or more:
    libs  122.6Mb
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is 139.0Mb
  sub-directories of 1Mb or more:
    libs  138.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.1Mb
installed size is 33.2Mb
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    libs  32.8Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Package suggested but not available for checking: ‘rCBA’
installed size is 81.7Mb
  sub-directories of 1Mb or more:
    libs  81.0Mb
installed size is 108.7Mb
  sub-directories of 1Mb or more:
    libs  107.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Packages suggested but not available for checking: 'glmmTMB', 'DHARMa'
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.6Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     32.8Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.6Mb
Packages suggested but not available for checking:
  'faraway', 'quantoptr', 'survminer'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   5.9Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Packages suggested but not available for checking: 'caret', 'xgboost'
'library' or 'require' call to ‘RDCOMClient’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs         16.2Mb
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.5Mb
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Package suggested but not available for checking: ‘quanteda.textmodels’
Error(s) in re-building vignettes:
--- re-building ‘fullpres.Rnw’ using Sweave
Loading required package: rngWELL
This is randtoolbox. For an overview, type 'help("randtoolbox")'.
Warning in sobol(10^3, 2, scrambling = 1) :
  scrambling is currently disabled.
Warning in sobol(10^3, 2, scrambling = 2) :
  scrambling is currently disabled.
Warning in coll.test(runif, 2^7, 2^10, 1, echo = FALSE) :
  p-values will be approximated in the presence of low expected collision number.
Warning in coll.test(congruRand, 2^8, 2^14, 1, echo = FALSE) :
  p-values will be approximated in the presence of low expected collision number.
Error: processing vignette 'fullpres.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'fullpres.tex' failed.
LaTeX errors:
! LaTeX Error: File `perpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.79 \MakePerPage
                 [1]{footnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘fullpres.Rnw’

--- re-building ‘shortintro.Rnw’ using Sweave
Loading required package: rngWELL
This is randtoolbox. For an overview, type 'help("randtoolbox")'.
Warning in RNGkind("default") :
  someone corrupted the random-number generator: re-initializing
Error: processing vignette 'shortintro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'shortintro.tex' failed.
LaTeX errors:
! LaTeX Error: File `perpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.87 \MakePerPage
                 [1]{footnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘shortintro.Rnw’

SUMMARY: processing the following files failed:
  ‘fullpres.Rnw’ ‘shortintro.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘RankAggreg.Rnw’ using Sweave
Loading required package: cluster
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: ‘kohonen’

The following object is masked from ‘package:mclust’:

    map

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘RankAggreg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   6.7Mb
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.6Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs  10.7Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs  56.5Mb
installed size is 60.1Mb
  sub-directories of 1Mb or more:
    libs  59.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.3Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 64.3Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.9Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs          12.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.5Mb
Package suggested but not available for checking: ‘evolMap’
Unavailable namespace imported from by a ':::' call: ‘evolMap’
  See the note in ?`:::` about the use of this operator.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rDNAse.Rnw’ using Sweave
Loading required package: rDNAse
Error: processing vignette 'rDNAse.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rDNAse.tex' failed.
LaTeX errors:
! LaTeX Error: File `tablefootnote.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘rDNAse.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
    libs   1.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.0Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs  14.6Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.8Mb
Packages suggested but not available for checking: 'cdparcoord', 'partools'
Package suggested but not available for checking: ‘ggpubr’
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.1Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  13.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     20.8Mb
    models    1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
Running ‘testthat.R’ [64s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    doc     3.0Mb
    fonts   1.5Mb
    libs   24.8Mb
Running examples in ‘ridge-Ex.R’ failed
The error most likely occurred in:

> ### Name: pvals
> ### Title: Compute p-values for ridgeLinear and ridgeLogistic models
> ### Aliases: pvals pvals.ridgeLinear pvals.ridgeLogistic
> ###   plot.pvalsRidgeLinear plot.pvalsRidgeLogistic print.pvalsRidgeLinear
> ###   print.pvalsRidgeLogistic
> 
> ### ** Examples
> 
> data(GenBin)
> mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))

Execution halted
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.3Mb
Package suggested but not available for checking: ‘portfolioBacktest’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs     18.4Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.0Mb
installed size is 106.7Mb
  sub-directories of 1Mb or more:
    libs  105.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rlibkriging.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Running ‘testthat.R’ [38s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─testthat::expect_warning(...) at test_downstream.R:245:9
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─testthat::expect_is(...) at test_downstream.R:246:13
    7. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    8. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    9. └─rliger::runGSEA(pbmcPlot, genesets = "Immune System")
   10.   └─cli::cli_abort("Package {.pkg reactome.db} is needed for this function to work.\n            Please install it by command:\n            {.code BiocManager::install('reactome.db')}")
   11.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 1039 ]
  Error: Test failures
  Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RMark.Rcheck/00install.out’ for details.
installed size is 135.1Mb
  sub-directories of 1Mb or more:
    libs  134.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmpi.Rcheck/00install.out’ for details.
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Package suggested but not available for checking: ‘recount3’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    2.2Mb
installed size is 102.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     99.9Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Package suggested but not available for checking: ‘robustbase’
Error(s) in re-building vignettes:
--- re-building ‘RobPer_vignette.Rnw’ using Sweave
Loading required package: robustbase
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: splines
Loading required package: BB
Loading required package: rgenoud
##  rgenoud (Version 5.9-0.3, Build Date: 2022-04-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error: processing vignette 'RobPer_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'RobPer_vignette.Rnw'

SUMMARY: processing the following file failed:
  'RobPer_vignette.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 87.8Mb
  sub-directories of 1Mb or more:
    libs  87.1Mb
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
Packages suggested but not available for checking: 'car', 'HH'
Package unavailable to check Rd xrefs: ‘HH’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         3.7Mb
    extdata   2.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ROracle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘MBESS’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.3Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs   7.8Mb
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.9Mb
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  52.0Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is 89.4Mb
  sub-directories of 1Mb or more:
    libs  88.8Mb
Packages suggested but not available for checking: 'fields', 'qgraph'
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is 299.3Mb
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installed size is 68.1Mb
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installed size is 37.4Mb
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installed size is 49.8Mb
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installed size is  5.2Mb
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installed size is 37.8Mb
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installed size is 28.0Mb
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installed size is 23.7Mb
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installed size is  5.9Mb
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installed size is  5.7Mb
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installed size is  7.3Mb
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installed size is 100.2Mb
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installed size is  8.4Mb
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installed size is 28.6Mb
  sub-directories of 1Mb or more:
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installed size is 222.2Mb
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installed size is  7.8Mb
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installed size is 11.7Mb
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installed size is 45.4Mb
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installed size is 59.2Mb
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installed size is  5.9Mb
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Package suggested but not available for checking: ‘partykit’
Package unavailable to check Rd xrefs: ‘partykit’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
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installed size is  6.4Mb
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installed size is  5.5Mb
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installed size is 16.0Mb
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installed size is 30.1Mb
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installed size is  9.5Mb
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installed size is  9.5Mb
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installed size is 10.3Mb
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installed size is 37.8Mb
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installed size is 16.8Mb
  sub-directories of 1Mb or more:
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installed size is 15.0Mb
  sub-directories of 1Mb or more:
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Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
installed size is 20.5Mb
  sub-directories of 1Mb or more:
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installed size is 44.8Mb
  sub-directories of 1Mb or more:
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installed size is 10.0Mb
  sub-directories of 1Mb or more:
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    libs   3.8Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'car', 'ergm', 'networkTomography',
  'org.Sc.sgd.db'
installed size is 47.7Mb
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installed size is  5.3Mb
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installed size is  5.2Mb
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
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installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
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installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using Sweave
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’

Attaching package: ‘scuba’

The following objects are masked _by_ ‘.GlobalEnv’:

    pedro902, pedro903, pedro904, pedro922, pedro943, pedro944,
    pedro945, pedro946, pedro948, pedro949, pedro950

Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \marginsize
               {2cm}{2cm}{2cm}{2cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.5Mb
installed size is 10.0Mb
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    libs   9.1Mb
installed size is 89.2Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
Error(s) in re-building vignettes:
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sealasso.Rnw’ using Sweave
Loading required package: lars
Loaded lars 1.3

Error: processing vignette 'sealasso.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sealasso.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \marginsize
               {2.5cm}{2.5cm}{2.5cm}{2.5cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sealasso.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.2Mb
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    R   8.6Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
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installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   7.8Mb
Packages suggested but not available for checking:
  'ArrayExpress', 'org.Mm.eg.db'
Package suggested but not available for checking: ‘Rmpfr’
Package suggested but not available for checking: ‘Ecdat’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Package which this enhances but not available for checking: ‘semPlot’
Packages suggested but not available for checking: 'blavaan', 'emmeans'
Package unavailable to check Rd xrefs: ‘blavaan’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
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installed size is 22.8Mb
  sub-directories of 1Mb or more:
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
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installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Packages suggested but not available for checking:
  'FactoMineR', 'descriptio'
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.2Mb
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    libs  17.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
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installed size is 16.0Mb
  sub-directories of 1Mb or more:
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installed size is 11.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘ggraph’
installed size is 268.6Mb
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    doc       1.7Mb
    libs    262.2Mb
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installed size is  7.2Mb
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    data   1.0Mb
    doc    3.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    ShinyItemAnalysis   2.3Mb
    data                2.3Mb
Package suggested but not available for checking: ‘edgeR’
Note: skipping ‘SIBER.Rnw’ due to unavailable dependencies: 'edgeR'
installed size is  5.1Mb
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    R      2.1Mb
    libs   1.9Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages suggested but not available for checking:
  'quantreg', 'semTools', 'OpenMx', 'copula'
Package unavailable to check Rd xrefs: ‘copula’
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  20.3Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   6.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.6Mb
    libs      5.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package suggested but not available for checking: ‘demography’
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.3Mb
    libs  10.4Mb
Packages suggested but not available for checking:
  'VariantAnnotation', 'org.Hs.eg.db',
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    doc   1.1Mb
Packages suggested but not available for checking:
  'raster', 'rasterVis', 'meteoForecast'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   9.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.0Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  11.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  34.3Mb
Package suggested but not available for checking: ‘fftwtools’
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 35.1Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  12.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.1Mb
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installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   9.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:34.091 R[19637:2290508776] XType: Using static font registry.

Quitting from lines 111-120 [Spectral_alignment] (classic_speaq_vignette.Rmd)
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:40.223 R[20964:2290511430] XType: Using static font registry.

