CRAN Package Check Results for Package vpc

Last updated on 2020-05-30 15:48:35 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.0 7.71 94.26 101.97 OK
r-devel-linux-x86_64-debian-gcc 1.2.0 6.95 73.67 80.62 ERROR
r-devel-linux-x86_64-fedora-clang 1.2.0 131.71 OK
r-devel-linux-x86_64-fedora-gcc 1.2.0 127.42 ERROR
r-devel-windows-ix86+x86_64 1.2.0 20.00 149.00 169.00 OK
r-patched-linux-x86_64 1.2.0 8.14 92.49 100.63 OK
r-patched-solaris-x86 1.2.0 174.00 ERROR
r-release-linux-x86_64 1.2.0 9.64 94.91 104.55 ERROR
r-release-osx-x86_64 1.2.0 OK
r-release-windows-ix86+x86_64 1.2.0 16.00 137.00 153.00 OK
r-oldrel-osx-x86_64 1.2.0 OK
r-oldrel-windows-ix86+x86_64 1.2.0 13.00 104.00 117.00 OK

Check Details

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in ‘vpc-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: vpc_cat
    > ### Title: VPC function for categorical
    > ### Aliases: vpc_cat
    >
    > ### ** Examples
    >
    >
    > ## See vpc.ronkeizer.com for more documentation and examples
    > library(vpc)
    >
    > # simple function to simulate categorical data for single individual
    > sim_id <- function(id = 1) {
    + n <- 10
    + logit <- function(x) exp(x) / (1+exp(x))
    + data.frame(id = id, time = seq(1, n, length.out = n),
    + dv = round(logit((1:n) - n/2 + rnorm(n, 0, 1.5))) )
    + }
    > ## simple function to simulate categorical data for a trial
    > sim_trial <- function(i = 1, n = 20) { # function to simulate categorical data for a trial
    + data.frame(sim = i, do.call("rbind", lapply(1:n, sim_id)))
    + }
    >
    > ## simulate single trial for 20 individuals
    > obs <- sim_trial(n = 20)
    >
    > ## simulate 200 trials of 20 individuals
    > sim <- do.call("rbind", lapply(1:200, sim_trial, n = 20))
    >
    > ## Plot categorical VPC
    > vpc_cat(sim = sim, obs = obs)
    New names:
    * sim -> sim...1
    * bin -> bin...2
    * `fact_perc(dv, lev[i])` -> `fact_perc(dv, lev[i])...3`
    * sim -> sim...4
    * bin -> bin...5
    * ...
    New names:
    * strat -> strat...1
    * bin -> bin...2
    * strat -> strat...4
    * bin -> bin...5
    * strat -> strat...7
    * ...
    Error in names(x) <- value :
     'names' attribute [6] must be the same length as the vector [4]
    Calls: vpc_cat -> colnames<-
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.2.0
Check: tests
Result: ERROR
     Running ‘test-add_sim_index_number.R’ [9s/14s]
     Running ‘test-filter_dv.R’ [0s/1s]
     Running ‘test-labeller.R’ [4s/6s]
     Running ‘test-softwaretype.R’ [0s/1s]
     Running ‘test-strat-col-detection.R’ [0s/1s]
     Running ‘test-vpc.R’ [3s/5s]
     Running ‘test-vpc_cat.R’ [2s/3s]
     Running ‘test-vpc_cens.R’ [5s/7s]
     Running ‘test-vpc_tte.R’ [7s/10s]
    Running the tests in ‘tests/test-vpc_cat.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > tmp <- simple_data
     > cat <- cut(tmp$obs$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$obs$DV <- match(cat, levels(cat))
     > cat2 <- cut(tmp$sim$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$sim$DV <- match(cat2, levels(cat2))
     > obj <- vpc_cat(sim = tmp$sim, obs = tmp$obs, vpcdb = TRUE)
     New names:
     * sim -> sim...1
     * bin -> bin...2
     * `fact_perc(dv, lev[i])` -> `fact_perc(dv, lev[i])...3`
     * sim -> sim...4
     * bin -> bin...5
     * ...
     New names:
     * strat -> strat...1
     * bin -> bin...2
     * strat -> strat...4
     * bin -> bin...5
     * strat -> strat...7
     * ...
