diff --git a/Rmd/installingHades.Rmd b/Rmd/installingHades.Rmd index e146ffb..aad483e 100644 --- a/Rmd/installingHades.Rmd +++ b/Rmd/installingHades.Rmd @@ -46,11 +46,12 @@ These releases are currently captured as [renv](https://rstudio.github.io/renv/a - 2023Q1: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q1/renv.lock) - 2023Q3: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock) - 2024Q1: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2024Q1/renv.lock) +- 2024Q3: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2024Q3/renv.lock) To build the R library corresponding to the latest release in your current RStudio project, you can use: ```r -download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2024Q1/renv.lock", "renv.lock") +download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2024Q3/renv.lock", "renv.lock") install.packages("renv") renv::restore() ``` diff --git a/Rmd/rSetup.Rmd b/Rmd/rSetup.Rmd index 92502b2..da41506 100644 --- a/Rmd/rSetup.Rmd +++ b/Rmd/rSetup.Rmd @@ -98,7 +98,7 @@ We will need to install C and Fortran compilers in order to build R packages fro 1. Open the App Store in Mac OS and install Xcode. Xcode is a large program. If disk space is scarce you could also try only installing Xcode command line tools by following the instructions [here](https://railsapps.github.io/xcode-command-line-tools.html). Verify that the C compiler gcc is installed by opening the terminal and running the command `clang`. You should see an error that says "no input files". -2. Download and install the gfortran compiler `gfortran-12.2-universal.pkg` from . Verify the installation by opening the terminal and running the command `/opt/gfortran/bin/gfortran`. You should see an error that says "no input files". R 4.2.3 will look in the wrong place for gfortran, so you must point it to the right location. Run `usethis::edit_r_makevars()` to open `~.R/Makevars` and add: +2. Download and install the gfortran compiler `gfortran-12.2-universal.pkg` from . Verify the installation by opening the terminal and running the command `/opt/gfortran/bin/gfortran`. You should see an error that says "no input files". R 4.4.1 will look in the wrong place for gfortran, so you must point it to the right location. Run `usethis::edit_r_makevars()` to open `~.R/Makevars` and add: ```{r, eval=FALSE} F77 = /opt/gfortran/bin/gfortran diff --git a/docs/codeStyle.html b/docs/codeStyle.html index ea40f5a..8411262 100644 --- a/docs/codeStyle.html +++ b/docs/codeStyle.html @@ -13,7 +13,7 @@ Code Style - + diff --git a/docs/community.html b/docs/community.html index d076ccc..5f43d95 100644 --- a/docs/community.html +++ b/docs/community.html @@ -13,7 +13,7 @@ Development Community - + diff --git a/docs/connecting.html b/docs/connecting.html index 709868b..351d9ef 100644 --- a/docs/connecting.html +++ b/docs/connecting.html @@ -13,7 +13,7 @@ Connecting to a Database - + diff --git a/docs/contribute.html b/docs/contribute.html index 6196e67..21b1402 100644 --- a/docs/contribute.html +++ b/docs/contribute.html @@ -13,7 +13,7 @@ Contribute - + diff --git a/docs/developerGuidelines.html b/docs/developerGuidelines.html index b24d374..21c97de 100644 --- a/docs/developerGuidelines.html +++ b/docs/developerGuidelines.html @@ -13,7 +13,7 @@ Developer Guidelines - + diff --git a/docs/developmentRoadmap.html b/docs/developmentRoadmap.html index b8541b6..de09c67 100644 --- a/docs/developmentRoadmap.html +++ b/docs/developmentRoadmap.html @@ -13,7 +13,7 @@ Development Roadmap - + diff --git a/docs/index.html b/docs/index.html index 5d5ec94..667c636 100644 --- a/docs/index.html +++ b/docs/index.html @@ -13,7 +13,7 @@ HADES - + diff --git a/docs/installingHades.html b/docs/installingHades.html index 42114d5..3fbd393 100644 --- a/docs/installingHades.html +++ b/docs/installingHades.html @@ -13,7 +13,7 @@ Installing HADES - + @@ -506,10 +506,13 @@