Quitting from lines 71-83 [detect winepeaks] (speaq2_illustrations.Rmd)
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.7Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Package suggested but not available for checking: ‘mboost’
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs     11.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.4Mb
Packages suggested but not available for checking: 'car', 'party'
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  48.3Mb
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    help   1.1Mb
    libs  10.8Mb
Package suggested but not available for checking: ‘ecpc’
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  25.5Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    lsndata   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SSsimple.Snw’ using Sweave
Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SSsimple.Snw’

SUMMARY: processing the following file failed:
  ‘SSsimple.Snw’

Error: Vignette re-building failed.
Execution halted
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs  49.3Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    include  11.6Mb
    lib       3.7Mb
installed size is 92.5Mb
  sub-directories of 1Mb or more:
    libs  91.7Mb
Package which this enhances but not available for checking: ‘CVXR’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.1Mb
Package suggested but not available for checking: ‘tweedie’
Package unavailable to check Rd xrefs: ‘tweedie’
Packages suggested but not available for checking:
  'semPlot', 'FactoMineR', 'FactoInvestigate', 'factoextra'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    libs  62.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘StMoMoVignette.Rnw’ using Sweave
Loading required package: gnm
Loading required package: forecast
Error: processing vignette 'StMoMoVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StMoMoVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [caption = false]{subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

SUMMARY: processing the following file failed:
  'StMoMoVignette.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.3Mb
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Package unavailable to check Rd xrefs: ‘HDoutliers’
installed size is 13.0Mb
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installed size is 34.6Mb
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installed size is  9.7Mb
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installed size is  5.5Mb
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installed size is 11.4Mb
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Package suggested but not available for checking: ‘networkD3’
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installed size is 10.1Mb
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installed size is 14.9Mb
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installed size is 65.0Mb
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installed size is  8.5Mb
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installed size is 45.4Mb
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installed size is  5.6Mb
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installed size is 44.8Mb
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installed size is 22.7Mb
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installed size is 24.3Mb
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installed size is 10.3Mb
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installed size is 15.5Mb
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Package suggested but not available for checking: ‘dearseq’
installed size is  9.8Mb
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installed size is 17.9Mb
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    data   2.4Mb
    libs  15.2Mb
installed size is 10.2Mb
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installed size is 297.8Mb
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    R       2.3Mb
    libs  294.2Mb
installed size is 31.7Mb
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    tessdata  22.2Mb
installed size is  8.3Mb
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installed size is  8.7Mb
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    R      2.0Mb
    libs   5.3Mb
installed size is  7.5Mb
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    libs   4.0Mb
installed size is  5.2Mb
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installed size is 21.6Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘btable.Rnw’ using Sweave
Loading required package: textutils
Error: processing vignette 'btable.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'btable.tex' failed.
LaTeX errors:
! LaTeX Error: File `DejaVuSansMono.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'btable.Rnw'

SUMMARY: processing the following file failed:
  'btable.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 27.9Mb
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    libs  27.6Mb
installed size is  5.4Mb
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    libs   2.2Mb
installed size is  9.1Mb
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    R      5.1Mb
    data   4.0Mb
installed size is 54.9Mb
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Package suggested but not available for checking: ‘ggplot2’
installed size is 46.7Mb
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installed size is 55.2Mb
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    tiledb  38.5Mb
installed size is 11.1Mb
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Packages suggested but not available for checking:
  'org.Rn.eg.db', 'org.Mm.eg.db'
installed size is  6.9Mb
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    data   6.1Mb
installed size is 63.0Mb
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    doc    1.9Mb
    libs  59.1Mb
installed size is  5.8Mb
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    doc    1.7Mb
    libs   3.5Mb
installed size is  7.2Mb
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installed size is  9.9Mb
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    libs   9.8Mb
installed size is 16.6Mb
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    examples  12.4Mb
    include    3.6Mb
installed size is 30.3Mb
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installed size is  6.2Mb
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installed size is 18.3Mb
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Error(s) in re-building vignettes:
--- re-building ‘ToolsForCoDa.Rnw’ using Sweave
Loading required package: mice

Attaching package: 'mice'

The following object is masked from 'package:stats':

    filter

The following objects are masked from 'package:base':

    cbind, rbind

Loading required package: Rsolnp
Loading required package: nnet
Loading required package: MASS
Loading required package: calibrate
Error: processing vignette 'ToolsForCoDa.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ToolsForCoDa.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'ToolsForCoDa.Rnw'

SUMMARY: processing the following file failed:
  'ToolsForCoDa.Rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
installed size is 200.0Mb
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    include    1.8Mb
    libs     189.3Mb
installed size is 49.2Mb
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    doc    2.1Mb
    libs  46.5Mb
Package suggested but not available for checking: ‘tramnet’
Note: skipping ‘tramvs.Rnw’ due to unavailable dependencies: 'tramnet'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   2.2Mb
installed size is  5.2Mb
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    R      1.1Mb
    libs   3.2Mb
Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
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    data      2.3Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 114.4Mb
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    doc     3.9Mb
    libs  109.4Mb
installed size is 39.5Mb
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    libs  39.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/triptych.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘fpc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathabx.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {microtype}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

SUMMARY: processing the following file failed:
  'tsglm.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
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installed size is 44.1Mb
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installed size is  8.5Mb
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    data   4.6Mb
    libs   2.5Mb
installed size is 96.9Mb
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Package unavailable to check Rd xrefs: ‘twang’
installed size is 110.0Mb
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    R       2.0Mb
    doc     1.0Mb
    libs  106.8Mb
installed size is 27.2Mb
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    doc         1.4Mb
    dummydata   1.4Mb
    libs       22.6Mb
installed size is  5.6Mb
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    data   5.3Mb
installed size is  6.6Mb
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    R      1.0Mb
    help   5.1Mb
2023-11-27 06:51:56.302 R[14525:2096614800] XType: Using static font registry.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
2023-11-27 06:52:00.054 R[16081:2096617951] XType: Using static font registry.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:02.337 R[16881:2096619572] XType: Using static font registry.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
2023-11-27 06:52:04.198 R[17365:2096620546] XType: Using static font registry.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:13.295 R[20905:2096627616] XType: Using static font registry.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:20.449 R[23405:2096632632] XType: Using static font registry.
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.
installed size is 10.0Mb
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    libs   8.9Mb
Package suggested but not available for checking: ‘adespatial’
installed size is  7.3Mb
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    data   7.1Mb
installed size is 19.0Mb
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    libs  18.5Mb
installed size is 39.1Mb
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    doc    1.8Mb
    libs  37.1Mb
installed size is 24.7Mb
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    doc    2.2Mb
    libs  22.3Mb
installed size is 257.0Mb
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    extdata    2.8Mb
    libs     252.8Mb
installed size is  8.3Mb
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    libs   7.6Mb
installed size is  7.9Mb
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    libs   7.6Mb
installed size is  5.1Mb
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    R      3.4Mb
    help   1.1Mb
installed size is 10.0Mb
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    R      5.0Mb
    help   3.6Mb
installed size is  5.2Mb
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    doc   2.7Mb
installed size is 52.0Mb
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    doc    1.4Mb
    libs  50.4Mb
installed size is 33.0Mb
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    libs  32.4Mb
installed size is 10.7Mb
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    doc           2.0Mb
    htmlwidgets   6.9Mb
installed size is  5.3Mb
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installed size is 32.9Mb
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    libs     31.0Mb
installed size is 57.0Mb
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installed size is  9.8Mb
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    extdata   8.4Mb
installed size is 100.5Mb
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    libs  99.1Mb
installed size is  9.5Mb
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    R     2.0Mb
    doc   6.3Mb
Package suggested but not available for checking: ‘NPRED’
Package suggested but not available for checking: ‘fftw’
installed size is  5.3Mb
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    libs   5.2Mb
installed size is 27.9Mb
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installed size is 12.4Mb
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    doc    1.2Mb
    libs  10.5Mb
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Package suggested but not available for checking: ‘classInt’
installed size is  8.8Mb
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    libs   7.9Mb
installed size is  5.4Mb
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    data   4.5Mb
installed size is 40.9Mb
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Package suggested but not available for checking: ‘preprocessCore’
installed size is  7.1Mb
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    data   3.7Mb
    help   1.9Mb
    libs   1.3Mb
Package suggested but not available for checking: ‘Rsymphony’
installed size is  9.6Mb
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    libs   9.4Mb
installed size is 53.5Mb
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    libs  52.6Mb
Package suggested but not available for checking: ‘nlmixr2’
installed size is 23.4Mb
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installed size is 41.4Mb
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    libs  41.1Mb
installed size is  8.7Mb
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    R      3.0Mb
    libs   4.6Mb
installed size is 41.2Mb
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Package suggested but not available for checking: ‘rJava’
Package suggested but not available for checking: ‘partitions’
installed size is  7.1Mb
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    R      1.4Mb
    data   2.9Mb
    libs   1.2Mb
installed size is  9.4Mb
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    data   9.3Mb
Package suggested but not available for checking: 'INLA'
installed size is 35.3Mb
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    R  35.3Mb
installed size is  5.2Mb
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    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
installed size is  5.2Mb
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    R      2.3Mb
    help   1.1Mb
installed size is 43.3Mb
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    R      4.3Mb
    libs  38.4Mb
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(assignR)
  knownOrig database version 0.2, 4352 samples from 1986 sites.
  > 
  > test_check("assignR")
  trying URL 'https://wateriso.utah.edu/waterisotopes/media/ArcGrids/CaribSr.zip'
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 96 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_getIsoscapes.R:2:1'): (code run outside of `test_that()`) ──────
  Error: [rast] file does not exist: CaribSr_Rock.tif
  Backtrace:
      ▆
   1. └─assignR::getIsoscapes("CaribSr") at test_getIsoscapes.R:2:1
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 96 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
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    doc    2.6Mb
    libs   1.1Mb
installed size is  7.3Mb
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    libs   5.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BALLI.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.6Mb
    doc   1.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.4Mb
installed size is 13.4Mb
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    doc   10.8Mb
    libs   1.5Mb
installed size is  6.6Mb
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    doc    2.8Mb
    libs   2.2Mb
S3 methods shown with full name in documentation object 'export.bce':
  'export.bce'

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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.6Mb
installed size is  5.6Mb
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    doc    2.8Mb
    libs   1.3Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
S3 methods shown with full name in documentation object 'select.cfs':
  'select.cfs'

S3 methods shown with full name in documentation object 'select.fast.filter':
  'select.fast.filter'

S3 methods shown with full name in documentation object 'select.forward.Corr':
  'select.forward.Corr'

S3 methods shown with full name in documentation object 'select.forward.wrapper':
  'select.forward.wrapper'

S3 methods shown with full name in documentation object 'select.inf.chi2':
  'select.inf.chi2'

S3 methods shown with full name in documentation object 'select.inf.gain':
  'select.inf.gain'

S3 methods shown with full name in documentation object 'select.inf.symm':
  'select.inf.symm'

S3 methods shown with full name in documentation object 'select.process':
  'select.process'

S3 methods shown with full name in documentation object 'select.relief':
  'select.relief'

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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.1Mb
    help   1.0Mb
    libs   1.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BRugs.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(canadianmaps)
  > 
  > test_check("canadianmaps")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-functions.R:14:3'): check-functions: scale_fill_map() returns a ggplot manual fill object ──
  output$scale_name (`actual`) not equal to "manual" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('manual')
  ── Failure ('test-functions.R:23:3'): check-functions: scale_color_map() returns a ggplot manual fill object ──
  output$scale_name (`actual`) not equal to "manual" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('manual')
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
installed size is 12.3Mb
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    libs  11.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(chronicler)
  > 
  > test_check("chronicler")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 15 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-test_chronicler.R:72:3'): first and only error message is ok ──
  grepl("Can't subset columns that don't exist", result_pipe$log_df$message) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-test_chronicler.R:89:3'): if multiple error messages, next ones are 'pipe failed' ──
  grepl("Can't subset columns that don't exist", result_pipe$log_df$message[1]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 15 ]
  Error: Test failures
  Execution halted
installed size is  6.6Mb
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    R         1.8Mb
    extdata   4.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.1Mb
installed size is  5.2Mb
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    R      1.0Mb
    libs   2.5Mb
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(cryptotrackr)
  > 
  > test_check("cryptotrackr")
  No encoding supplied: defaulting to UTF-8.
  [1] " {\"jsonrpc\":\"2.0\",\"error\":{\"code\":429,\"message\":\"Too many requests for a specific RPC call, contact your app developer or support@rpcpool.com.\"}, \"id\": null } \r\n"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-solana.R:4:3'): the "solana_get_signature_for_address" function returns a list ──
  Error in `solana_api_call(url, request_body)`: Request failed with status code: 429
  Backtrace:
      ▆
   1. └─cryptotrackr::solana_get_signature_for_address(url, address) at test-solana.R:4:3
   2.   └─cryptotrackr::solana_api_call(url, request_body)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
Package required but not available: 'signatureSearchData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/DiNAMIC.Duo.Rcheck/00install.out' for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Package which this enhances but not available for checking: 'INLA'
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
S3 methods shown with full name in documentation object 'add.joint.mean.many':
  'all.cond.mean.PO' 'all.cond.mean2.PO'