     Error in names(x) <- value :
     'names' attribute [6] must be the same length as the vector [4]
     Calls: vpc_cat -> colnames<-
     Execution halted
    Running the tests in ‘tests/test-vpc_cens.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > ## Test regular vpc in presence of lloq / uloq data
     > obj1 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, uloq = 120, vpcdb = TRUE)
     > obj2 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 20, vpcdb = TRUE)
     > assert("6 values in upper percentile flagged as >uloq", vpc:::is_equal(sum(is.na(obj1$aggr_obs$obs95)), 6))
     > assert("4 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs5)), 4))
     > assert("1 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs50)), 1))
     >
     > ## test vpc func
     > obj <- vpc_cens(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs,
     + lloq = 30, n_bins = 8, vpcdb = TRUE)
     New names:
     * strat -> strat...1
     * sim -> sim...2
     * bin -> bin...3
     * strat -> strat...5
     * sim -> sim...6
     * ...
     Error: Must group by variables found in `.data`.
     * Column `strat` is not found.
     * Column `bin` is not found.
     Backtrace:
     █
     1. └─vpc::vpc_cens(...)
     2. └─aggr_sim %>% dplyr::group_by(strat, bin)
     3. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     4. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     6. └─vpc:::`_fseq`(`_lhs`)
     7. └─magrittr::freduce(value, `_function_list`)
     8. ├─base::withVisible(function_list[[k]](value))
     9. └─function_list[[k]](value)
     10. ├─dplyr::group_by(., strat, bin)
     11. └─dplyr:::group_by.data.frame(., strat, bin)
     12. └─dplyr::group_by_prepare(.data, ..., .add = .add)
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in ‘vpc-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: vpc_cat
    > ### Title: VPC function for categorical
    > ### Aliases: vpc_cat
    >
    > ### ** Examples
    >
    >
    > ## See vpc.ronkeizer.com for more documentation and examples
    > library(vpc)
    >
    > # simple function to simulate categorical data for single individual
    > sim_id <- function(id = 1) {
    + n <- 10
    + logit <- function(x) exp(x) / (1+exp(x))
    + data.frame(id = id, time = seq(1, n, length.out = n),
    + dv = round(logit((1:n) - n/2 + rnorm(n, 0, 1.5))) )
    + }
    > ## simple function to simulate categorical data for a trial
    > sim_trial <- function(i = 1, n = 20) { # function to simulate categorical data for a trial
    + data.frame(sim = i, do.call("rbind", lapply(1:n, sim_id)))
    + }
    >
    > ## simulate single trial for 20 individuals
    > obs <- sim_trial(n = 20)
    >
    > ## simulate 200 trials of 20 individuals
    > sim <- do.call("rbind", lapply(1:200, sim_trial, n = 20))
    >
    > ## Plot categorical VPC
    > vpc_cat(sim = sim, obs = obs)
    New names:
    * sim -> sim...1
    * bin -> bin...2
    * `fact_perc(dv, lev[i])` -> `fact_perc(dv, lev[i])...3`
    * sim -> sim...4
    * bin -> bin...5
    * ...
    New names:
    * strat -> strat...1
    * bin -> bin...2
    * strat -> strat...4
    * bin -> bin...5
    * strat -> strat...7
    * ...
    Error in names(x) <- value :
     'names' attribute [6] must be the same length as the vector [4]
    Calls: vpc_cat -> colnames<-
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 1.2.0
Check: tests
Result: ERROR
     Running ‘test-add_sim_index_number.R’ [15s/27s]
     Running ‘test-filter_dv.R’
     Running ‘test-labeller.R’ [6s/11s]
     Running ‘test-softwaretype.R’
     Running ‘test-strat-col-detection.R’
     Running ‘test-vpc.R’
     Running ‘test-vpc_cat.R’
     Running ‘test-vpc_cens.R’
     Running ‘test-vpc_tte.R’ [12s/18s]
    Running the tests in ‘tests/test-vpc_cat.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > tmp <- simple_data
     > cat <- cut(tmp$obs$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$obs$DV <- match(cat, levels(cat))
     > cat2 <- cut(tmp$sim$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$sim$DV <- match(cat2, levels(cat2))
     > obj <- vpc_cat(sim = tmp$sim, obs = tmp$obs, vpcdb = TRUE)
     New names:
     * sim -> sim...1
     * bin -> bin...2
     * `fact_perc(dv, lev[i])` -> `fact_perc(dv, lev[i])...3`
     * sim -> sim...4
     * bin -> bin...5
     * ...
