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ggPMXdevelopment / ggPMX

ggPMX R package
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ggPMX cannot use of absolute filepath for results folder #151

Closed combefr1 closed 2 years ago

combefr1 commented 3 years ago

Hi Just to let you know, when monolix .mlxtran file is using absolute path, the pmx_mlxtran cannot find the results folder

Error in parse_mlxtran(file_name) : No results directory provided.

in that case, the monolix file contains: 

[SETTINGS]
GLOBAL:
exportpath = '/view/combefr1_view/vob/CLCI699C/pool/pkpd_003/pgm_05/MT-34425_Renal_hepatic_impairment_Aug2018/monolix/HEPAT/Second_Covariate/V2_merged/project'

it works if I duplicate the project.mlxtran file and convert absolute by relative path: 

[SETTINGS]
GLOBAL:
exportpath = 'project'

To Reproduce:

Package and platform:

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /CHBS/apps/intel/15.3.187/composer_xe_2015.3.187/mkl/lib/intel64/libmkl_gf_lp64.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] gridExtra_2.3           lixoftConnectors_2019.2 RJSONIO_1.3-1.3        
[4] rmarkdown_1.16          mlxR_4.1.0              ggPMX_1.0              
[7] ggplot2_3.2.1           tidyr_1.0.0             dplyr_0.8.3            

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3         highr_0.8          pillar_1.4.2       compiler_3.6.1    
 [5] RColorBrewer_1.1-2 plyr_1.8.4         tools_3.6.1        digest_0.6.22     
 [9] zeallot_0.1.0      lattice_0.20-38    evaluate_0.14      lifecycle_0.1.0   
[13] tibble_2.1.3       gtable_0.3.0       pkgconfig_2.0.3    rlang_0.4.1       
[17] rstudioapi_0.10    GGally_1.4.0       yaml_2.2.0         xfun_0.10         
[21] stringr_1.4.0      withr_2.1.2        knitr_1.25         vctrs_0.2.0       
[25] tidyselect_0.2.5   reshape_0.8.8      glue_1.3.1         data.table_1.12.6 
[29] R6_2.4.0           purrr_0.3.3        magrittr_1.5       htmltools_0.4.0   
[33] backports_1.1.5    scales_1.0.0       assertthat_0.2.1   colorspace_1.4-1  
[37] stringi_1.4.3      lazyeval_0.2.2     munsell_0.5.0      crayon_1.3.4
biethbr1 commented 3 years ago

@combefr1: Hi Francois - can you share project.mlxtran and project2.mlxtran? Thanks

combefr1 commented 3 years ago

here it is! not sure you can use them directly. you can always paste directly the code above to test it

project.mlxtran.txt project2.mlxtran.txt

tynsci commented 2 years ago