Allow vpc to be an s3 method.

[mattfidler]

Addresses Issue #92

[mattfidler]

Hi @guiastrennec I have fixed the VPC issues. I think you have some problems with the tibbles they have a new type of output based on pillar. I'm not sure what you want to do with these tests.

[mattfidler]

The first failure is

> sum_term(model, "nonmem")
# A tibble: 1 x 4
  problem subprob label value                                                  
    <dbl>   <dbl> <chr> <chr>                                                  
1    1.00       0 term  "MINIMIZATION TERMINATED\nDUE TO PROXIMITY OF NEXT ITE 
> expected_result
# A tibble: 1 x 4
  problem subprob label value                                                  
    <dbl>   <dbl> <chr> <chr>                                                  
1    1.00       0 term  "MINIMIZATION TERMINATED\nDUE TO PROXIMITY OF NEXT ITE 
> 

The structure is the same too

> str(sum_term(model, "nonmem"))
Classes 'tbl_df', 'tbl' and 'data.frame':	1 obs. of  4 variables:
 $ problem: num 1
 $ subprob: num 0
 $ label  : chr "term"
 $ value  : chr "MINIMIZATION TERMINATED\nDUE TO PROXIMITY OF NEXT ITERATION EST. TO A VALUE\nAT WHICH THE OBJ. FUNC. IS INFINIT"| __truncated__
> str(expected_result)
Classes 'tbl_df', 'tbl' and 'data.frame':	1 obs. of  4 variables:
 $ problem: num 1
 $ subprob: num 0
 $ label  : chr "term"
 $ value  : chr "MINIMIZATION TERMINATED\nDUE TO PROXIMITY OF NEXT ITERATION EST. TO A VALUE\nAT WHICH THE OBJ. FUNC. IS INFINIT"| __truncated__
> 

[mattfidler]

Note, that running test-xpose_data line by line yeilds no errors. So to me there something has changed in stringr or the like.

[mattfidler]

To test my hypothesis, I tested your package without any modifications on my system (which has some of the latest packages) and get the same failures:

Here is my output

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> > if (identical(getOption('pager'), file.path(R.home('bin'), 'pager'))) options(pager='console') # rather take the ESS one 
> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> devtools::check()
Updating xpose documentation
Loading xpose
Loading required package: ggplot2
Do you like the new xpose? Give us some feedback on github:
https://github.com/UUPharmacometrics/xpose
Writing NAMESPACE
Writing xpdb_ex_pk.Rd
Writing data_opt.Rd
Writing only_obs.Rd
Writing only_distinct.Rd
Writing reorder_factors.Rd
Writing fetch_data.Rd
Writing list_nm_tables.Rd
Writing manual_nm_import.Rd
Writing list_nm_tables_manual.Rd
Writing amt_vs_idv.Rd
Writing distrib_plot.Rd
Writing dv_vs_pred.Rd
Writing ind_plots.Rd
Writing minimization_plots.Rd
Writing qq_plot.Rd
Writing res_vs_pred.Rd
Writing res_vs_idv.Rd
Writing pred_vs_idv.Rd
Writing vpc.Rd
Writing print.xpose_data.Rd
Writing print.xpose_plot.Rd
Writing prm_table.Rd
Writing read_nm_files.Rd
Writing parse_nm_files.Rd
Writing raw_to_tibble.Rd
Writing read_nm_model.Rd
Writing read_nm_tables.Rd
Writing read_funs.Rd
Writing read_args.Rd
Writing combine_tables.Rd
Writing merge_firstonly.Rd
Writing index_table.Rd
Writing summary.xpose_data.Rd
Writing template_titles.Rd
Writing gg_themes.Rd
Writing xp_themes.Rd
Writing transform_prm.Rd
Writing update_themes.Rd
Writing reexports.Rd
Writing is.xp.theme.Rd
Writing is.xpdb.Rd
Writing is.nm.model.Rd
Writing is.nm.table.list.Rd
Writing as.nm.table.list.Rd
Writing is.xpose.plot.Rd
Writing is.formula.Rd
Writing as.ctime.Rd
Writing msg.Rd
Writing file_path.Rd
Writing get_extension.Rd
Writing make_extension.Rd
Writing update_extension.Rd
Writing software.Rd
Writing list_vars.Rd
Writing set_vars.Rd
Writing vpc_data.Rd
Writing vpc_opt.Rd
Writing get_code.Rd
Writing get_data.Rd
Writing get_file.Rd
Writing get_summary.Rd
Writing get_prm.Rd
Writing grab_iter.Rd
Writing get_prm_transformation_formulas.Rd
Writing get_special.Rd
Writing subset_xpdb.Rd
Writing modify_xpdb.Rd
Writing summarize_xpdb.Rd
Writing edit_xpose_data.Rd
Writing xpdb_index_update.Rd
Writing check_quo_vars.Rd
Writing irep.Rd
Writing list_xpdb.Rd
Writing xplot_distrib.Rd
Writing check_problem.Rd
Writing check_xpdb.Rd
Writing check_plot_type.Rd
Writing check_scales.Rd
Writing append_suffix.Rd
Writing parse_title.Rd
Writing filter_xp_theme.Rd
Writing all_data_problem.Rd
Writing last_data_problem.Rd
Writing default_plot_problem.Rd
Writing all_file_problem.Rd
Writing last_file_problem.Rd
Writing last_file_subprob.Rd
Writing last_file_method.Rd
Writing drop_fixed_cols.Rd
Writing xp_var.Rd
Writing aes_c.Rd
Writing aes_filter.Rd
Writing aes_rename.Rd
Writing add_facet_var.Rd
Writing xplot_qq.Rd
Writing xplot_scatter.Rd
Writing xpose-package.Rd
Writing xpose_data.Rd
Writing parse_arg.Rd
Writing update_args.Rd
Writing xp_map.Rd
Writing xp_geoms.Rd
Writing xpose_panels.Rd
Writing xpose_save.Rd
Setting env vars --------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building xpose ----------------------------------------------------------------
"c:/Users/fidlema3/AppData/Local/nlmixr/R/bin/x64/R" --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD build  \
  "c:/SVN/Wenping/xpose" --no-resave-data --no-manual 