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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/dplyr.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bin       3.1Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'lavaan.survey'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
S3 methods shown with full name in documentation object 'addDrug.Lexis':
  'addDrug.Lexis'

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.
S3 methods shown with full name in documentation object 'summary.error_interval':
  'summary.error_interval'

S3 methods shown with full name in documentation object 'summary.measure':
  'summary.measure'

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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      1.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.8Mb
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installed size is  5.1Mb
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installed size is  8.6Mb
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installed size is  5.8Mb
  sub-directories of 1Mb or more:
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    doc    1.1Mb
    libs   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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installed size is  5.9Mb
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installed size is  6.3Mb
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installed size is  7.5Mb
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installed size is  9.2Mb
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installed size is  7.2Mb
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    libs      1.2Mb
installed size is  5.5Mb
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installed size is 14.1Mb
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    libs  12.8Mb
installed size is  5.0Mb
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    data   3.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
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    libs   1.6Mb
installed size is  5.9Mb
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installed size is 23.3Mb
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installed size is 10.8Mb
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    libs   1.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
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    libs   3.6Mb
installed size is  5.7Mb
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    R   5.6Mb
installed size is 20.8Mb
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installed size is 33.6Mb
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    doc   31.8Mb
    libs   1.2Mb
installed size is 106.0Mb
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    extdata   9.0Mb
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installed size is 106.0Mb
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    gdal     3.0Mb
    libs    91.0Mb
    proj     8.4Mb
installed size is 103.0Mb
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    gdal   3.0Mb
    libs  89.3Mb
    proj   8.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.1Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

--- re-building 'geoAr_leaflet.Rmd' using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_leaflet.Rmd'

--- re-building 'georefar.Rmd' using rmarkdown
--- finished re-building 'georefar.Rmd'

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.1Mb
Running examples in 'ggdag-Ex.R' failed
The error most likely occurred in:

> ### Name: ggdag_classic
> ### Title: Quickly plot a DAG in ggplot2
> ### Aliases: ggdag_classic
> 
> ### ** Examples
> 
> 
> dag <- dagify(
+   y ~ x + z2 + w2 + w1,
+   x ~ z1 + w1,
+   z1 ~ w1 + v,
+   z2 ~ w2 + v,
+   w1 ~ ~w2
+ )
> 
> ggdag_classic(dag)
> ggdag_classic(dag) + theme_dag_blank()
> 
> ggdag_classic(dagitty::randomDAG(5, .5))
Error in `dplyr::select()`:
! Can't select columns that don't exist.
✖ Column `x` doesn't exist.
Backtrace:
     ▆
  1. ├─ggdag::ggdag_classic(dagitty::randomDAG(5, 0.5))
  2. │ └─ggdag:::if_not_tidy_daggity(.tdy_dag, ...)
  3. │   └─ggdag::tidy_dagitty(.dagitty, ...)
  4. │     └─ggdag:::get_dagitty_edges(.dagitty)
  5. │       └─.edges %>% dplyr::select(-x, -y) %>% ...
  6. ├─dplyr::rename(., name = v, to = w, direction = e)
  7. ├─dplyr::select(., -x, -y)
  8. ├─dplyr:::select.data.frame(., -x, -y)
  9. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
 10. │   └─tidyselect:::eval_select_impl(...)
 11. │     ├─tidyselect:::with_subscript_errors(...)
 12. │     │ └─base::withCallingHandlers(...)
 13. │     └─tidyselect:::vars_select_eval(...)
 14. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 15. │         └─tidyselect:::eval_c(expr, data_mask, context_mask)
 16. │           └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 17. │             └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 18. │               └─tidyselect:::as_indices_sel_impl(...)
 19. │                 └─tidyselect:::as_indices_impl(...)
 20. │                   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 21. │                     └─vctrs::vec_as_location(...)
 22. └─vctrs (local) `<fn>`()
 23.   └─vctrs:::stop_subscript_oob(...)
 24.     └─vctrs:::stop_subscript(...)
 25.       └─rlang::abort(...)
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.3Mb
    help   1.0Mb
Running examples in 'ggprism-Ex.R' failed
The error most likely occurred in:

> ### Name: annotation_ticks
> ### Title: Add ticks as ggplot annotation
> ### Aliases: annotation_ticks
> 
> ### ** Examples
> 
> ## Generally it is better to use the guide_prism_minor function.
> ## However annotation_ticks is useful in a few specific situations.
> library(ggplot2)
> 
> ## easily put ticks without labels around a plot with a border
> ggplot(mtcars, aes(x = mpg, y = disp)) +
+   geom_point() +
+   theme_prism(border = TRUE) +
+   coord_cartesian(clip = "off") +
+   annotation_ticks(sides = "tr", type = "major", outside = TRUE) +
+   theme(plot.margin = unit(c(4, 4, 4, 4), "mm"))
Error in `plot_theme()`:
! The `legend.text.align` theme element is not defined in the element
  hierarchy.
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. └─ggplot2:::print.ggplot(x)
  3.   ├─ggplot2::ggplot_gtable(data)
  4.   └─ggplot2:::ggplot_gtable.ggplot_built(data)
  5.     └─ggplot2:::plot_theme(plot)
  6.       └─ggplot2:::validate_theme(theme)
  7.         └─base::mapply(...)
  8.           └─ggplot2 (local) `<fn>`(...)
  9.             └─cli::cli_abort(...)
 10.               └─rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'axes.Rmd' using rmarkdown

Quitting from lines 38-48 [unnamed-chunk-2] (axes.Rmd)
Error: processing vignette 'axes.Rmd' failed with diagnostics:
<Guide> classes have been rewritten as <ggproto> classes.
The old S3 guide methods have been superseded.
--- failed re-building 'axes.Rmd'

--- re-building 'colours.Rmd' using rmarkdown

Quitting from lines 44-51 [unnamed-chunk-2] (colours.Rmd)
Error: processing vignette 'colours.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'colours.Rmd'

--- re-building 'ggprism.Rmd' using rmarkdown

Quitting from lines 45-59 [unnamed-chunk-2] (ggprism.Rmd)
Error: processing vignette 'ggprism.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'ggprism.Rmd'

--- re-building 'pvalues.Rmd' using rmarkdown

Quitting from lines 66-74 [unnamed-chunk-3] (pvalues.Rmd)
Error: processing vignette 'pvalues.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'pvalues.Rmd'

--- re-building 'themes.Rmd' using rmarkdown

Quitting from lines 53-63 [unnamed-chunk-3] (themes.Rmd)
Error: processing vignette 'themes.Rmd' failed with diagnostics:
The `legend.text.align` theme element is not defined in the element
hierarchy.
--- failed re-building 'themes.Rmd'

SUMMARY: processing the following files failed:
  'axes.Rmd' 'colours.Rmd' 'ggprism.Rmd' 'pvalues.Rmd' 'themes.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ggtern.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(glancedata)
  > 
  > test_check("glancedata")
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_numerical_vars.R:7:3'): histogram mode is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:14:3'): density is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:22:3'): boxplot is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:30:3'): violin is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:37:3'): qqplot is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
installed size is  9.8Mb
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    test_data       2.2Mb
    vignette_data   1.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
installed size is 267.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  264.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.6Mb
    libs   1.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.6Mb
    libs   1.0Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   1.9Mb
    libs   6.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
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    libs     10.2Mb
Package unavailable to check Rd xrefs: 'INLA'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs   3.1Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
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installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
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S3 methods shown with full name in documentation object 'bw.abram.temp':
  'bw.abram.temp'

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.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
Package suggested but not available for checking: 'EnsDb.Hsapiens.v75'
Note: skipping 'locuszoomr.Rmd' due to unavailable dependencies:
  'EnsDb.Hsapiens.v75'
Found the following significant warnings:
  Warning: replacing previous import 'ggmulti::coord_radial' by 'ggplot2::coord_radial' when loading 'loon.ggplot'
See 'd:/Rcompile/CRANpkg/local/4.3/loon.ggplot.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    gdal   3.0Mb
    libs  17.4Mb
    proj   8.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs          3.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
Package suggested but not available for checking: 'BSgenome.Hsapiens.NCBI.GRCh38'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.7Mb
installed size is  5.5Mb
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installed size is  6.0Mb
  sub-directories of 1Mb or more:
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    libs      1.2Mb
installed size is  5.2Mb
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    libs   1.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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    libs   2.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.2Mb
    libs   1.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
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installed size is 27.2Mb
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installed size is  8.6Mb
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installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    4.3Mb
    libs  11.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    6.5Mb
    libs   1.2Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    CppCode   4.8Mb
    R         7.5Mb
    include  11.7Mb
    libs      1.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.6Mb
    mods   3.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.1Mb
    libs   1.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.1Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.4Mb
    libs     5.2Mb
    models   4.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
Error(s) in re-building vignettes:
--- re-building 'MultipleComparisons.Rmd' using rmarkdown
--- finished re-building 'MultipleComparisons.Rmd'

--- re-building 'PairVizIntroduction.Rmd' using rmarkdown

Quitting from lines 312-320 [unnamed-chunk-21] (PairVizIntroduction.Rmd)
Error: processing vignette 'PairVizIntroduction.Rmd' failed with diagnostics:
At vendor/cigraph/src/core/vector.pmt:515 : Assertion failed: v->stor_begin != NULL. This is an unexpected igraph error; please report this as a bug, along with the steps to reproduce it.
Please restart your R session to avoid crashes or other surprising behavior.
--- failed re-building 'PairVizIntroduction.Rmd'

--- re-building 'pcp.Rmd' using rmarkdown
--- finished re-building 'pcp.Rmd'

SUMMARY: processing the following file failed:
  'PairVizIntroduction.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    library  14.2Mb
S3 methods shown with full name in documentation object 'pamr-internal':
  'print.nsc' 'print.nsccv'

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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    help   2.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    help   3.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   3.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   3.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.4Mb
Found the following significant warnings:
  d:/rtools43/x86_64-w64-mingw32.static.posix/include/coin/Clp_C_Interface.h:68:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/pcaL1.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      1.0Mb
Error(s) in re-building vignettes:
--- re-building 'PhyloTree_vignette_1.Rmd' using rmarkdown
--- finished re-building 'PhyloTree_vignette_1.Rmd'

--- re-building 'PhyloTree_vignette_2.Rmd' using rmarkdown

Quitting from lines 149-159 [unnamed-chunk-10] (PhyloTree_vignette_2.Rmd)
Error: processing vignette 'PhyloTree_vignette_2.Rmd' failed with diagnostics:
DNA sequences in list not of the same length.
--- failed re-building 'PhyloTree_vignette_2.Rmd'

SUMMARY: processing the following file failed:
  'PhyloTree_vignette_2.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'pinnacle.API'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    libs   1.6Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
    libs   1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   1.6Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
    proj   8.4Mb
Error(s) in re-building vignettes:
--- re-building 'prWarp-homo-example.Rmd' using rmarkdown

Quitting from lines 70-76 [plot non aff] (prWarp-homo-example.Rmd)
Error: processing vignette 'prWarp-homo-example.Rmd' failed with diagnostics:
unused argument (plot.param = list(pt.cex = 0.3, mean.cex = 0.8, mean.col = "red"))
--- failed re-building 'prWarp-homo-example.Rmd'

