* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/morse.Rcheck’
* using R Under development (unstable) (2024-06-30 r86853)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘morse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘morse’ version ‘3.3.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘morse’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/17s] OK
* checking Rd files ... NOTE
checkRd: (-1) plot.LCx.Rd:34: Lost braces
34 | \\code{LCx} class. It plots the survival probability as a function of concentration.
| ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [161s/162s] ERROR
Running examples in ‘morse-Ex.R’ failed
The error most likely occurred in:
> ### Name: MFx
> ### Title: Predict the Multiplication Factor leading to x% of reduction in
> ### survival at a specific time.
> ### Aliases: MFx MFx.survFit MFx_ode MFx_ode.survFit
>
> ### ** Examples
>
>
> # (1) Load the data
> data("propiconazole")
>
> # (2) Create an object of class 'survData'
> dataset <- survData(propiconazole)
>
> ## No test:
> # (3) Run the survFit function with model_type SD (or IT)
> out_SD <- survFit(dataset, model_type = "SD")
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 40
Unobserved stochastic nodes: 84
Total graph size: 1240
Initializing model
>
> # (4) data to predict
> data_4prediction <- data.frame(time = 1:10, conc = c(0,0.5,3,3,0,0,0.5,3,1.5,0))
>
> # (5) estimate MF(x=30, t=4), that is for 30% reduction of survival at time 4
> MFx_SD_30.4 <- MFx(out_SD, data_predict = data_4prediction , X = 30, time_MFx = 4)
q50 1 accuracy: 0.6462912 with multiplication factor: 1000
q50 2 accuracy: 0.6462912 with multiplication factor: 500
q50 3 accuracy: 0.6462912 with multiplication factor: 250
q50 4 accuracy: 0.6462912 with multiplication factor: 125
q50 5 accuracy: 0.6462912 with multiplication factor: 62.5
q50 6 accuracy: 0.6462384 with multiplication factor: 31.25
q50 7 accuracy: 0.6104681 with multiplication factor: 15.625
q50 8 accuracy: 0.03347525 with multiplication factor: 7.8125
q50 9 accuracy: 0.2769819 with multiplication factor: 3.90625
q50 10 accuracy: 0.2717134 with multiplication factor: 5.859375
q50 11 accuracy: 0.1472467 with multiplication factor: 6.835938
q50 12 accuracy: 0.05543355 with multiplication factor: 7.324219
q50 13 accuracy: 0.01075896 with multiplication factor: 7.568359
q50 14 accuracy: 0.01142361 with multiplication factor: 7.69043
q50 15 accuracy: 0.0004065483 with multiplication factor: 7.629395
qinf95 1 accuracy: 0.6462912 with multiplication factor: 1000
qinf95 2 accuracy: 0.6462912 with multiplication factor: 500
qinf95 3 accuracy: 0.6462912 with multiplication factor: 250
qinf95 4 accuracy: 0.6462912 with multiplication factor: 125
qinf95 5 accuracy: 0.6462912 with multiplication factor: 62.5
qinf95 6 accuracy: 0.6462903 with multiplication factor: 31.25
qinf95 7 accuracy: 0.635502 with multiplication factor: 15.625
qinf95 8 accuracy: 0.1174724 with multiplication factor: 7.8125
qinf95 9 accuracy: 0.2176563 with multiplication factor: 3.90625
qinf95 10 accuracy: 0.2112206 with multiplication factor: 5.859375
qinf95 11 accuracy: 0.0710002 with multiplication factor: 6.835938
qinf95 12 accuracy: 0.02314409 with multiplication factor: 7.324219
qinf95 13 accuracy: 0.02426829 with multiplication factor: 7.080078
qinf95 14 accuracy: 0.0006439577 with multiplication factor: 7.202148
qsup95 1 accuracy: 0.6462912 with multiplication factor: 1000
qsup95 2 accuracy: 0.6462912 with multiplication factor: 500
qsup95 3 accuracy: 0.6462912 with multiplication factor: 250
qsup95 4 accuracy: 0.6462912 with multiplication factor: 125
qsup95 5 accuracy: 0.6462911 with multiplication factor: 62.5
qsup95 6 accuracy: 0.6452254 with multiplication factor: 31.25
qsup95 7 accuracy: 0.554416 with multiplication factor: 15.625
qsup95 8 accuracy: 0.05169158 with multiplication factor: 7.8125
qsup95 9 accuracy: 0.3838515 with multiplication factor: 11.71875
qsup95 10 accuracy: 0.2168242 with multiplication factor: 9.765625
qsup95 11 accuracy: 0.09849466 with multiplication factor: 8.789062
qsup95 12 accuracy: 0.02747805 with multiplication factor: 8.300781
qsup95 13 accuracy: 0.01127919 with multiplication factor: 8.056641
qsup95 14 accuracy: 0.008250363 with multiplication factor: 8.178711
>
> # (5bis) estimate MF(x,t) along the MF_range from 5 to 10 (50) (X = NULL)
> MFx_SD_range <- MFx(out_SD, data_predict = data_4prediction ,
+ X = NULL, time_MFx = 4, MFx_range = seq(5, 10, length.out = 50))
> ## End(No test)
>
>
>
> # (1) Load the data
> data("propiconazole")
>
> # (2) Create an object of class 'survData'
> dataset <- survData(propiconazole)
>
> ## No test:
> # (3) Run the survFit function with model_type SD (or IT)
> out_SD <- survFit(dataset, model_type = "SD")
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 40
Unobserved stochastic nodes: 84
Total graph size: 1240
Initializing model
>
> # (4) data to predict
> data_4prediction <- data.frame(time = 1:10, conc = c(0,0.5,3,3,0,0,0.5,3,1.5,0))
>
> # (5) estimate MF(x=30, t=4), that is for 30% reduction of survival at time 4
> MFx_SD_30.4 <- MFx_ode(out_SD, data_predict = data_4prediction , X = 30, time_MFx = 4)
Warning in MFx_ode.survFit(out_SD, data_predict = data_4prediction, X = 30, :
The function 'MFx_ode' uses 'predict_ode' to compute the predictions for calculating the multiplication factors.
This can take a very long time to compute (minutes to hours).
Prefer the function 'MFx' when possible.
Error in predict_ode.survFit(object = object, data_predict = ls_data_predict[[1]], :
Please provide value for `hb` using `hb_valueFORCED`.
Calls: MFx_ode ... MFx_ode.survFit -> predict_ode -> predict_ode.survFit
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [113s/113s]
[113s/113s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/data/blackswan/ripley/R/packages/tests-devel/morse.Rcheck/00check.log’
for details.
Command exited with non-zero status 1
Time 5:41.77, 332.23 + 8.07