* checking for file 'c:/SVN/Wenping/xpose/DESCRIPTION' ... OK
* preparing 'xpose':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'xpose_0.4.2.tar.gz'

Setting env vars --------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_           : FALSE
_R_CHECK_FORCE_SUGGESTS_          : FALSE
Checking xpose ----------------------------------------------------------------
"c:/Users/fidlema3/AppData/Local/nlmixr/R/bin/x64/R" --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD check  \
  "C:\Users\fidlema3\AppData\Local\Temp\ep\Rtmpu6EfqF/xpose_0.4.2.tar.gz"  \
  --as-cran --timings --no-manual 

* using log directory 'C:/Users/fidlema3/AppData/Local/Temp/ep/Rtmpu6EfqF/xpose.Rcheck'
* using R version 3.4.3 (2017-11-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'xpose/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'xpose' version '0.4.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'webshot'
* 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 whether package 'xpose' can be installed ... OK
* checking installed package size ... OK
* 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 R 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 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 ... OK
* checking Rd files ... OK
* 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 data for ASCII and uncompressed saves ... OK
 WARNING
'qpdf' is needed for checks on size reduction of PDFs
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
ind_plots 5.41   0.03    5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R' [40s]
Warning message:
running command '"c:/Users/fidlema3/AppData/Local/nlmixr/R/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  7: all.equal(target[[i]], current[[i]], check.attributes = check.attributes, use.names = use.names, 
         ...)
  8: all.equal.tbl_df(target[[i]], current[[i]], check.attributes = check.attributes, 
         use.names = use.names, ...)
  9: equal_data_frame(target, current, ignore_col_order = ignore_col_order, ignore_row_order = ignore_row_order, 
         convert = convert)
  
  == testthat results  ===========================================================
  OK: 528 SKIPPED: 0 FAILED: 3
  1. Failure: Termination messages are parsed when minimization is terminated (@test-model-summary.R#121) 
  2. Error: properly creates the xpdb when using the file argument (@test-xpose_data.R#47) 
  3. Error: properly creates the xpdb when using the runno argument (@test-xpose_data.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  'C:/Users/fidlema3/AppData/Local/Temp/ep/Rtmpu6EfqF/xpose.Rcheck/00check.log'
for details.

R CMD check results
1 error  | 0 warnings | 1 note 
checking tests ... ERROR
  Running 'testthat.R' [40s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  7: all.equal(target[[i]], current[[i]], check.attributes = check.attributes, use.names = use.names, 
         ...)
  8: all.equal.tbl_df(target[[i]], current[[i]], check.attributes = check.attributes, 
         use.names = use.names, ...)
  9: equal_data_frame(target, current, ignore_col_order = ignore_col_order, ignore_row_order = ignore_row_order, 
         convert = convert)
  
  == testthat results  ===========================================================
  OK: 528 SKIPPED: 0 FAILED: 3
  1. Failure: Termination messages are parsed when minimization is terminated (@test-model-summary.R#121) 
  2. Error: properly creates the xpdb when using the file argument (@test-xpose_data.R#47) 
  3. Error: properly creates the xpdb when using the runno argument (@test-xpose_data.R#64) 
  
  Error: testthat unit tests failed
  Execution halted

checking package dependencies ... NOTE
Package suggested but not available for checking: 'webshot'
> 

[mattfidler]

My session info

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xpose_0.4.2   ggplot2_2.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16     pillar_1.1.0     compiler_3.4.3   plyr_1.8.4      
 [5] bindr_0.1        tools_3.4.3      testthat_2.0.0   digest_0.6.15   
 [9] memoise_1.1.0    tibble_1.4.2     gtable_0.2.0     pkgconfig_2.0.1 
[13] rlang_0.2.0      commonmark_1.4   bindrcpp_0.2     withr_2.1.1     
[17] dplyr_0.7.4      stringr_1.3.0    roxygen2_6.0.1   xml2_1.1.1      
[21] desc_1.1.1       devtools_1.13.4  hms_0.4.0        rprojroot_1.3-2 
[25] grid_3.4.3       glue_1.2.0       R6_2.2.2         tweenr_0.1.5    
[29] purrr_0.2.4      readr_1.1.1      tidyr_0.8.0      udunits2_0.13   
[33] magrittr_1.5     backports_1.1.2  vpc_1.0.2        scales_0.5.0    
[37] MASS_7.3-47      units_0.5-1      assertthat_0.2.0 ggforce_0.1.1   
[41] colorspace_1.3-2 stringi_1.1.7    lazyeval_0.2.1   munsell_0.4.3   
[45] crayon_1.3.4    
> 

[bguiastr]

Thanks for the PR. I am aware of the issues with the tests, they are the result of a bug introduced in stringr back in December. I reported the issue but it has not yet been fixed (tidyverse/stringr#203).

[mattfidler]

Let me know if it gets fixed.

For now, since there is really no issue with the xpose package, I am going to include this branch in the nlmixr installer (FYI), unless you have some strong objection to this.

[vrognas]

The issue in stringr has been fixed in tidyverse/stringr#206