--- re-building 'prWarp-papionin-example.Rmd' using rmarkdown

Quitting from lines 80-87 [plot total shape] (prWarp-papionin-example.Rmd)
Error: processing vignette 'prWarp-papionin-example.Rmd' failed with diagnostics:
unused argument (plot.param = list(pt.cex = 0.5))
--- failed re-building 'prWarp-papionin-example.Rmd'

SUMMARY: processing the following files failed:
  'prWarp-homo-example.Rmd' 'prWarp-papionin-example.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    libs   1.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.5Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(quickmatch)
  Loading required package: distances
  Please cite the `quickmatch` package as:
     Savje, Fredrik, Michael J. Higgins and Jasjeet S. Sekhon (2017),
     "Generalized Full Matching", arXiv 1703.03882.
     https://arxiv.org/abs/1703.03882
  > 
  > test_check("quickmatch")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 599 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_quickmatch.R:240:3'): `quickmatch` handles discrete covariates ──
  `quickmatch(my_distances, my_data$treatment)` did not produce any warnings.
  ── Failure ('test_quickmatch.R:241:3'): `quickmatch` handles discrete covariates ──
  `expect_identical(...)` did not produce any warnings.
  ── Failure ('test_quickmatch.R:243:3'): `quickmatch` handles discrete covariates ──
  `quickmatch(my_distances, my_data$treatment, secondary_unassigned_method = "closest_seed")` did not throw an error.
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 599 ]
  Error: Test failures
  Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(receptiviti)
  > 
  > test_check("receptiviti")
  Status: ERROR
  Message: URL is unreachable
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 16 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • no API key (2): 'test-receptiviti.R:31:1', 'test-receptiviti_status.R:17:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-receptiviti_status.R:6:3'): failures works ───────────────────
  ...[] (`actual`) not identical to "Message: 404" (`expected`).
  
  `actual`:   "Message: 500"
  `expected`: "Message: 404"
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 16 ]
  Error: Test failures
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/reshape2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/restfulr.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc     3.0Mb
    fonts   1.5Mb
    libs    2.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs      2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
Error(s) in re-building vignettes:
--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

SUMMARY: processing the following file failed:
  'rnaCrosslinkOO.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   1.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/RSQLite.Rcheck/00install.out' for details.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.6Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  40.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    help   2.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
S3 methods shown with full name in documentation object 'matmult':
  '%*%.rv'

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.
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.5Mb
'sandwich-CL.Rnw'... [14s] NOTE
differences from 'sandwich-CL.Rout.save'
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  'sandwich-OOP.Rnw'... [3s] OK
  'sandwich.Rnw'... [1s] OK
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 107.3Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     3.0Mb
    libs    89.7Mb
    proj     8.4Mb
    sqlite   1.5Mb
Found the following significant warnings:

  Warning: 'lwgeom::st_perimeter' is deprecated.
  Warning: 'lwgeom::st_perimeter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SIGN.Rcheck/00install.out' for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs   1.7Mb
S3 methods shown with full name in documentation object 'plot.predictions':
  'plot.predictions'

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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   4.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    libs   1.9Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
Running 'testthat.R' [59s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(statgenGxE)
  > 
  > test_check("statgenGxE")
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 448 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3',
    'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3',
    'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3',
    'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3',
    'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3',
    'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3',
    'test-report.R:41:3', 'test-summaries.R:75:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plots.R:440:3'): option colorGenoBy in megaEnv plot functions correctly ──
  setdiff(layout[["name"]], layout0[["name"]]) not equal to "guide-box".
  Lengths differ: 0 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 448 ]
  Error: Test failures
  Execution halted
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.1Mb
S3 methods shown with full name in documentation object 'size.penalize':
  'size.penalize'

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.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
installed size is 107.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    gdal   3.0Mb
    libs  92.5Mb
    proj   8.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/tibble.Rcheck/00install.out' for details.
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
Found the following significant warnings:
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.6Mb
    include   1.8Mb
    libs     17.4Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TPCselect)
  > 
  > test_check("TPCselect")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-TPC.R:51:3'): test the main functions (TPC) with simple algorithm ──
  as.vector(TPC.fit$beta) (`actual`) not equal to `truebeta` (`expected`).
  
    `actual[1:8]`: 2.8 1.4 0.0 0.0 1.9 0.0 0.0 0.0
  `expected[1:8]`: 3.0 1.5 0.0 0.0 2.0 0.0 0.0 0.0
  
    `actual[197:200]`: 0.0 0.0 0.0 0.3
  `expected[197:200]`: 0.0 0.0 0.0 0.0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    libs  14.8Mb
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  22.0Mb
installed size is 104.4Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.9Mb
    proj      8.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   3.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
Found the following significant warnings:

  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
  Warning: 'ggiraph' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     19.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    6.3Mb
    libs   1.0Mb
S3 methods shown with full name in documentation object 'QIC.gee':
  'QIC.gee'

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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/xLLiM.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
Running ‘testthat.R’ [300s/301s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3. ├─base::suppressWarnings(...) at test-simulateabn.R:799:7
   4. │ └─base::withCallingHandlers(...)
   5. └─abn::buildScoreCache(...) at test-simulateabn.R:800:9
   6.   └─abn::buildScoreCache.bayes(...)
   7.     └─... %do% ...
   8.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
   9.         └─base::library(p, character.only = TRUE)
  
  [ FAIL 30 | WARN 0 | SKIP 35 | PASS 485 ]
  Deleting unused snapshots:
  • tographviz/graph.dot
  • tographviz/graph1.dot
  • tographviz/graph_group.dot
  Error: Test failures
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/adbcpostgresql.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    1.3Mb
    files   1.7Mb
Found the following apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset summary.amCluster
  summary.amPairwise summary.amUnique
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   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(...)
  ── Error ('test-update.R:111:5'): render_docs also transform new/modified vignettes if specified: docsify ──
  Error in `render_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
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    30.2Mb
Error: package or namespace load failed for ‘ao’:
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
In addition: Warning message:
In utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Execution halted
Error: .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
Execution halted

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.
Error: .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
In addition: Warning message:
In utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Execution halted
Loading required package: optimizeR
Error: package or namespace load failed for ‘ao’:
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
In addition: Warning message:
In utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error: package or namespace load failed for ‘ao’:
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
Call sequence:
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.6Mb
    doc    1.7Mb
Packages suggested but not available for checking:
  'oligo', 'oligoClasses', 'pdInfoBuilder', 'AffymetrixDataTestFiles'
Packages unavailable to check Rd xrefs: ‘oligo’, ‘oligoClasses’
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs  62.2Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 115.0Mb
  sub-directories of 1Mb or more:
    libs  113.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is 70.3Mb
  sub-directories of 1Mb or more:
    libs  68.8Mb
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    libs  95.6Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  21.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 86.3Mb
  sub-directories of 1Mb or more:
    libs  86.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.5Mb
Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Running ‘testthat.R’ [31s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:61:1
   2. │ └─... %>% xml2::read_xml()
   3. ├─xml2::read_xml(.)
   4. └─xml2:::read_xml.character(x = .)
   5.   └─xml2:::check_string(x)
   6.     └─xml2:::stop_input_type(...)
   7.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 238 ]
  Error: Test failures
  Execution halted
  Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs  45.5Mb
installed size is 60.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  57.3Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
    libs   7.5Mb
installed size is 163.0Mb
  sub-directories of 1Mb or more:
    include  162.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 92.3Mb
  sub-directories of 1Mb or more:
    libs  91.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
installed size is 95.2Mb
  sub-directories of 1Mb or more:
    libs  94.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.5Mb
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs  27.4Mb
installed size is 110.9Mb
  sub-directories of 1Mb or more:
    libs  110.0Mb
installed size is 116.7Mb
  sub-directories of 1Mb or more:
    libs  114.3Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is 128.3Mb
  sub-directories of 1Mb or more:
    libs  127.9Mb
Package required but not available: ‘org.Dr.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bluster’

Package suggested but not available for checking: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  19.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   9.4Mb
Packages suggested but not available for checking:
  'GenomicInteractions', 'GenomicRanges', 'Gviz', 'countreg'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   4.3Mb
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.0Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.1Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Package required but not available: ‘GenomicInteractions’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  10.5Mb
Running examples in ‘colorspace-Ex.R’ failed
The error most likely occurred in:

> ### Name: scale_colour_binned_diverging
> ### Title: HCL-Based Binned Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_binned_diverging scale_color_binned_diverging
> ###   scale_fill_binned_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
Error: package or namespace load failed for ‘ggplot2’:
 .onAttach failed in attachNamespace() for 'ggplot2', details:
  call: loadNamespace(x)
  error: there is no package called ‘withr’
Execution halted
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    libs  49.6Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.3Mb
Packages required and available but unsuitable versions:
  'stats', 'grDevices'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cec2005benchmark’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
installed size is 177.3Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    2.1Mb
    libs  171.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    doc    1.2Mb
    libs   4.6Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
str:
  function(object, ...)
str.language:
  function(expr, name, indent)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  str.language
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.4Mb
Package required but not available: ‘RedeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.6Mb
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.4Mb
Packages required but not available: 'zinbwave', 'scran'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
installed size is 69.8Mb
  sub-directories of 1Mb or more:
    libs  69.0Mb
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  12.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/DRviaSPCN.Rcheck/00install.out’ for details.
installed size is 53.7Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 366.0Mb
  sub-directories of 1Mb or more:
    libs  365.3Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    data   9.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
    libs   2.9Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   8.5Mb
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs        9.1Mb
    shiny_app   1.1Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs  10.7Mb
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  11.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
installed size is 142.4Mb
  sub-directories of 1Mb or more:
    libs  142.3Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 95.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  92.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc      3.4Mb
    images   1.1Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.2/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    doc    4.2Mb
    help   1.7Mb
    libs  12.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.1Mb
    libs   2.6Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.5Mb
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   8.3Mb
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    lib   10.3Mb
    libs  19.5Mb
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   6.9Mb
installed size is 80.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  73.1Mb
Packages suggested but not available for checking: 'foba', 'rrlda'
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Package suggested but not available for checking: ‘IRanges’
Package unavailable to check Rd xrefs: ‘IRanges’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  10.1Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/gdalBindings.Rcheck/00install.out’ for details.
installed size is 273.6Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    270.1Mb
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.5Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R        10.0Mb
    extdata   2.5Mb
    help      3.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
                                                  {and}\,\,\mathcal H_0: \ma...
l.238 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.249 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.251 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.252 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.265 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.266 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      3.1Mb
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Packages required but not available: 'lefser', 'Maaslin2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.3Mb
    help   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
installed size is 114.6Mb
  sub-directories of 1Mb or more:
    doc     1.4Mb
    libs  112.2Mb
installed size is 57.9Mb
  sub-directories of 1Mb or more:
    libs  56.7Mb
installed size is 96.4Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs           90.9Mb
    test_data       2.3Mb
    vignette_data   1.1Mb
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.97 ...ong to a compact set of \eqn{\mathbb{R}}{}
                                                  .
! Undefined control sequence.
<recently read> \mathbb 
                        
l.161 ... to a compact set of \eqn{\mathbb{R}^2}{}
                                                  .
Package suggested but not available for checking: ‘SeqArray’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is 184.5Mb
  sub-directories of 1Mb or more:
    libs  183.6Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.6Mb
    libs   6.0Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  18.3Mb
Package required but not available: ‘fmrs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        8.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Package suggested but not available for checking: ‘HiddenMarkov’
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  59.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
Package suggested but not available for checking: ‘webshot2’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.8Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Found the following significant warnings:
  vendor/cigraph/vendor/glpk/api/mps.c:1297:19: warning: explicitly assigning value of variable of type 'GLPAIJ *' (aka 'struct GLPAIJ *') to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/draft/glpapi06.c:565:26: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/draft/glpapi06.c:574:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/draft/glpios01.c:224:17: warning: explicitly assigning value of variable of type 'IOSNPD *' (aka 'struct IOSNPD *') to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/misc/ks.c:428:14: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/mpl/mpl6.c:687:17: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/mpl/mpl6.c:854:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/igraph.Rcheck/00install.out’ for details.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.2Mb
    help   2.8Mb
    libs  18.4Mb
File ‘igraph/libs/igraph.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Objects: ‘vendor/cigraph/vendor/glpk/env/stdout.o’,
      ‘vendor/cigraph/vendor/glpk/misc/mygmp.o’,
      ‘vendor/cigraph/vendor/glpk/mpl/mpl4.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Object: ‘vendor/cigraph/vendor/glpk/proxy/main.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘vendor/cigraph/vendor/glpk/proxy/main.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘vendor/cigraph/vendor/glpk/proxy/main.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
logLik:
  function(object, ...)
logLik.displacement:
  function(model, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  logLik.displacement
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'logLik.displacement':
  ‘logLik.displacement’

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.
filter:
  function(x, filter, method, sides, circular, init)
filter.sort.matrix:
  function(weight_matrix, regulators, targets)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  filter.sort.matrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'filter.sort.matrix':
  ‘filter.sort.matrix’

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.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  28.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/intrinsicFRP.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: 6
  ── Failure ('test-dday.R:10:3'): dday works ────────────────────────────────────
  dday(df, "2023-08-01", d = 1, x = "x") (`actual`) not identical to 13 (`expected`).
  