HADES-wide releases

  • 2024Q1: renv lock file
  • +
  • 2024Q3: renv +lock file
  • To build the R library corresponding to the latest release in your current RStudio project, you can use:

    -
    download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2024Q1/renv.lock", "renv.lock")
    +
    download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2024Q3/renv.lock", "renv.lock")
     install.packages("renv")
     renv::restore()
    diff --git a/docs/packageRequirements.html b/docs/packageRequirements.html index 53ae595..42d31f4 100644 --- a/docs/packageRequirements.html +++ b/docs/packageRequirements.html @@ -13,7 +13,7 @@ HADES Package Requirements - + diff --git a/docs/packageStatuses.html b/docs/packageStatuses.html index 5ccbfd9..304ab07 100644 --- a/docs/packageStatuses.html +++ b/docs/packageStatuses.html @@ -13,7 +13,7 @@ Package statuses - + diff --git a/docs/packages.html b/docs/packages.html index 9d6b5e8..04a702f 100644 --- a/docs/packages.html +++ b/docs/packages.html @@ -13,7 +13,7 @@ Packages - + diff --git a/docs/publications.html b/docs/publications.html index 8f94235..d277183 100644 --- a/docs/publications.html +++ b/docs/publications.html @@ -13,7 +13,7 @@ Publications - + diff --git a/docs/rSetup.html b/docs/rSetup.html index edffdab..62f2673 100644 --- a/docs/rSetup.html +++ b/docs/rSetup.html @@ -13,7 +13,7 @@ Setting up the R environment - + @@ -450,8 +450,8 @@

    Setting up the R environment

  • R is a statistical computing environment. It comes with a basic user interface that is primarily a command-line interface. For stability, we’ve picked one R version that we aim to support for a -while moving forward. Since 2023-04-01 our target is R -4.2.3. We highly recommend installing R 4.2.3 for maximum +while moving forward. Since 2024-06-14 our target is R +4.4.1. We highly recommend installing R 4.4.1 for maximum compatibility.
  • RTools is a set of programs that is required on Windows to build R packages from source.
  • @@ -482,8 +482,8 @@

    Instructions for Windows

    Installing R

    1. Go to https://cran.r-project.org/bin/windows/base/old/4.2.3/, -click on ‘R-4.2.3-win.exe’ to download.

    2. +href="https://cran.r-project.org/bin/windows/base/old/4.4.1/">https://cran.r-project.org/bin/windows/base/old/4.4.1/, +click on ‘R-4.4.1-win.exe’ to download.

    3. After the download has completed, run the installer. Use the default options everywhere, with two exceptions: First, it is better not to install into program files. Instead, just make R a subfolder of your @@ -501,7 +501,7 @@

      Installing R

      Installing RTools

      1. Go to https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html, +href="https://cran.r-project.org/bin/windows/Rtools/rtools44/rtools.html">https://cran.r-project.org/bin/windows/Rtools/rtools44/rtools.html, and download the RTools installer.

      2. After downloading has completed run the installer. Select the default options everywhere.

      3. @@ -549,7 +549,7 @@

        Installing R

        1. Go to https://cran.r-project.org/bin/macosx/base/, click on -‘R-4.2.3.pkg’ to download.

        2. +‘R-4.4.1.pkg’ to download.

        3. After the download has completed, run the installer and accept all of the default options. You should see a screen indicating that the installation was successful.

          @@ -575,7 +575,7 @@

          Installing R build tools

          class="uri">https://cran.r-project.org/bin/macosx/tools/. Verify the installation by opening the terminal and running the command /opt/gfortran/bin/gfortran. You should see an error that -says “no input files”. R 4.2.3 will look in the wrong place for +says “no input files”. R 4.4.1 will look in the wrong place for gfortran, so you must point it to the right location. Run usethis::edit_r_makevars() to open ~.R/Makevars and add:

