Added time log to function, updated log

extras/1695023475_pare_log.txt

@@ -0,0 +1,58 @@
+[*] Generated PaRe report for BrokenAdaptiveRidge [53.08 secs]
+[*] Generated PaRe report for CohortExplorer [55.26 secs]
+[*] Generated PaRe report for Eunomia [1 mins]
+[*] Generated PaRe report for OhdsiSharing [1.04 mins]
+[*] Generated PaRe report for Characterization [1.09 mins]
+[*] Generated PaRe report for ResultModelManager [1.14 mins]
+[*] Generated PaRe report for MethodEvaluation [1.17 mins]
+[*] Generated PaRe report for Andromeda [33.57 secs]
+[*] Generated PaRe report for BigKnn [26.67 secs]
+[*] Generated PaRe report for Capr [1.09 mins]
+[*] Generated PaRe report for FeatureExtraction [1.34 mins]
+[*] Generated PaRe report for ROhdsiWebApi [1.47 mins]
+[*] Generated PaRe report for CirceR [30.25 secs]
+[*] Generated PaRe report for Hydra [36.18 secs]
+[*] Generated PaRe report for CohortMethod [2.97 mins]
+[*] Generated PaRe report for ShinyAppBuilder [32.39 secs]
+[*] Generated PaRe report for PhenotypeLibrary [3.29 mins]
+[*] Generated PaRe report for IterativeHardThresholding [23.39 secs]
+[*] Generated PaRe report for Achilles [2.44 mins]
+[*] Generated PaRe report for Cyclops [2.52 mins]
+[*] Generated PaRe report for CohortGenerator [58.45 secs]
+[*] Generated PaRe report for SqlRender [37.9 secs]
+[*] Generated PaRe report for DataQualityDashboard [41.97 secs]
+[*] Generated PaRe report for SelfControlledCaseSeries [1.47 mins]
+[*] Generated PaRe report for PatientLevelPrediction [4.48 mins]
+[*] Generated PaRe report for CohortDiagnostics [1.24 mins]
+[*] Generated PaRe report for OhdsiShinyModules [3.68 mins]
+[*] Generated PaRe report for DatabaseConnector [1.5 mins]
+[*] Generated PaRe report for SelfControlledCohort [29.46 secs]
+[!] Generating PaRe report for DeepPatientLevelPrediction failed
+! error in pak subprocess
+Caused by error: 
+! Could not solve package dependencies:
+* dplyr: dependency conflict
+* ParallelLogger: dependency conflict
+* rlang: dependency conflict
+* withr: dependency conflict
+* reticulate: dependency conflict
+* ohdsi/PatientLevelPrediction: Can't install dependency ohdsi/ParallelLogger (>= 2.0.0)
+* ohdsi/ParallelLogger: Conflicts with ParallelLogger
+
+
+[*] Generated PaRe report for EmpiricalCalibration [1.01 mins]
+[*] Generated PaRe report for PheValuator [39.94 secs]
+[*] Generated PaRe report for ParallelLogger [35.9 secs]
+[*] Generated PaRe report for EvidenceSynthesis [56.65 secs]
+[!] Generating PaRe report for EnsemblePatientLevelPrediction failed
+! error in pak subprocess
+Caused by error: 
+! Could not solve package dependencies:
+* dplyr: dependency conflict
+* ParallelLogger: dependency conflict
+* rlang: dependency conflict
+* tidyr: dependency conflict
+* ohdsi/PatientLevelPrediction: Can't install dependency ohdsi/ParallelLogger (>= 2.0.0)
+* ohdsi/ParallelLogger: Conflicts with ParallelLogger
+
+

extras/runPaRe.R

@@ -17,6 +17,7 @@ pareHades <- function(
     packagesPath = "extras/packages.csv",
     logPath = "./",
     nCores = 10) {
+  start <- Sys.time()
   pkgs <- read.csv(packagesPath)
   pkgNames <- pkgs$name
 
@@ -35,6 +36,7 @@ pareHades <- function(
 
   parallel::parLapply(cl = cl, X = pkgNames, fun = function(pkg) {
     tryCatch({
+      start <- Sys.time()
       repoDir <- file.path(tempdir(), pkg)
 
       git2r::clone(
@@ -48,9 +50,9 @@ pareHades <- function(
         repo = repo,
         outputFile = file.path("docs/pare_reports/", sprintf("%s.html", pkg))
       )
-
+      timeDiff <- round(Sys.time() - start, 2)
       write(
-        x = sprintf("[*] Generated PaRe report for %s\n\n", pkg),
+        x = sprintf("[*] Generated PaRe report for %s [%s %s]", pkg, as.numeric(timeDiff), units(timeDiff)),
         file = logFile,
         append = TRUE
       )
@@ -66,7 +68,9 @@ pareHades <- function(
       )
     })
   })
-  message(sprintf("Worte reports to\n\t%s", "docs/pare_reports/"))
+  timeDiff <- round(Sys.time() - start, 2)
+  message(sprintf("Worte reports to: %s", "docs/pare_reports/"))
+  message(sprintf("Time: %s %s", as.numeric(timeDiff), units(timeDiff)))
   return(NULL)
 }