    `actual`:  0
  `expected`: 13
  ── Failure ('test-ytd.R:12:3'): ytd works ──────────────────────────────────────
  ytd(df, "2023-08-01", x = "x") (`actual`) not equal to dday(df, "2023-08-01", x = "x") (`expected`).
  
    `actual`: 10
  `expected`:  0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/JavaGD.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.2Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.7Mb
    help   1.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  49.2Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave

Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics:
 chunk 4 (label = generating artificial SNPs) 
Error in library(LFDR.MLE) : there is no package called ‘LFDR.MLE’

--- failed re-building ‘LFDREmpiricalBayes.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      9.0Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
installed size is 64.9Mb
  sub-directories of 1Mb or more:
    libs  64.4Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  31.7Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/longclust.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
Package suggested but not available for checking: ‘miceadds’
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.9Mb
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Packages suggested but not available for checking: 'pdInfoBuilder', 'oligo'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
    libs   5.0Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'wiggleplotr'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.2Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is 155.1Mb
  sub-directories of 1Mb or more:
    libs  153.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘merlin.Rmd’ using rmarkdown

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.4Mb
installed size is 107.2Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
Packages suggested but not available for checking:
  'hgu133a.db', 'hgu95av2.db'
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dada2’
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    8.8Mb
    libs   4.4Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 116.7Mb
  sub-directories of 1Mb or more:
    libs  116.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.3Mb
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.3Mb
Warning: declared S3 method 'smooth.construct.unc_pcre.smooth.spec' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is 237.0Mb
  sub-directories of 1Mb or more:
    include    9.6Mb
    libs     226.9Mb
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.8Mb
installed size is 110.0Mb
  sub-directories of 1Mb or more:
    libs  108.1Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Package which this enhances but not available for checking: ‘MoBPSmaps’
Packages required but not available:
  'plyranges', 'RaggedExperiment', 'MultiAssayExperiment', 'ggbio'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/MPCR.Rcheck/00install.out’ for details.
installed size is 68.9Mb
  sub-directories of 1Mb or more:
    libs  68.5Mb
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
Found the following apparent S3 methods exported but not registered:
  plot.prevalence.msm plot.survfit.msm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘mtvc-Ex.R’ failed
The error most likely occurred in:

> ### Name: mtvc
> ### Title: (mtvc) Multiple Time Varying Covariates
> ### Aliases: mtvc
> 
> ### ** Examples
> 
> data(simwide)
> cp.dataframe=mtvc(data=simwide,
+ origin='1970-01-01',
+ dates=c(FIRST_CHRONIC,FIRST_ACUTE,FIRST_RELAPSE),
+ complications=c(CHRONIC,ACUTE,RELAPSE),
+ start=DATETRAN,
+ stop=DLASTSE,
+ event=EVENT)
Error in `mutate()`:
ℹ In argument: `FIRST_CHRONIC = (structure(function (..., .x = ..1, .y =
  ..2, . = ..1) ...`.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
Backtrace:
     ▆
  1. ├─mtvc::mtvc(...)
  2. │ └─data %>% ungroup() %>% mutate(id = row_number()) %>% ...
  3. ├─dplyr::mutate_at(...)
  4. │ ├─dplyr::mutate(.tbl, !!!funs)
  5. │ └─dplyr:::mutate.data.frame(.tbl, !!!funs)
  6. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │     ├─base::withCallingHandlers(...)
  8. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │       └─mask$eval_all_mutate(quo)
 10. │         └─dplyr (local) eval()
 11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
 12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
 13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 16. │ └─base::stop("'origin' must be supplied")
 17. └─base::.handleSimpleError(...)
 18.   └─dplyr (local) h(simpleError(msg, call))
 19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. │       └─mask$eval_all_mutate(quo)
   10. │         └─dplyr (local) eval()
   11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
   12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
   13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   16. │ └─base::stop("'origin' must be supplied")
   17. └─base::.handleSimpleError(...)
   18.   └─dplyr (local) h(simpleError(msg, call))
   19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.TetraDualStatis summary.TetraDualStatis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Package required but not available: ‘GFDmcv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 106.9Mb
  sub-directories of 1Mb or more:
    libs  106.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

The following objects are masked from ‘package:base’:

    levels, rbind

--- finished re-building ‘cias.Rnw’

--- re-building ‘multivator.Rnw’ using Sweave
Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'multivator.Rnw'

SUMMARY: processing the following file failed:
  'multivator.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    22.9Mb
    models   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • gg-miss-case/gg-miss-case-plot-show-pct.svg
  • gg-miss-case/gg-miss-case-sort-show-pct.svg
  • gg-miss-case/gg-miss-case-sort.svg
  • gg-miss-case/gg-miss-case.svg
  • gg-miss-fct/gg-miss-fct.svg
  • gg-miss-span/gg-miss-span-group.svg
  • gg-miss-span/gg-miss-span.svg
  • gg-miss-var-cumsum/gg-miss-var-cumsum.svg
  • gg-miss-var-plot/gg-miss-var-group-pct.svg
  • gg-miss-var-plot/gg-miss-var-pct.svg
  • gg-miss-var-plot/gg-miss-var-plot-group.svg
  • gg-miss-var-plot/gg-miss-var.svg
  • gg-miss-which/gg-miss-which.svg
  Error: Test failures
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.1Mb
    mods   3.3Mb
Found the following apparent S3 methods exported but not registered:
  print.fkk.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  14.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.4Mb
    libs   3.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   6.3Mb
Packages suggested but not available for checking: 'org.Dr.eg.db', 'scde'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    library   7.5Mb
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  43.0Mb
‘constparty.Rnw’... [3s/3s] OK
  ‘ctree.Rnw’ using ‘UTF-8’... [4s/4s] NOTE
differences from ‘ctree.Rout.save’
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  ‘mob.Rnw’... [5s/5s] OK
  ‘partykit.Rnw’... [1s/1s] OK
Package required but not available: ‘Mfuzz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/pbdMPI.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    help   1.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  14.0Mb
installed size is 134.4Mb
  sub-directories of 1Mb or more:
    libs  133.5Mb
Package suggested but not available for checking: ‘ptmixed’
installed size is 56.2Mb
  sub-directories of 1Mb or more:
    libs  55.0Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  10.2Mb
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   4.2Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.7Mb
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 79.8Mb
  sub-directories of 1Mb or more:
    libs  79.1Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2230 ...to a user-specified \eqn{K_\text{max}}{}
                                                  )
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2256 ...er}{integer} scalar \eqn{K_\text{max}}{}
                                                  ,
! Undefined control sequence.
<argument> K^c+1=K_\text 
                         {max}
l.2282 ...is stopped if \eqn{K^c+1=K_\text{max}}{}
                                                  ,
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs         16.0Mb
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.6Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  11.3Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.7Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rblpapi.Rcheck/00install.out’ for details.
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
installed size is 66.1Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.5Mb
    po    2.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking: 'ROntoTools', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  17.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  13.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     19.5Mb
    models    1.6Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rJava.Rcheck/00install.out’ for details.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rlibkriging.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RMark.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RmecabKo.Rcheck/00install.out’ for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ... (t+(r-1))\neq \mu (t+(s-1))\ \text 
                                                  {for some}\ t\in [0,1],\\ ...
l.380 \end{array}\right.}{}
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   5.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.2Mb
    minizinc   3.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rmpi.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is 101.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     98.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.3Mb
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.0Mb
    simulationStudy   1.5Mb
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
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.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/ROracle.Rcheck/00install.out’ for details.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   7.7Mb
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    libs  58.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RQuantLib.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  24.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
installed size is 99.8Mb
  sub-directories of 1Mb or more:
    libs  98.1Mb
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-slope_rast.R:9:3'): slope_rast works ───────────────────────────
  Error in `as.POSIXlt.numeric(x, tz = tz(x))`: 'origin' must be supplied
  Backtrace:
      ▆
   1. ├─rtrend::slope_rast(...) at test-slope_rast.R:9:3
   2. │ └─r %<>% rast_filter_time(period)
   3. └─rtrend::rast_filter_time(., period)
   4.   ├─lubridate::year(time(r))
   5.   └─lubridate:::year.default(time(r))
   6.     ├─base::as.POSIXlt(x, tz = tz(x))
   7.     └─base::as.POSIXlt.numeric(x, tz = tz(x))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘slope_rast.Rmd’ using rmarkdown

Quitting from lines 20-33 [setup] (slope_rast.Rmd)
Error: processing vignette 'slope_rast.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘slope_rast.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.3Mb
Package required but not available: ‘rWikiPathways’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
installed size is 63.3Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     57.9Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  44.3Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \dfrac 
                       
l.192 ...omputed by  \eqn{\dfrac{|I|-ec}{|I|-1}}{}
                                                  .
! Undefined control sequence.
<argument> 1 - \dfrac 
                      {\hat {\ell }_{k,n}(1_I,0_{I^c})}{|I|}
l.280 ...ac{\hat{\ell}_{k,n}(1_I,0_{I^c})}{|I|}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1278 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1364 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> \hat {S}_{I,k,n}=\dfrac 
                                   {\hat {D}_{I,k,n}}{\hat {D}_{k,n}}
l.1374 ...dfrac{\hat{D}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                  
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...hat{\Upsilon}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                   the empirical counterpart...
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...n{\dfrac{\Upsilon_I(\ell)}{D_I(\ell)}}{}
                                                  .
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1609 ... by \eqn{\dfrac{(2|I|+2)!}{2(|I|!)^2}}{}
                                                  .
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.6Mb
Packages suggested but not available for checking:
  'DropletUtils', 'Nebulosa'
Package required but not available: ‘glmGamPoi’

Packages suggested but not available for checking: 'scran', 'Linnorm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Packages suggested but not available for checking: 'ontoProc', 'rrvgo'
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.2Mb
installed size is 75.3Mb
  sub-directories of 1Mb or more:
    libs  73.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.0Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  14.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   7.7Mb
Found the following apparent S3 methods exported but not registered:
  model.matrix.segmented model.matrix.stepmented vcov.stepmented
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flowMerge’
Package unavailable to check Rd xrefs: ‘flowMerge’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs    21.4Mb
    models   1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
Package required but not available: ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   8.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/shide.Rcheck/00install.out’ for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> X \in \mathbb 
                         {R}{n\times p}
l.3264 ...data \eqn{X \in \mathbb{R}{n\times p}}{}
                                                   such that its rows are
! Undefined control sequence.
<argument> ...Delta _{p-1} =\lbrace z \in \mathbb 
                                                  {R}^p~|~z_j > 0, \sum _{i=...
l.3267 }{}
           test whether the data is uniformly distributed.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      4.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.7Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  19.9Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.6Mb
    libs      5.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
Package suggested but not available for checking: ‘SMITIDstruct’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.9Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [18s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: "0427" "1946"
  ── Failure ('test-audioblastProcessors.R:103:3'): .calcTimesOfDay() works as expected ──
  as.character(o[2, ]) (`actual`) not equal to c("2248", "0124") (`expected`).
  