     New names:
     * strat -> strat...1
     * bin -> bin...2
     * strat -> strat...4
     * bin -> bin...5
     * strat -> strat...7
     * ...
     Error in names(x) <- value :
     'names' attribute [6] must be the same length as the vector [4]
     Calls: vpc_cat -> colnames<-
     Execution halted
    Running the tests in ‘tests/test-vpc_cens.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > ## Test regular vpc in presence of lloq / uloq data
     > obj1 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, uloq = 120, vpcdb = TRUE)
     > obj2 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 20, vpcdb = TRUE)
     > assert("6 values in upper percentile flagged as >uloq", vpc:::is_equal(sum(is.na(obj1$aggr_obs$obs95)), 6))
     > assert("4 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs5)), 4))
     > assert("1 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs50)), 1))
     >
     > ## test vpc func
     > obj <- vpc_cens(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs,
     + lloq = 30, n_bins = 8, vpcdb = TRUE)
     New names:
     * strat -> strat...1
     * sim -> sim...2
     * bin -> bin...3
     * strat -> strat...5
     * sim -> sim...6
     * ...
     Error: Must group by variables found in `.data`.
     * Column `strat` is not found.
     * Column `bin` is not found.
     Backtrace:
     █
     1. └─vpc::vpc_cens(...)
     2. └─aggr_sim %>% dplyr::group_by(strat, bin)
     3. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     4. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     6. └─vpc:::`_fseq`(`_lhs`)
     7. └─magrittr::freduce(value, `_function_list`)
     8. ├─base::withVisible(function_list[[k]](value))
     9. └─function_list[[k]](value)
     10. ├─dplyr::group_by(., strat, bin)
     11. └─dplyr:::group_by.data.frame(., strat, bin)
     12. └─dplyr::group_by_prepare(.data, ..., .add = .add)
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2.0
Check: tests
Result: ERROR
     Running ‘test-add_sim_index_number.R’ [18s/18s]
     Running ‘test-filter_dv.R’
     Running ‘test-labeller.R’
     Running ‘test-softwaretype.R’
     Running ‘test-strat-col-detection.R’
     Running ‘test-vpc.R’
     Running ‘test-vpc_cat.R’
     Running ‘test-vpc_cens.R’
     Running ‘test-vpc_tte.R’ [15s/15s]
    Running the tests in ‘tests/test-vpc_cat.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > tmp <- simple_data
     > cat <- cut(tmp$obs$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$obs$DV <- match(cat, levels(cat))
     > cat2 <- cut(tmp$sim$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$sim$DV <- match(cat2, levels(cat2))
     > obj <- vpc_cat(sim = tmp$sim, obs = tmp$obs, vpcdb = TRUE)
     New names:
     * sim -> sim...1
     * bin -> bin...2
     * `fact_perc(dv, lev[i])` -> `fact_perc(dv, lev[i])...3`
     * sim -> sim...4
     * bin -> bin...5
     * ...
     New names:
     * strat -> strat...1
     * bin -> bin...2
     * strat -> strat...4
     * bin -> bin...5
     * strat -> strat...7
     * ...
     Error in names(x) <- value :
     'names' attribute [6] must be the same length as the vector [4]
     Calls: vpc_cat -> colnames<-
     Execution halted
    Running the tests in ‘tests/test-vpc_cens.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > ## Test regular vpc in presence of lloq / uloq data
     > obj1 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, uloq = 120, vpcdb = TRUE)
     > obj2 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 20, vpcdb = TRUE)
     > assert("6 values in upper percentile flagged as >uloq", vpc:::is_equal(sum(is.na(obj1$aggr_obs$obs95)), 6))
     > assert("4 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs5)), 4))
     > assert("1 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs50)), 1))
     >
     > ## test vpc func
     > obj <- vpc_cens(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs,
     + lloq = 30, n_bins = 8, vpcdb = TRUE)
     New names:
     * strat -> strat...1
     * sim -> sim...2
     * bin -> bin...3
     * strat -> strat...5
     * sim -> sim...6
     * ...
