Debugging prints

docker/vtg.survfit.Dockerfile

@@ -14,13 +14,21 @@ COPY ./vtg.preprocessing/ /usr/local/R/vtg.preprocessing/
 RUN Rscript -e 'install.packages("/usr/local/R/vtg.preprocessing", \
                                  repos = NULL, type = "source")'
 
-# Install federated survfit package
-COPY ./${PKG_NAME}/src /usr/local/R/${PKG_NAME}/
+RUN R -e "remove.packages('prettyunits')"
+RUN R -e "install.packages('prettyunits', repos='http://cran.rstudio.com/')"
 
-WORKDIR /usr/local/R/${PKG_NAME}
 RUN Rscript -e 'library(devtools)' -e 'install_github("IKNL/vtg")'
 RUN Rscript -e 'install.packages("RCurl", repos = "http://cran.rstudio.com/")'
-RUN Rscript -e 'devtools::install_deps(".")'
+
+COPY ./${PKG_NAME}/src/DESCRIPTION /usr/local/R/${PKG_NAME}/DESCRIPTION
+
+WORKDIR /usr/local/R/${PKG_NAME}
+# Somehow prettyunit crashes when installed using the `install_deps`
+RUN Rscript -e 'devtools::install_deps(".", dependencies = TRUE)'
+
+# Install federated survfit package
+COPY ./${PKG_NAME}/src /usr/local/R/${PKG_NAME}/
+
 RUN Rscript -e 'install.packages(".", repos = NULL, type = "source", INSTALL_opts = "--no-multiarch")'
 
 # Change directory to '/app’ and create files that will be

vtg.survfit/src/DESCRIPTION

@@ -11,7 +11,7 @@ Type: Package
 Version: 1.0.0
 Title: vtg.survfit
 Description: This package can be used with vantage6
-  (see https://github.com/vantage6/vantage6).
+    (see https://github.com/vantage6/vantage6).
 Encoding: UTF-8
 LazyData: true
 Imports:

vtg.survfit/src/R/dsurvfit.R

@@ -69,6 +69,8 @@ dsurvfit <- function(client, formula, conf.int = 0.95, conf.type = "log", tmax =
 
 
   KM <- function(vars, stratum = NULL) {
+    vtg::log$debug("  - [KM]")
+    vtg::log$debug("  - stratum: {stratum}")
     master <-
       if (length(vars) > 3) {
         list(
@@ -139,7 +141,9 @@ dsurvfit <- function(client, formula, conf.int = 0.95, conf.type = "log", tmax =
       extend_data = extend_data
     )
     stratum <- unique(unlist(node_strata))
-    print(stratum)
+    vtg::log$info("stratum:")
+    lapply(stratum, function (k) vtg::log$info(k))
+    vtg::log$info("stratum end")
     master <- lapply(stratum, function(k) KM(vars, k))
     names(master) <- paste0(vars[3], "=", stratum)
   }

vtg.survfit/test.R

@@ -1,24 +1,17 @@
 # Clear the environment completely
 rm(list = ls(all.names = TRUE))
-devtools::load_all("./vtg.preprocessing/src")
+devtools::load_all("./vtg.preprocessing/R")
 devtools::load_all("./vtg.survfit/src")
-# This seems to be equivalent to "import x as y"
-library(namespace)
-tryCatch({
-    invisible(registerNamespace('vtg', loadNamespace('vtg')))
-}, error = function(e) {
-    vtg::writeln("Package 'vantage.infrastructure' already loaded.")
-})
 
 library(vtg.survfit)
 
-d1 <- read.csv("C:\\data\\euracan-node-a.csv")
+d1 <- read.csv("~/data/euracan-node-a.csv")
 dataset=list(d1, d1, d1)
 ###exapl
 
 # formula = Surv(time, status) ~ trt
 #formula = Surv(time,, status) ~ trt
-formula = 'Surv(surv, deadOS) ~ b04_sex'
+formula = 'Surv(surv, deadOS) ~ site'
 
 conf.int=0.95
 conf.type='log'