  `actual`:   "2254" "0119"
  `expected`: "2248" "0124"
  ── Failure ('test-audioblastProcessors.R:105:3'): .calcTimesOfDay() works as expected ──
  as.character(o[4, ]) (`actual`) not equal to c("1206", "2248") (`expected`).
  
  `actual`:   "1207" "2254"
  `expected`: "1206" "2248"
  
  [ FAIL 18 | WARN 0 | SKIP 7 | PASS 811 ]
  Error: Test failures
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
Packages required but not available:
  'SpatialExperiment', 'zinbwave', 'scran'

Package suggested but not available for checking: ‘bluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    libs  53.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.9Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  10.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs     11.2Mb
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─... %>% as_preview() at test-spork.R:297:1
    2. ├─spork::as_preview(.)
    3. └─spork:::as_preview.plotmath(.)
    4.   ├─latexpdf::as.png(...)
    5.   └─spork:::as.png.plotmath(...)
    6.     ├─ggplot2::ggplot(x, ...)
    7.     └─spork:::ggplot.plotmath(x, ...)
    8.       ├─ggplot2::ggplot(data.frame(x = 1, y = 1, label = (x)))
    9.       └─base::data.frame(x = 1, y = 1, label = (x))
   10.         ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
   11.         └─base::as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 101 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  49.5Mb
Package suggested but not available for checking: ‘scanstatistics’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.0Mb
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  64.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Missing or unexported objects:
  ‘GSVA::gsvaParam’ ‘GSVA::ssgseaParam’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'gsvaParam' is not an exported object from 'namespace:GSVA'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.2Mb
    libs   1.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    libs   2.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    doc    3.9Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  13.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   7.3Mb
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Package required and available but unsuitable version: ‘spork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \text 
                  {logit} \big ( E(Y) \big ) = \tau + \alpha + \delta (r - 1), 
l.172 ...g ) = \tau + \alpha + \delta (r - 1), }{}
Package suggested but not available for checking: ‘MultiAssayExperiment’
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package which this enhances but not available for checking: ‘mnlogit’
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
Warning: declared S3 method 'filter.edsurvey.data.frame' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Warning: declared S3 method 'filter.Seurat' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
Packages required but not available: 'EnhancedVolcano', 'Mfuzz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 211.7Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       1.6Mb
    include    1.8Mb
    libs     201.6Mb
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  46.4Mb
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  116.2Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/triptych.Rcheck/00install.out’ for details.
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.1Mb
installed size is 108.5Mb
  sub-directories of 1Mb or more:
    libs  107.5Mb
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.cla_fs' not found
Warning: declared S3 method 'transform.ts_aug_awareness' not found
Warning: declared S3 method 'transform.ts_aug_awaresmooth' not found
Warning: declared S3 method 'transform.ts_aug_flip' not found
Warning: declared S3 method 'transform.ts_aug_jitter' not found
Warning: declared S3 method 'transform.ts_aug_none' not found
Warning: declared S3 method 'transform.ts_aug_shrink' not found
Warning: declared S3 method 'transform.ts_aug_stretch' not found
Warning: declared S3 method 'transform.ts_aug_wormhole' not found
Warning: declared S3 method 'transform.ts_fil_ema' not found
Warning: declared S3 method 'transform.ts_fil_hp' not found
Warning: declared S3 method 'transform.ts_fil_kalman' not found
Warning: declared S3 method 'transform.ts_fil_lowess' not found
Warning: declared S3 method 'transform.ts_fil_ma' not found
Warning: declared S3 method 'transform.ts_fil_none' not found
Warning: declared S3 method 'transform.ts_fil_qes' not found
Warning: declared S3 method 'transform.ts_fil_recursive' not found
Warning: declared S3 method 'transform.ts_fil_seas_adj' not found
Warning: declared S3 method 'transform.ts_fil_ses' not found
Warning: declared S3 method 'transform.ts_fil_smooth' not found
Warning: declared S3 method 'transform.ts_fil_spline' not found
Warning: declared S3 method 'transform.ts_fil_winsor' not found
Warning: declared S3 method 'transform.ts_norm_none' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is 106.5Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    doc     1.0Mb
    libs  103.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   4.4Mb
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.4Mb
    libs  47.5Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.8Mb
installed size is 271.2Mb
  sub-directories of 1Mb or more:
    extdata    2.8Mb
    libs     267.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     29.5Mb
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  54.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘changing_default_parameters.Rmd’ using rmarkdown
--- finished re-building ‘changing_default_parameters.Rmd’

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

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

Quitting from lines 68-71 [unnamed-chunk-2] (process_bouts.Rmd)
Error: processing vignette 'process_bouts.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘process_bouts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [60s/94s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  19: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  20: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  21: source_file(path, env = env(env), desc = desc, error_call = error_call)
  22: FUN(X[[i]], ...)
  23: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  28: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  29: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  30: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  31: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  32: test_check("wallace")
  An irrecoverable exception occurred. R is aborting now ...
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.3Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    help   1.9Mb
    libs   1.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘RNRCS’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      2.0Mb
Error(s) in re-building vignettes:
--- re-building 'data_simulation.Rmd' using rmarkdown
File fit_model-1.png not found in resource path
Error: processing vignette 'data_simulation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'data_simulation.Rmd'

--- re-building 'mixed_effect_BN_model.Rmd' using rmarkdown
--- finished re-building 'mixed_effect_BN_model.Rmd'

--- re-building 'model_specification.Rmd' using rmarkdown
--- finished re-building 'model_specification.Rmd'

--- re-building 'multiprocessing.Rmd' using rmarkdown
File benchmarkBoxPlot-1.png not found in resource path
Error: processing vignette 'multiprocessing.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'multiprocessing.Rmd'

--- re-building 'paper.Rmd' using rmarkdown
--- finished re-building 'paper.Rmd'

--- re-building 'parameter_learning.Rmd' using rmarkdown
File unnamed-chunk-3-1.png not found in resource path
Error: processing vignette 'parameter_learning.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'parameter_learning.Rmd'

--- re-building 'quick_start_example.Rmd' using rmarkdown
--- finished re-building 'quick_start_example.Rmd'

--- re-building 'structure_learning.Rmd' using rmarkdown
--- finished re-building 'structure_learning.Rmd'

SUMMARY: processing the following files failed:
  'data_simulation.Rmd' 'multiprocessing.Rmd' 'parameter_learning.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Found the following problems:
errorevol_ranking_vector_IW.Rd:68:38: Warning: nested emphasis <code>
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/adbcpostgresql.Rcheck/00install.out' for details.
Encountered the following conversion/validation errors:
absindex.Rd:110: condition must be plain text
feemscatter.Rd:47: condition must be plain text
write.openfluor.Rd:43: condition must be plain text
Found the following apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset summary.amCluster
  summary.amPairwise summary.amUnique
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.7Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/arcpbf.Rcheck/00install.out' for details.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   11.8Mb
    misc   2.1Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(atrrr)
  > 
  > test_check("atrrr")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 167 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • !dir.exists(tools::R_user_dir("atrrr", "cache")) is TRUE (2):
    'test-convert.R:6:3', 'test-convert.R:16:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-actors.R:17:3'): user info pagination ──────────────────────────
  Error in `basename(req$url)`: path too long
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(nrow(get_user_info(actor = actors)), 75L) at test-actors.R:17:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::nrow(get_user_info(actor = actors))
    5. └─atrrr::get_user_info(actor = actors)
    6.   ├─base::append(...)
    7.   ├─purrr::pluck(...)
    8.   │ └─purrr:::pluck_raw(.x, list2(...), .default = .default)
    9.   ├─base::do.call(...)
   10.   └─atrrr (local) `<fn>`(`<chr>`, .token = NULL, .return = "json")
   11.     └─atrrr:::make_request(...)
   12.       └─httr2::req_perform(...)
   13.         └─atrrr (local) mock(req)
   14.           ├─base::sub("\\?.*", "", basename(req$url)) at D:\RCompile\CRANpkg\local\4.2\atrrr.Rcheck\tests\testthat\setup-mock.R:6:3
   15.           │ └─base::is.factor(x)
   16.           └─base::basename(req$url)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 167 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/b64.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.6Mb
    doc   1.8Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bigrquerystorage.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'vol2birdR'
Running examples in 'bioRad-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_vp
> ### Title: Calculate a vertical profile ('vp') from a polar volume ('pvol')
> ###   file
> ### Aliases: calculate_vp
> 
> ### ** Examples
> 
> # Locate and read the polar volume example file
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> 
> # Copy the file to a home directory with read/write permissions
> file.copy(pvolfile, "~/volume.h5")
[1] TRUE
> 
> # Calculate the profile
> vp <- calculate_vp("~/volume.h5")
Error in calculate_vp("~/volume.h5") : 
  The package "vol2birdR" is required to run `calculate_vp`.
Calls: calculate_vp -> <Anonymous>
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.6Mb
Found the following significant warnings:
  bnlearn/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/loglikelihood/../../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/rinterface/../../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  minimal/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  predict/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  sanitization/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.2/bnlearn.Rcheck/00install.out' for details.
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      30.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BRugs.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.0Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/clarabel.Rcheck/00install.out' for details.
Found the following problems:
fitEmaxB.Rd:191:38: Warning: nested emphasis <code>
fishp: no visible binding for global variable 'markname'
fishp: no visible binding for global variable 'sum_chisq'
fishp: no visible binding for global variable 'sum_z'
pvalues_to_zscores: no visible binding for global variable 'markname'
tetracorr: no visible binding for global variable 'PLCORR'
Undefined global functions or variables:
  PLCORR markname sum_chisq sum_z
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(cryptotrackr)
  > 
  > test_check("cryptotrackr")
  No encoding supplied: defaulting to UTF-8.
  [1] " {\"jsonrpc\":\"2.0\",\"error\":{\"code\":429,\"message\":\"Too many requests for a specific RPC call, contact your app developer or support@rpcpool.com.\"}, \"id\": null } \r\n"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-solana.R:4:3'): the "solana_get_signature_for_address" function returns a list ──
  Error in `solana_api_call(url, request_body)`: Request failed with status code: 429
  Backtrace:
      ▆
   1. └─cryptotrackr::solana_get_signature_for_address(url, address) at test-solana.R:4:3
   2.   └─cryptotrackr::solana_api_call(url, request_body)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 92 ]
  Error: Test failures
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Package required and available but unsuitable version: 'IRanges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  ./src/common/stddecl.h:481:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.2/cubature.Rcheck/00install.out' for details.
str:
  function(object, ...)
str.language:
  function(expr, name, indent)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  str.language
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
Packages required and available but unsuitable versions: 'utils', 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Error(s) in re-building vignettes:
--- re-building 'introduction_to_dnapath.Rmd' using rmarkdown