          diff --git a/docs/releaseProcess.html b/docs/releaseProcess.html index b20ffb2..ce3cd62 100644 --- a/docs/releaseProcess.html +++ b/docs/releaseProcess.html @@ -13,7 +13,7 @@ Release Process - + diff --git a/docs/renv.html b/docs/renv.html index e0d7a7b..2893fcc 100644 --- a/docs/renv.html +++ b/docs/renv.html @@ -13,7 +13,7 @@ Using Renv for Dependencies - + diff --git a/docs/site_libs/header-attrs-2.27/header-attrs.js b/docs/site_libs/header-attrs-2.28/header-attrs.js similarity index 100% rename from docs/site_libs/header-attrs-2.27/header-attrs.js rename to docs/site_libs/header-attrs-2.28/header-attrs.js diff --git a/docs/support.html b/docs/support.html index d94c453..edf9a0e 100644 --- a/docs/support.html +++ b/docs/support.html @@ -13,7 +13,7 @@ Questions and Bug Reports - + diff --git a/docs/supportedPlatforms.html b/docs/supportedPlatforms.html index fd6856d..1687ffd 100644 --- a/docs/supportedPlatforms.html +++ b/docs/supportedPlatforms.html @@ -13,7 +13,7 @@ Supported Database Platforms - + diff --git a/docs/testServerUsage.html b/docs/testServerUsage.html index ec6e7cb..acd4b84 100644 --- a/docs/testServerUsage.html +++ b/docs/testServerUsage.html @@ -13,7 +13,7 @@ Test server usage - + diff --git a/docs/validation.html b/docs/validation.html index e8fb4ea..9bdcadd 100644 --- a/docs/validation.html +++ b/docs/validation.html @@ -13,7 +13,7 @@ Validation & Evaluation - + diff --git a/extras/Releasing/Dependencies.rds b/extras/Releasing/Dependencies.rds deleted file mode 100644 index f7be6df..0000000 Binary files a/extras/Releasing/Dependencies.rds and /dev/null differ diff --git a/extras/Releasing/RunCheckOnAllHadesPackages.R b/extras/Releasing/RunCheckOnAllHadesPackages.R index 8194421..aaa2ab3 100644 --- a/extras/Releasing/RunCheckOnAllHadesPackages.R +++ b/extras/Releasing/RunCheckOnAllHadesPackages.R @@ -9,10 +9,12 @@ saveRDS(prepareForPackageCheck(), "Dependencies.rds") dependencies <- readRDS("Dependencies.rds") # Skipping Hydra, as renv seems to clash with skeleton renv environments: dependencies <- dependencies[dependencies$name != "Hydra", ] -for (i in 1:nrow(dependencies)) { - if (dependencies$name[i] == "PatientLevelPrediction") { - # Temp workaround for https://github.com/OHDSI/PatientLevelPrediction/issues/435 - additionalCheckArgs <- c("--no-build-vignettes", "--ignore-vignettes") +for (i in 29:nrow(dependencies)) { + if (dependencies$name[i] == "DeepPatientLevelPrediction") { + # This package is failing unit tests, it seems because Python modules are + # missing. Skipping for now. Hoping DeepPlp users are savy enough to figure + # this out + additionalCheckArgs <- c("--no-tests") } else { additionalCheckArgs <- c() } diff --git a/extras/Releasing/SetupPython.R b/extras/Releasing/SetupPython.R index 58185bc..29ff9ba 100644 --- a/extras/Releasing/SetupPython.R +++ b/extras/Releasing/SetupPython.R @@ -6,7 +6,7 @@ reticulate::use_virtualenv("r-reticulate") # Test: np <- reticulate::import('numpy') # Packages needed by DeepPatientLevelPrediction -------------------------------- -reticulate::py_install(c("polars", "tqdm", "connectorx", "scikit-learn", "pyarrow")) +reticulate::py_install(c("polars", "tqdm", "connectorx", "scikit-learn", "pyarrow", "pynvml")) reticulate::py_install("torch") # Test: torch <- reticulate::import('torch') # Error in py_module_import(module, convert = convert) : diff --git a/extras/rVersion.csv b/extras/rVersion.csv index a52e309..1939342 100644 --- a/extras/rVersion.csv +++ b/extras/rVersion.csv @@ -1,2 +1,2 @@ rVersion,fromDate -4.2.3,2023-04-01 +4.4.1,2024-06-14 diff --git a/hadesWideReleases/2024Oct01/renv.lock b/hadesWideReleases/2024Oct01/renv.lock new file mode 100644 index 0000000..4761271 --- /dev/null +++ b/hadesWideReleases/2024Oct01/renv.lock @@ -0,0 +1,1595 @@ +{ + "R" : { + "Version" : "4.4.1", + "Repositories" : [ + { + "Name" : "CRAN", + "URL" : "https://cloud.r-project.org" + } + ] + }, + "Packages" : { + "cli" : { + "Package" : "cli", + "Version" : "3.6.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "glue" : { + "Package" : "glue", + "Version" : "1.7.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "rlang" : { + "Package" : "rlang", + "Version" : "1.1.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "lifecycle" : { + "Package" : "lifecycle", + "Version" : "1.0.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "fansi" : { + "Package" : "fansi", + "Version" : "1.0.6", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "utf8" : { + "Package" : "utf8", + "Version" : "1.2.