From c3fde90b3b801767fb3d762740b976d3b6acd013 Mon Sep 17 00:00:00 2001 From: schuemie Date: Thu, 21 Mar 2024 10:22:28 +0100 Subject: [PATCH] Fix error when calling `groupApply()` with `dbplyr` >= 2.5.0. Increasing version number. Regenerating documentation. --- DESCRIPTION | 4 +-- NEWS.md | 24 +++++++++++++++--- R/Operations.R | 2 +- cran-comments.md | 6 +++-- docs/404.html | 2 +- docs/articles/UsingAndromeda.html | 6 ++--- docs/articles/index.html | 2 +- docs/authors.html | 10 ++++---- docs/index.html | 6 ++--- docs/news/index.html | 18 +++++++++---- docs/pkgdown.yml | 2 +- docs/reference/Andromeda-class.html | 2 +- docs/reference/Andromeda-package.html | 8 +++--- docs/reference/andromeda_constructor.html | 2 +- docs/reference/appendToTable.html | 2 +- docs/reference/batchApply.html | 2 +- docs/reference/batchTest.html | 2 +- docs/reference/copyAndromeda.html | 2 +- docs/reference/createIndex.html | 2 +- docs/reference/getAndromedaTempDiskSpace.html | 4 +-- docs/reference/groupApply.html | 2 +- docs/reference/index.html | 2 +- docs/reference/isAndromeda.html | 2 +- docs/reference/isAndromedaTable.html | 2 +- docs/reference/isValidAndromeda.html | 2 +- docs/reference/listIndices.html | 4 +-- docs/reference/loadAndromeda.html | 2 +- docs/reference/names-set-.tbl_Andromeda.html | 2 +- .../reference/names-set-Andromeda-method.html | 2 +- docs/reference/names.tbl_Andromeda.html | 2 +- docs/reference/removeIndex.html | 2 +- docs/reference/restoreDate.html | 2 +- docs/reference/restorePosixct.html | 2 +- docs/reference/saveAndromeda.html | 2 +- extras/Andromeda.pdf | Bin 124505 -> 124504 bytes extras/PackageMaintenance.R | 1 - inst/doc/UsingAndromeda.pdf | Bin 219677 -> 219758 bytes tests/testthat/test-batching.R | 1 + 38 files changed, 84 insertions(+), 56 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3dd36d9..4a32ae2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Andromeda Type: Package Title: Asynchronous Disk-Based Representation of Massive Data -Version: 0.6.5 -Date: 2024-01-19 +Version: 0.6.6 +Date: 2024-03-21 Authors@R: c( person("Adam", "Black", , "black@ohdsi.org", role = c("aut")), person("Egill", "Fridgeirsson", , "e.fridgeirsson@erasmusmc.nl", role = c("aut")), diff --git a/NEWS.md b/NEWS.md index 7432e8a..01ea475 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,25 +1,43 @@ +Andromeda 0.6.6 +=============== + +Bugfixes + +- Fix error when calling `groupApply()` with `dbplyr` >= 2.5.0. + Andromeda 0.6.5 =============== +Bugfixes + - Ensuring package passes R check even when `arrow` is not installed. Required to stay in CRAN. Andromeda 0.6.4 =============== + +Bugfixes + - Fix a bug causing Andromeda saving not to respect andromeda temp folder Andromeda 0.6.3 =============== + +Bugfixes + - Fix workflow Andromeda 0.6.2 =============== -- add isAndromedaTable -- update docs -- add weekly r check yaml + +Changes + +- Added `isAndromedaTable()` function. Andromeda 0.6.1 =============== +Bugfixes + - Fix compatibility with dbplyr. diff --git a/R/Operations.R b/R/Operations.R index d31b1d8..8486427 100644 --- a/R/Operations.R +++ b/R/Operations.R @@ -161,7 +161,7 @@ groupApply <- function(tbl, groupVariable, fun, ..., batchSize = 100000, progres env$groupData <- groups[[length(groups)]] env$groupValue <- groups[[length(groups)]][1, groupVariable] } - batchApply(tbl = tbl %>% arrange(rlang::sym(groupVariable)), + batchApply(tbl = tbl %>% arrange(groupVariable), fun = wrapper, userFun = fun, env = env, diff --git a/cran-comments.md b/cran-comments.md index e500622..349f256 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,7 +1,7 @@ -Andromeda v0.6.5 +Andromeda v0.6.6 --- -This is a patch release that fixes the error observed on r-devel-linux-x86_64-fedora-clang. +This is a patch release that fixes the error observed on various CRAN testing instances following the release of dbplyr 2.5.0. ## Test environments * Windows-latest, R-release (Github Actions) @@ -15,4 +15,6 @@ This is a patch release that fixes the error observed on r-devel-linux-x86_64-fe There were no ERRORs or WARNINGs on any platform. +## Downstream dependencies +DatabaseConnector is used by Cyclops, TreatmentPatterns, CohortAlgebra, DatabaseConnector, which were tested with this new version. No issues were found. diff --git a/docs/404.html b/docs/404.html index 5947f1f..3226fa8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ Andromeda - 0.6.5 + 0.6.6 diff --git a/docs/articles/UsingAndromeda.html b/docs/articles/UsingAndromeda.html index abcacc2..70a47c0 100644 --- a/docs/articles/UsingAndromeda.html +++ b/docs/articles/UsingAndromeda.html @@ -33,7 +33,7 @@ Andromeda - 0.6.5 + 0.6.6 @@ -85,7 +85,7 @@

Using Andromeda

Martijn J. Schuemie

-

2024-01-19

+

2024-03-21

Source: vignettes/UsingAndromeda.Rmd @@ -137,7 +137,7 @@

Creating an Andromeda objectandr$cars <- cars andr 
## # Andromeda object
-## # Physical location:  /var/folders/d5/7zcm15t57p3_91m486y3qtw40000gn/T//Rtmpnl94ws/file29b931c42ed1.sqlite
+## # Physical location:  /var/folders/d5/7zcm15t57p3_91m486y3qtw40000gn/T//RtmpbkC3SQ/file28593f76001e.sqlite
 ## 
 ## Tables:
 ## $cars (speed, dist)
diff --git a/docs/articles/index.html b/docs/articles/index.html index 25081af..5e70bcb 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ Andromeda - 0.6.5 + 0.6.6 diff --git a/docs/authors.html b/docs/authors.html index 5424a74..c48f5e0 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ Andromeda - 0.6.5 + 0.6.6 @@ -62,7 +62,7 @@

Authors