Quitting from lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd)
Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
--- failed re-building 'introduction_to_dnapath.Rmd'

--- re-building 'package_data.Rmd' using rmarkdown

Quitting from lines 234-239 [unnamed-chunk-17] (package_data.Rmd)
Error: processing vignette 'package_data.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
--- failed re-building 'package_data.Rmd'

SUMMARY: processing the following files failed:
  'introduction_to_dnapath.Rmd' 'package_data.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/dplyr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/DRviaSPCN.Rcheck/00install.out' for details.
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    bin       3.5Mb
    extdata   1.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Rcgi      3.1Mb
    cgi-bin   2.9Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/fcl.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following problems:
fRegress.Rd:321:38: Warning: nested emphasis <code>
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/fdrDiscreteNull.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.1Mb
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(fishRman)
  > 
  > test_check("fishRman")
  The resource you requested cannot be served. Error message:
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fish.R:16:3'): the right dataframe is returned from the API ────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [fishrman.ddnsfree.com] Failed to connect to fishrman.ddnsfree.com port 443 after 10013 ms: Timeout was reached
  Backtrace:
      ▆
   1. └─fishRman::fish(bait) at test-fish.R:16:3
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       ├─base (local) tryCatchOne(...)
   5.       │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   6.       └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
   7.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
Error(s) in re-building vignettes:
--- re-building 'Air_Quality.Rmd' using rmarkdown
--- finished re-building 'Air_Quality.Rmd'

--- re-building 'Atmospheric_Radiation.Rmd' using rmarkdown
--- finished re-building 'Atmospheric_Radiation.Rmd'

--- re-building 'Basic_Functions.Rmd' using rmarkdown
--- finished re-building 'Basic_Functions.Rmd'

--- re-building 'Particle_Size_Distribution.Rmd' using rmarkdown
Could not fetch https://s1.ax1x.com/2022/04/05/qLbLef.png
HttpExceptionRequest Request {
  host                 = "s1.ax1x.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/2022/04/05/qLbLef.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 NoResponseDataReceived
Error: processing vignette 'Particle_Size_Distribution.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building 'Particle_Size_Distribution.Rmd'

--- re-building 'Plot_Functions.Rmd' using rmarkdown
--- finished re-building 'Plot_Functions.Rmd'

--- re-building 'Trace_Gas_Chemistry.Rmd' using rmarkdown
--- finished re-building 'Trace_Gas_Chemistry.Rmd'

SUMMARY: processing the following file failed:
  'Particle_Size_Distribution.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    help   2.6Mb
    libs   3.6Mb
installed size is 77.5Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
    libs     60.1Mb
    proj      8.2Mb
installed size is 76.4Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.8Mb
    libs    62.3Mb
    proj     7.7Mb
installed size is 73.6Mb
  sub-directories of 1Mb or more:
    gdal   2.8Mb
    libs  60.8Mb
    proj   7.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Running 'testthat.R' [50s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("gfpop")
  Loading required package: gfpop
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 40 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sn.R:3:1'): (code run outside of `test_that()`) ────────────────
  <install_error/error/condition>
  Error: Failed to install 'unknown package' from GitHub:
    HTTP error 403.
    API rate limit exceeded for 129.217.207.166. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
  
    Rate limit remaining: 0/60
    Rate limit reset at: 2024-03-20 13:06:53 UTC
  
    To increase your GitHub API rate limit
    - Use `usethis::create_github_token()` to create a Personal Access Token.
    - Use `gitcreds::gitcreds_set()` to add the token.
  Backtrace:
      ▆
   1. └─devtools::install_github("vrunge/gfpop.data") at test-sn.R:3:1
   2.   ├─pkgbuild::with_build_tools(...)
   3.   │ └─pkgbuild:::withr_with_path(rtools_path(), code)
   4.   │   └─base::force(code)
   5.   └─remotes:::install_remotes(...)
   6.     └─base::tryCatch(...)
   7.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 40 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ggtern.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/gifski.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(glancedata)
  > 
  > test_check("glancedata")
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_numerical_vars.R:7:3'): histogram mode is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:14:3'): density is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:22:3'): boxplot is a list of length 9 ──
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:30:3'): violin is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plot_numerical_vars.R:37:3'): qqplot is a list of length 9 ───
  mymode == "list" & mylength == 9 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            4.5Mb
    test_data       2.3Mb
    vignette_data   1.1Mb
Found the following problems:
get_k_stages_adjacency_tensor.Rd:58:38: Warning: nested emphasis <code>
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
Found the following problems:
GWASinlps.Rd:187:1: Warning: trimming empty <h4>
Error(s) in re-building vignettes:
--- re-building 'GWRLASSO.Rmd' using rmarkdown

Quitting from lines 18-55 [unnamed-chunk-1] (GWRLASSO.Rmd)
Error: processing vignette 'GWRLASSO.Rmd' failed with diagnostics:
system is computationally singular: reciprocal condition number = 6.72386e-17
--- failed re-building 'GWRLASSO.Rmd'

SUMMARY: processing the following file failed:
  'GWRLASSO.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following problems:
KMHFA.Rd:128:38: Warning: nested emphasis <code>


KMHFA.Rd:132:38: Warning: nested emphasis <code>


KPCA.Rd:73:38: Warning: nested emphasis <code>


KPCA.Rd:77:38: Warning: nested emphasis <code>


KPE.Rd:83:38: Warning: nested emphasis <code>


KPE.Rd:87:38: Warning: nested emphasis <code>
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.3Mb
Package required but not available: 'unigd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following problems:
baseflow.Rd:167:38: Warning: nested emphasis <code>


baseflow.Rd:171:38: Warning: nested emphasis <code>
Found the following problems:
KIALS.Rd:92:38: Warning: nested emphasis <code>


KIALS.Rd:96:38: Warning: nested emphasis <code>
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.6Mb
    libs   1.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   1.9Mb
    libs   6.4Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      9.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
logLik:
  function(object, ...)
logLik.displacement:
  function(model, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  logLik.displacement
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
S3 methods shown with full name in documentation object 'logLik.displacement':
  'logLik.displacement'

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.
filter:
  function(x, filter, method, sides, circular, init)
filter.sort.matrix:
  function(weight_matrix, regulators, targets)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  filter.sort.matrix
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
S3 methods shown with full name in documentation object 'filter.sort.matrix':
  'filter.sort.matrix'

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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/intrinsicFRP.Rcheck/00install.out' for details.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(iperform)
  > 
  > test_check("iperform")
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-dday.R:7:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-03", x = "x") (`actual`) not identical to 8 (`expected`).
  
    `actual`: 0
  `expected`: 8
  ── Failure ('test-dday.R:8:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-05", d = -1, x = "x") (`actual`) not identical to 12 (`expected`).
  
    `actual`:  0
  `expected`: 12
  ── Failure ('test-dday.R:9:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-05", d = 0, x = "x") (`actual`) not identical to 6 (`expected`).
  
    `actual`: 0
  `expected`: 6
  ── Failure ('test-dday.R:10:3'): dday works ────────────────────────────────────
  dday(df, "2023-08-01", d = 1, x = "x") (`actual`) not identical to 13 (`expected`).
  
    `actual`:  0
  `expected`: 13
  ── Failure ('test-ytd.R:12:3'): ytd works ──────────────────────────────────────
  ytd(df, "2023-08-01", x = "x") (`actual`) not equal to dday(df, "2023-08-01", x = "x") (`expected`).
  
    `actual`: 10
  `expected`:  0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           9.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/journalabbr.Rcheck/00install.out' for details.
apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/longclust.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'ggmulti::coord_radial' by 'ggplot2::coord_radial' when loading 'loon.ggplot'
See 'd:/Rcompile/CRANpkg/local/4.2/loon.ggplot.Rcheck/00install.out' for details.
installed size is 71.4Mb
  sub-directories of 1Mb or more:
    gdal   2.8Mb
    libs  60.7Mb
    proj   7.7Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  36.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.3Mb
qr.X: no visible binding for global variable 'R'
Undefined global functions or variables:
  R
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.8Mb
    libs   2.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.3Mb
    libs   1.2Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
Warning: declared S3 method 'smooth.construct.unc_pcre.smooth.spec' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    include   9.7Mb
    libs     17.5Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Found the following apparent S3 methods exported but not registered:
  plot.prevalence.msm plot.survfit.msm
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
Running examples in 'mtvc-Ex.R' failed
The error most likely occurred in:

> ### Name: mtvc
> ### Title: (mtvc) Multiple Time Varying Covariates
> ### Aliases: mtvc
> 
> ### ** Examples
> 
> data(simwide)
> cp.dataframe=mtvc(data=simwide,
+ origin='1970-01-01',
+ dates=c(FIRST_CHRONIC,FIRST_ACUTE,FIRST_RELAPSE),
+ complications=c(CHRONIC,ACUTE,RELAPSE),
+ start=DATETRAN,
+ stop=DLASTSE,
+ event=EVENT)
Error in `mutate()`:
ℹ In argument: `FIRST_CHRONIC = (structure(function (..., .x = ..1, .y =
  ..2, . = ..1) ...`.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
Backtrace:
     ▆
  1. ├─mtvc::mtvc(...)
  2. │ └─data %>% ungroup() %>% mutate(id = row_number()) %>% ...
  3. ├─dplyr::mutate_at(...)
  4. │ ├─dplyr::mutate(.tbl, !!!funs)
  5. │ └─dplyr:::mutate.data.frame(.tbl, !!!funs)
  6. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │     ├─base::withCallingHandlers(...)
  8. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │       └─mask$eval_all_mutate(quo)
 10. │         └─dplyr (local) eval()
 11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
 12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
 13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 16. │ └─base::stop("'origin' must be supplied")
 17. └─base::.handleSimpleError(...)
 18.   └─dplyr (local) h(simpleError(msg, call))
 19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.TetraDualStatis summary.TetraDualStatis
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'multivariate_sex_differences_in_personality.Rmd' using rmarkdown
trying URL 'http://openpsychometrics.org/_rawdata/BIG5.zip'
Content type 'application/zip' length 523351 bytes (511 KB)
==============================================
downloaded 471 KB


Quitting from lines 60-80 [importdata] (multivariate_sex_differences_in_personality.Rmd)
Error: processing vignette 'multivariate_sex_differences_in_personality.Rmd' failed with diagnostics:
download from 'http://openpsychometrics.org/_rawdata/BIG5.zip' failed
--- failed re-building 'multivariate_sex_differences_in_personality.Rmd'

SUMMARY: processing the following file failed:
  'multivariate_sex_differences_in_personality.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    CppCode   4.9Mb
    R         7.4Mb
    include  11.7Mb
    libs      1.2Mb
Found the following apparent S3 methods exported but not registered:
  print.fkk.test
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.1Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs   19.6Mb
    share  10.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    data     1.5Mb
    libs     5.1Mb
    models   4.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/orbweaver.Rcheck/00install.out' for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    library  14.4Mb
'ctree.Rnw' using 'UTF-8'... [12s] NOTE
differences from 'ctree.Rout.save'
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  'partykit.Rnw'... [3s] OK
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    help   3.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.7Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs    6.9Mb
    share  12.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    libs   1.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.2Mb
Error(s) in re-building vignettes:
--- re-building 'a_posteriori_dosing.Rmd' using rmarkdown
--- finished re-building 'a_posteriori_dosing.Rmd'

--- re-building 'a_priori_dosing.Rmd' using rmarkdown
--- re-building 'auc_based_dosing.Rmd' using rmarkdown
--- finished re-building 'auc_based_dosing.Rmd'

--- re-building 'multiple_endpoints.Rmd' using rmarkdown
--- finished re-building 'multiple_endpoints.Rmd'