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "vctrs" : { + "Package" : "vctrs", + "Version" : "0.6.5", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "magrittr" : { + "Package" : "magrittr", + "Version" : "2.0.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "pillar" : { + "Package" : "pillar", + "Version" : "1.9.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "pkgconfig" : { + "Package" : "pkgconfig", + "Version" : "2.0.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "withr" : { + "Package" : "withr", + "Version" : "3.0.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "colorspace" : { + "Package" : "colorspace", + "Version" : "2.1-1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "generics" : { + "Package" : "generics", + "Version" : "0.1.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "lattice" : { + "Package" : "lattice", + "Version" : "0.22-6", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "R6" : { + "Package" : "R6", + "Version" : "2.5.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "stringi" : { + "Package" : "stringi", + "Version" : "1.8.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "tibble" : { + "Package" : "tibble", + "Version" : "3.2.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "tidyselect" : { + "Package" : "tidyselect", + "Version" : "1.2.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "cpp11" : { + "Package" : "cpp11", + "Version" : "0.5.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "dplyr" : { + "Package" : "dplyr", + "Version" : "1.1.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "farver" : { + "Package" : "farver", + "Version" : "2.1.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "labeling" : { + "Package" : "labeling", + "Version" : "0.4.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "Matrix" : { + "Package" : "Matrix", + "Version" : "1.7-0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "munsell" : { + "Package" : "munsell", + "Version" : "0.5.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "nlme" : { + "Package" : "nlme", + "Version" : "3.1-166", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "purrr" : { + "Package" : "purrr", + "Version" : "1.0.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "RColorBrewer" : { + "Package" : "RColorBrewer", + "Version" : "1.1-3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "stringr" : { + "Package" : "stringr", + "Version" : "1.5.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "viridisLite" : { + "Package" : "viridisLite", + "Version" : "0.4.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "backports" : { + "Package" : "backports", + "Version" : "1.5.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "gtable" : { + "Package" : "gtable", + "Version" : "0.3.5", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "isoband" : { + "Package" : "isoband", + "Version" : "0.2.7", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "MASS" : { + "Package" : "MASS", + "Version" : "7.3-61", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "mgcv" : { + "Package" : "mgcv", + "Version" : "1.9-1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "scales" : { + "Package" : "scales", + "Version" : "1.3.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "tidyr" : { + "Package" : "tidyr", + "Version" : "1.3.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "base64enc" : { + "Package" : "base64enc", + "Version" : "0.1-3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "broom" : { + "Package" : "broom", + "Version" : "1.0.7", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "digest" : { + "Package" : "digest", + "Version" : "0.6.37", + "Source" : 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: "4.5.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "crayon" : { + "Package" : "crayon", + "Version" : "1.5.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "doBy" : { + "Package" : "doBy", + "Version" : "4.6.22", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "evaluate" : { + "Package" : "evaluate", + "Version" : "1.0.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "highr" : { + "Package" : "highr", + "Version" : "0.11", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "hms" : { + "Package" : "hms", + "Version" : "1.1.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "jquerylib" : { + "Package" : "jquerylib", + "Version" : "0.1.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "jsonlite" : { + "Package" : "jsonlite", + "Version" : "1.8.9", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "lme4" : { + "Package" : "lme4", + "Version" : "1.1-35.5", + "Source" : "Repository", + "Repository" : 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