CRAN Package Check Results for Package msmtools

Last updated on 2024-09-27 17:51:25 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.1 10.76 87.93 98.69 ERROR
r-devel-linux-x86_64-debian-gcc 2.0.1 7.92 61.76 69.68 ERROR
r-devel-linux-x86_64-fedora-clang 2.0.1 150.37 ERROR
r-devel-linux-x86_64-fedora-gcc 2.0.1 157.90 ERROR
r-devel-windows-x86_64 2.0.1 12.00 96.00 108.00 ERROR
r-patched-linux-x86_64 2.0.1 10.42 82.12 92.54 ERROR
r-release-linux-x86_64 2.0.1 8.74 81.71 90.45 ERROR
r-release-macos-arm64 2.0.1 61.00 OK
r-release-macos-x86_64 2.0.1 141.00 OK
r-release-windows-x86_64 2.0.1 11.00 93.00 104.00 ERROR
r-oldrel-macos-arm64 2.0.1 89.00 OK
r-oldrel-macos-x86_64 2.0.1 107.00 OK
r-oldrel-windows-x86_64 2.0.1 14.00 115.00 129.00 ERROR

Check Details

Version: 2.0.1
Check: examples
Result: ERROR Running examples in ‘msmtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.036 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘msmtools.Rmd’ using rmarkdown_notangle Quitting from lines 300-318 [multistate_model] (msmtools.Rmd) Error: processing vignette 'msmtools.Rmd' failed with diagnostics: object 'augmented_int' not found --- failed re-building ‘msmtools.Rmd’ SUMMARY: processing the following file failed: ‘msmtools.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.0.1
Check: examples
Result: ERROR Running examples in ‘msmtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.078 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.0.1
Check: examples
Result: ERROR Running examples in ‘msmtools-Ex.R’ failed The error most likely occurred in: > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.063 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘msmtools.Rmd’ using rmarkdown_notangle Quitting from lines 300-318 [multistate_model] (msmtools.Rmd) Error: processing vignette 'msmtools.Rmd' failed with diagnostics: object 'augmented_int' not found --- failed re-building ‘msmtools.Rmd’ SUMMARY: processing the following file failed: ‘msmtools.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 2.0.1
Check: examples
Result: ERROR Running examples in ‘msmtools-Ex.R’ failed The error most likely occurred in: > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.067 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.0.1
Check: examples
Result: ERROR Running examples in 'msmtools-Ex.R' failed The error most likely occurred in: > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.03 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavors: r-devel-windows-x86_64, r-release-windows-x86_64

Version: 2.0.1
Check: examples
Result: ERROR Running examples in ‘msmtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.039 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-patched-linux-x86_64

Version: 2.0.1
Check: examples
Result: ERROR Running examples in ‘msmtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.068 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-release-linux-x86_64

Version: 2.0.1
Check: examples
Result: ERROR Running examples in 'msmtools-Ex.R' failed The error most likely occurred in: > ### Name: polish > ### Title: Remove observations with different states occurring at the same > ### time > ### Aliases: polish > > ### ** Examples > > > # loading data > data( hosp ) > > # augmenting longitudinal data > hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number, + pattern = label_3, t_start = dateIN, t_end = dateOUT, + t_cens = dateCENS ) Warning in augment(data = hosp, data_key = subj, n_events = adm_number, : no t_death has been passed. Assuming that dateCENS contains both censoring and death times ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking monotonicity of adm_number Ok, adm_number is monotonic --- checking label_3 and defining patterns Ok, detected 3 values --- augmenting data Ok, data have been augmented --- defining dimesions Ok, dimensions computed --- adding status flag status flag has been added successfully --- adding numeric status flag numeric status has been added successfully --- adding sequential status flag sequential status flag has been added successfully --- adding variable augmented as new time variable variables "augmented" and "augmented_int" successfully added and repositioned --- --------------------------- augment() took: 0.04 sec. --------------------------- > > # cleaning any targeted occurrence > hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 ) ------------------------------------- # # # # setting everything up # # # # ------------------------------------- checking label_3 and defining patterns Ok, detected 3 values --- Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : argument "time" is missing, with no default Calls: polish -> duplicated -> duplicated.data.table -> eval Execution halted Flavor: r-oldrel-windows-x86_64