--- re-building 'patient_data_input.Rmd' using rmarkdown
--- finished re-building 'patient_data_input.Rmd'

--- re-building 'posologyr_user_defined_models.Rmd' using rmarkdown
--- finished re-building 'posologyr_user_defined_models.Rmd'

SUMMARY: processing the following file failed:
  'a_priori_dosing.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required and available but unsuitable versions:
  'graphics', 'grDevices', 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.7Mb
    libs   1.6Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
    proj   7.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/prqlr.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs          2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/Rcplex.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  Shallalist Data saved to the following destination: ./ 
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-pkg-style.R:5:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dmoz-cat.R:5:3'): dmoz cat ─────────────────────────────────────
  Error in `curl_download(paste0("https://github.com/themains/rdomains/blob/master/data-raw/dmoz/", 
      "dmoz_domain_category.zip?raw=TRUE"), tmp)`: Timeout was reached: [] SSL/TLS connection timeout
  Backtrace:
      ▆
   1. └─rdomains::get_dmoz_data() at test-dmoz-cat.R:5:3
   2.   └─curl::curl_download(...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2 ]
  Error: Test failures
  Execution halted
Running 'test-all.R' [4s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > test_check('rebird')
  Loading required package: rebird
  [ FAIL 1 | WARN 0 | SKIP 28 | PASS 3 ]
  
  ══ Skipped tests (28) ══════════════════════════════════════════════════════════
  • On CRAN (28): 'test-ebirdchecklistfeed.R:4:3',
    'test-ebirdchecklistfeed.R:14:3', 'test-ebirdfreq.R:4:3',
    'test-ebirdfreq.R:23:3', 'test-ebirdgeo.R:4:3', 'test-ebirdhistorical.R:4:3',
    'test-ebirdhistorical.R:45:3', 'test-ebirdhotspot.R:4:3',
    'test-ebirdhotspotlist.R:4:3', 'test-ebirdhotspotlist.R:32:3',
    'test-ebirdloc.R:4:3', 'test-ebirdloc.R:22:3', 'test-ebirdnotable.R:4:3',
    'test-ebirdregion.R:4:3', 'test-ebirdregioncheck.R:4:3',
    'test-ebirdregioncheck.R:19:3', 'test-ebirdregioninfo.R:4:3',
    'test-ebirdregioninfo.R:27:3', 'test-ebirdregionspecies.R:4:3',
    'test-ebirdregionspecies.R:25:3', 'test-ebirdsubregionlist.R:4:3',
    'test-ebirdsubregionlist.R:28:3', 'test-ebirdtaxonomy.R:4:3',
    'test-ebirdtaxonomy.R:19:3', 'test-nearestobs.R:4:3',
    'test-nearestobs.R:20:3', 'test-species_code.R:4:3',
    'test-species_code.R:16:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ebirdtaxonomy.R:29:3'): ebirdtaxonomy works without an API key ──
  Error: Please install xml2 package
  Backtrace:
      ▆
   1. └─rebird::ebirdtaxonomy() at test-ebirdtaxonomy.R:29:3
   2.   └─rebird:::ebird_GET(...)
   3.     └─httr::content(tt)
   4.       └─httr:::parse_auto(raw, type, encoding, ...)
   5.         └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
   6.           └─httr:::need_package("xml2")
  
  [ FAIL 1 | WARN 0 | SKIP 28 | PASS 3 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(receptiviti)
  > 
  > test_check("receptiviti")
  Status: ERROR
  Message: URL is unreachable
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 16 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • no API key (2): 'test-receptiviti.R:31:1', 'test-receptiviti_status.R:17:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-receptiviti_status.R:6:3'): failures works ───────────────────
  ...[] (`actual`) not identical to "Message: 404" (`expected`).
  
  `actual`:   "Message: 500"
  `expected`: "Message: 404"
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 16 ]
  Error: Test failures
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/restfulr.Rcheck/00install.out' for details.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
Warnings in file 'R/shinyFSSA.R':
  unable to translate 'f(<U+03C4>)' to native encoding
  unable to translate 'g(<U+03C4>)' to native encoding
  unable to translate 'f(<U+03C4>) + g(<U+03C4>)' to native encoding

Warnings in file 'R/shinyMFSSA.R':
  unable to translate 'A.1t(<U+03C9>1,<U+2113>) F1 +' to native encoding
  unable to translate 'A.2t(<U+03C9>2) F2' to native encoding
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    lib    3.4Mb
    libs   4.2Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'

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.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ROracle.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/rsgeo.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/rshift.Rcheck/00install.out' for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    2.1Mb
    libs   1.5Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  37.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.6Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   9.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  13.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package required and available but unsuitable version: 'pcaMethods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
Warning in file 'R/label-number.R':
  unable to translate '<U+03BC>s' to native encoding
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Found the following apparent S3 methods exported but not registered:
  model.matrix.segmented model.matrix.stepmented vcov.stepmented
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is 78.5Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     2.8Mb
    libs    61.7Mb
    proj     7.7Mb
    sqlite   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/shide.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/SIGN.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/smcryptoR.Rcheck/00install.out' for details.
Running examples in 'SMDIC-Ex.R' failed
The error most likely occurred in:

> ### Name: exp2cell
> ### Title: exp2cell
> ### Aliases: exp2cell
> 
> ### ** Examples
> 
> #get breast cancer gene expression profile.
> exp.example<-GetExampleData("exp.example")
> 
> #perform the exp2cell method. Method must be one of "xCell","ssGSEA" and "CIBERSORT".
> cellmatrix<-exp2cell(exp=exp.example,method="ssGSEA") #cell abundance matrix
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SMDIC.Rmd' using rmarkdown

Quitting from lines 63-70 [unnamed-chunk-2] (SMDIC.Rmd)
Error: processing vignette 'SMDIC.Rmd' failed with diagnostics:
useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
--- failed re-building 'SMDIC.Rmd'

SUMMARY: processing the following file failed:
  'SMDIC.Rmd'

Error: Vignette re-building failed.
Execution halted
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R   4.6Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.0Mb
Warnings in file 'R/import_csv_settings.R':
  unable to translate '(W/m<U+00B2>*nm)' to native encoding
  unable to translate '(mW/m<U+00B2>*nm)' to native encoding
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spork)
  > 
  > test_check("spork")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 101 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-spork.R:451:3', 'test-spork.R:469:3',
    'test-spork.R:490:3', 'test-spork.R:540:3', 'test-spork.R:567:3',
    'test-spork.R:615:3', 'test-spork.R:623:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-spork.R:297:1'): spork to plotmath is stable ───────────────────
  Error in `as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)`: cannot coerce class '"plotmath"' to a data.frame
  Backtrace:
       ▆
    1. ├─... %>% as_preview() at test-spork.R:297:1
    2. ├─spork::as_preview(.)
    3. └─spork:::as_preview.plotmath(.)
    4.   ├─latexpdf::as.png(...)
    5.   └─spork:::as.png.plotmath(...)
    6.     ├─ggplot2::ggplot(x, ...)
    7.     └─spork:::ggplot.plotmath(x, ...)
    8.       ├─ggplot2::ggplot(data.frame(x = 1, y = 1, label = (x)))
    9.       └─base::data.frame(x = 1, y = 1, label = (x))
   10.         ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
   11.         └─base::as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 101 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/string2path.Rcheck/00install.out' for details.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.1Mb
Missing or unexported objects:
  'GSVA::gsvaParam' 'GSVA::ssgseaParam'
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown

Quitting from lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'gsvaParam' is not an exported object from 'namespace:GSVA'
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'svHttp.Rmd' using rmarkdown
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
installed size is 78.7Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    gdal   2.8Mb
    libs  64.6Mb
    proj   7.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       7.2Mb
    tessdata  14.0Mb
Warning: declared S3 method 'filter.edsurvey.data.frame' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Warning: declared S3 method 'filter.Seurat' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/timeless.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/tok.Rcheck/00install.out' for details.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.6Mb
    include   1.8Mb
    libs     17.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.2Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.cla_fs' not found
Warning: declared S3 method 'transform.ts_aug_awareness' not found
Warning: declared S3 method 'transform.ts_aug_awaresmooth' not found
Warning: declared S3 method 'transform.ts_aug_flip' not found
Warning: declared S3 method 'transform.ts_aug_jitter' not found
Warning: declared S3 method 'transform.ts_aug_none' not found
Warning: declared S3 method 'transform.ts_aug_shrink' not found
Warning: declared S3 method 'transform.ts_aug_stretch' not found
Warning: declared S3 method 'transform.ts_aug_wormhole' not found
Warning: declared S3 method 'transform.ts_fil_ema' not found
Warning: declared S3 method 'transform.ts_fil_hp' not found
Warning: declared S3 method 'transform.ts_fil_kalman' not found
Warning: declared S3 method 'transform.ts_fil_lowess' not found
Warning: declared S3 method 'transform.ts_fil_ma' not found
Warning: declared S3 method 'transform.ts_fil_none' not found
Warning: declared S3 method 'transform.ts_fil_qes' not found
Warning: declared S3 method 'transform.ts_fil_recursive' not found
Warning: declared S3 method 'transform.ts_fil_seas_adj' not found
Warning: declared S3 method 'transform.ts_fil_ses' not found
Warning: declared S3 method 'transform.ts_fil_smooth' not found
Warning: declared S3 method 'transform.ts_fil_spline' not found
Warning: declared S3 method 'transform.ts_fil_winsor' not found
Warning: declared S3 method 'transform.ts_norm_none' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/unigd.Rcheck/00install.out' for details.
Running examples in 'uniswappeR-Ex.R' failed
The error most likely occurred in:

> ### Name: liquidity_range_all_v3
> ### Title: Forecast Price for liquidity range for a pair's tokens UniswapV3
> ### Aliases: liquidity_range_all_v3
> 
> ### ** Examples
> 
> liquidity_range_all_v3(pair_address = "0x1d42064fc4beb5f8aaf85f4617ae8b3b5b8bd801",
+                        days = 30, cap = 10, sims = 1000)
Warning: tz(): Don't know how to compute timezone for object of class NULL; returning "UTC".
Error in `[.data.frame`(data, , c("Date", "token0Price", "token1Price")) : 
  undefined columns selected
Calls: liquidity_range_all_v3 -> [ -> [.data.frame
Execution halted
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.3Mb
Package required and available but unsuitable version: 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 74.9Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      2.8Mb
    libs     60.3Mb
    proj      7.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/vol2birdR.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'changing_default_parameters.Rmd' using rmarkdown
--- finished re-building 'changing_default_parameters.Rmd'

--- re-building 'generate_data.Rmd' using rmarkdown
--- finished re-building 'generate_data.Rmd'

--- re-building 'process_bouts.Rmd' using rmarkdown

Quitting from lines 68-71 [unnamed-chunk-2] (process_bouts.Rmd)
Error: processing vignette 'process_bouts.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building 'process_bouts.Rmd'

SUMMARY: processing the following file failed:
  'process_bouts.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    help   1.9Mb
    libs   1.0Mb
Found the following problems:
retrieveFunctionReturnTypes.Rd:48:38: Warning: nested emphasis <code>


retrieveFunctionReturnTypes.Rd:52:38: Warning: nested emphasis <code>


retrieveFunctionReturnTypes.Rd:56:38: Warning: nested emphasis <code>


retrieveTestCaseDefinitions.Rd:52:38: Warning: nested emphasis <code>


retrieveTestCaseDefinitions.Rd:56:38: Warning: nested emphasis <code>


retrieveTestCaseDefinitions.Rd:61:38: Warning: nested emphasis <code>
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/x13binary.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/ymd.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/zoomerjoin.Rcheck/00install.out' for details.