     Error: Must group by variables found in `.data`.
     * Column `strat` is not found.
     * Column `bin` is not found.
     Backtrace:
     █
     1. └─vpc::vpc_cens(...)
     2. └─aggr_sim %>% dplyr::group_by(strat, bin)
     3. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     4. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     6. └─vpc:::`_fseq`(`_lhs`)
     7. └─magrittr::freduce(value, `_function_list`)
     8. ├─base::withVisible(function_list[[k]](value))
     9. └─function_list[[k]](value)
     10. ├─dplyr::group_by(., strat, bin)
     11. └─dplyr:::group_by.data.frame(., strat, bin)
     12. └─dplyr::group_by_prepare(.data, ..., .add = .add)
     Execution halted
Flavor: r-patched-solaris-x86

Version: 1.2.0
Check: tests
Result: ERROR
     Running ‘test-add_sim_index_number.R’ [13s/15s]
     Running ‘test-filter_dv.R’ [0s/1s]
     Running ‘test-labeller.R’ [5s/5s]
     Running ‘test-softwaretype.R’ [0s/1s]
     Running ‘test-strat-col-detection.R’ [0s/1s]
     Running ‘test-vpc.R’ [5s/5s]
     Running ‘test-vpc_cat.R’ [2s/3s]
     Running ‘test-vpc_cens.R’ [6s/7s]
     Running ‘test-vpc_tte.R’ [9s/10s]
    Running the tests in ‘tests/test-vpc_cat.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > tmp <- simple_data
     > cat <- cut(tmp$obs$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$obs$DV <- match(cat, levels(cat))
     > cat2 <- cut(tmp$sim$DV, breaks = c(-1, 10, 40, 1000))
     > tmp$sim$DV <- match(cat2, levels(cat2))
     > obj <- vpc_cat(sim = tmp$sim, obs = tmp$obs, vpcdb = TRUE)
     New names:
     * sim -> sim...1
     * bin -> bin...2
     * `fact_perc(dv, lev[i])` -> `fact_perc(dv, lev[i])...3`
     * sim -> sim...4
     * bin -> bin...5
     * ...
     New names:
     * strat -> strat...1
     * bin -> bin...2
     * strat -> strat...4
     * bin -> bin...5
     * strat -> strat...7
     * ...
     Error in names(x) <- value :
     'names' attribute [6] must be the same length as the vector [4]
     Calls: vpc_cat -> colnames<-
     Execution halted
    Running the tests in ‘tests/test-vpc_cens.R’ failed.
    Complete output:
     > library(vpc)
     > library(testit)
     > Sys.setenv("R_TESTS" = "")
     >
     > ## Test regular vpc in presence of lloq / uloq data
     > obj1 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, uloq = 120, vpcdb = TRUE)
     > obj2 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 20, vpcdb = TRUE)
     > assert("6 values in upper percentile flagged as >uloq", vpc:::is_equal(sum(is.na(obj1$aggr_obs$obs95)), 6))
     > assert("4 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs5)), 4))
     > assert("1 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs50)), 1))
     >
     > ## test vpc func
     > obj <- vpc_cens(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs,
     + lloq = 30, n_bins = 8, vpcdb = TRUE)
     New names:
     * strat -> strat...1
     * sim -> sim...2
     * bin -> bin...3
     * strat -> strat...5
     * sim -> sim...6
     * ...
     Error: Must group by variables found in `.data`.
     * Column `strat` is not found.
     * Column `bin` is not found.
     Backtrace:
     █
     1. └─vpc::vpc_cens(...)
     2. └─aggr_sim %>% dplyr::group_by(strat, bin)
     3. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     4. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
     6. └─vpc:::`_fseq`(`_lhs`)
     7. └─magrittr::freduce(value, `_function_list`)
     8. ├─base::withVisible(function_list[[k]](value))
     9. └─function_list[[k]](value)
     10. ├─dplyr::group_by(., strat, bin)
     11. └─dplyr:::group_by.data.frame(., strat, bin)
     12. └─dplyr::group_by_prepare(.data, ..., .add = .add)
     Execution halted
Flavor: r-release-linux-x86_64