diff --git a/extras/1694775778_pare_log.txt b/extras/1694775778_pare_log.txt deleted file mode 100644 index a52bf1a..0000000 --- a/extras/1694775778_pare_log.txt +++ /dev/null @@ -1,124 +0,0 @@ -[*] Generated PaRe report for BrokenAdaptiveRidge - - -[*] Generated PaRe report for CohortExplorer - - -[*] Generated PaRe report for Eunomia - - -[*] Generated PaRe report for Characterization - - -[*] Generated PaRe report for ResultModelManager - - -[*] Generated PaRe report for OhdsiSharing - - -[*] Generated PaRe report for MethodEvaluation - - -[*] Generated PaRe report for Andromeda - - -[*] Generated PaRe report for Capr - - -[*] Generated PaRe report for FeatureExtraction - - -[*] Generated PaRe report for BigKnn - - -[*] Generated PaRe report for ROhdsiWebApi - - -[*] Generated PaRe report for CirceR - - -[*] Generated PaRe report for Hydra - - -[*] Generated PaRe report for CohortMethod - - -[*] Generated PaRe report for ShinyAppBuilder - - -[*] Generated PaRe report for Cyclops - - -[*] Generated PaRe report for Achilles - - -[*] Generated PaRe report for IterativeHardThresholding - - -[*] Generated PaRe report for PhenotypeLibrary - - -[*] Generated PaRe report for CohortGenerator - - -[*] Generated PaRe report for SqlRender - - -[*] Generated PaRe report for DataQualityDashboard - - -[*] Generated PaRe report for SelfControlledCaseSeries - - -[*] Generated PaRe report for PatientLevelPrediction - - -[*] Generated PaRe report for CohortDiagnostics - - -[*] Generated PaRe report for OhdsiShinyModules - - -[*] Generated PaRe report for DatabaseConnector - - -[*] Generated PaRe report for EmpiricalCalibration - - -[*] Generated PaRe report for SelfControlledCohort - - -[!] 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 ParallelLogger - - -[*] Generated PaRe report for PheValuator - - -[*] Generated PaRe report for EvidenceSynthesis - - -[!] 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 - - diff --git a/extras/1695023475_pare_log.txt b/extras/1695023475_pare_log.txt new file mode 100644 index 0000000..ab7ccad --- /dev/null +++ b/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 + + diff --git a/extras/runPaRe.R b/extras/runPaRe.R index 53c8ac4..9285883 100644 --- a/extras/runPaRe.R +++ b/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) }