From ea1bb7215cfaca517a0a4b10a84f8d4780f393b9 Mon Sep 17 00:00:00 2001 From: Dirk Eddelbuettel Date: Thu, 7 Sep 2023 11:01:35 -0500 Subject: [PATCH 1/6] [r] Use current main of tiledb-r in CI --- .github/workflows/r-ci.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml index 1c063ca8d8..bdb01fe7b9 100644 --- a/.github/workflows/r-ci.yml +++ b/.github/workflows/r-ci.yml @@ -39,6 +39,14 @@ jobs: - name: Install BioConductor package SingleCellExperiment run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment + + - name: Install rc version of tiledb-r (macOS) + if: ${{ matrix.os == 'macOS-latest' }} + run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))" + + - name: Install rc version of tiledb-r (linux) + if: ${{ matrix.os != 'macOS-latest' }} + run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" - name: Dependencies run: cd apis/r && tools/r-ci.sh install_all From 84110ecdb733ad49e51862d1ae11717503fd930b Mon Sep 17 00:00:00 2001 From: Dirk Eddelbuettel Date: Thu, 7 Sep 2023 11:13:49 -0500 Subject: [PATCH 2/6] [r] Whitespace-only change in DESCRIPTION plain to tickle CI --- apis/r/DESCRIPTION | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/apis/r/DESCRIPTION b/apis/r/DESCRIPTION index e043a2f6a5..c6160004b5 100644 --- a/apis/r/DESCRIPTION +++ b/apis/r/DESCRIPTION @@ -8,25 +8,17 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices, . Version: 1.4.3.1 Authors@R: c( - person(given = "Aaron", - family = "Wolen", - role = c("cre", "aut"), - email = "aaron@tiledb.com", + person(given = "Aaron", family = "Wolen", + role = c("cre", "aut"), email = "aaron@tiledb.com", comment = c(ORCID = "0000-0003-2542-2202")), - person(given = "Dirk", - family = "Eddelbuettel", - email = "dirk@tiledb.com", - role = "aut", + person(given = "Dirk", family = "Eddelbuettel", + role = "aut", email = "dirk@tiledb.com", comment = c(ORCID = "0000-0001-6419-907X")), - person(given = "Paul", - family = "Hoffman", - email = "paul.hoffman@tiledb.com", - role = "aut", + person(given = "Paul", family = "Hoffman", + role = "aut", email = "paul.hoffman@tiledb.com", comment = c(ORCID = "0000-0002-7693-8957")), - person(given = "John", - family = "Kerl", - email = "john.kerl@tiledb.com", - role = "aut"), + person(given = "John", family = "Kerl", + role = "aut", email = "john.kerl@tiledb.com"), person(given = "TileDB, Inc.", role = c("cph", "fnd")) ) From 1daa71bb1b383c9b972b785ebdfe23583343d3cf Mon Sep 17 00:00:00 2001 From: John Kerl Date: Thu, 7 Sep 2023 11:16:38 -0400 Subject: [PATCH 3/6] ./scripts/update-tiledb-version.py 2.17.0-rc0 --- .../cmake/Modules/FindTileDB_EP.cmake | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake index c6efe9aaaa..c973a109de 100644 --- a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake +++ b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake @@ -58,8 +58,8 @@ else() # NB When updating the pinned URLs here, please also update in file apis/r/tools/get_tarball.R if(DOWNLOAD_TILEDB_PREBUILT) if (WIN32) # Windows - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.2/tiledb-windows-x86_64-2.16.2-07b65de.zip") - SET(DOWNLOAD_SHA1 "1cda23235ceeff70cb2b30e0c0e22fcd9fd83b51") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-windows-x86_64-2.17.0-rc0-46b9ca5.zip") + SET(DOWNLOAD_SHA1 "740c7885b5191a467cb742b3420a51ae7b2a0a99") elseif(APPLE) # OSX # Status quo as of 2023-05-18: @@ -76,22 +76,22 @@ else() # o CMAKE_SYSTEM_PROCESSOR is x86_64 if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64) - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.2/tiledb-macos-x86_64-2.16.2-07b65de.tar.gz") - SET(DOWNLOAD_SHA1 "355233cee1515857c91b2f12fe4f7bbc1ac02465") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-x86_64-2.17.0-rc0-46b9ca5.tar.gz") + SET(DOWNLOAD_SHA1 "a3280bfaad8697080f9804b2d0756887962bdaa5") elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64) - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.2/tiledb-macos-arm64-2.16.2-07b65de.tar.gz") - SET(DOWNLOAD_SHA1 "5aad92b76e6fe3f7129f514ed926ef1c8af4bfa3") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-arm64-2.17.0-rc0-46b9ca5.tar.gz") + SET(DOWNLOAD_SHA1 "1b15a9aad373d491224f586fcbd677d47c2b86e8") elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)") - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.2/tiledb-macos-x86_64-2.16.2-07b65de.tar.gz") - SET(DOWNLOAD_SHA1 "355233cee1515857c91b2f12fe4f7bbc1ac02465") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-x86_64-2.17.0-rc0-46b9ca5.tar.gz") + SET(DOWNLOAD_SHA1 "a3280bfaad8697080f9804b2d0756887962bdaa5") elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm") - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.2/tiledb-macos-arm64-2.16.2-07b65de.tar.gz") - SET(DOWNLOAD_SHA1 "5aad92b76e6fe3f7129f514ed926ef1c8af4bfa3") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-arm64-2.17.0-rc0-46b9ca5.tar.gz") + SET(DOWNLOAD_SHA1 "1b15a9aad373d491224f586fcbd677d47c2b86e8") endif() else() # Linux - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.16.2/tiledb-linux-x86_64-2.16.2-07b65de.tar.gz") - SET(DOWNLOAD_SHA1 "b9fc44a104f31a9348a399e55ef9e32903b99590") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-linux-x86_64-2.17.0-rc0-46b9ca5.tar.gz") + SET(DOWNLOAD_SHA1 "f7fe14f444ab3ea9799844ebed247f18f6e40a90") endif() ExternalProject_Add(ep_tiledb @@ -113,8 +113,8 @@ else() else() # Build from source ExternalProject_Add(ep_tiledb PREFIX "externals" - URL "https://github.com/TileDB-Inc/TileDB/archive/2.16.2.zip" - URL_HASH SHA1=d54ff7fc4c3a1c5afb1027bab1ba011ae47c3d79 + URL "https://github.com/TileDB-Inc/TileDB/archive/2.17.0-rc0.zip" + URL_HASH SHA1=54c229897ead5fb578d28ba3c134e7f17a95c3a3 DOWNLOAD_NAME "tiledb.zip" CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX} From f64140d07eb66ccc6141ff178e3c96924995a255 Mon Sep 17 00:00:00 2001 From: Dirk Eddelbuettel Date: Thu, 7 Sep 2023 13:29:32 -0500 Subject: [PATCH 4/6] Also update tools/get_tarball.R --- apis/r/tools/get_tarball.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/apis/r/tools/get_tarball.R b/apis/r/tools/get_tarball.R index 7d5eac3270..daaea5c3ab 100644 --- a/apis/r/tools/get_tarball.R +++ b/apis/r/tools/get_tarball.R @@ -1,8 +1,8 @@ #!/usr/bin/env Rscript ## version pinning info -tiledb_core_version <- "2.16.2" -tiledb_core_sha1 <- "07b65de" +tiledb_core_version <- "2.17.0-rc0" +tiledb_core_sha1 <- "46b9ca5" if ( ! dir.exists("inst/") ) { stop("No 'inst/' directory. Exiting.", call. = FALSE) From 133f59cf245730a99b0c2a8242825ae37913a5b5 Mon Sep 17 00:00:00 2001 From: Dirk Eddelbuettel Date: Thu, 7 Sep 2023 14:11:39 -0500 Subject: [PATCH 5/6] Ensure bspm version check is enabled --- .github/workflows/r-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml index bdb01fe7b9..c99e098f49 100644 --- a/.github/workflows/r-ci.yml +++ b/.github/workflows/r-ci.yml @@ -46,7 +46,7 @@ jobs: - name: Install rc version of tiledb-r (linux) if: ${{ matrix.os != 'macOS-latest' }} - run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" + run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" - name: Dependencies run: cd apis/r && tools/r-ci.sh install_all From 394da9977a2394193a48abe0571f58886d72b39d Mon Sep 17 00:00:00 2001 From: John Kerl Date: Fri, 15 Sep 2023 09:20:54 -0400 Subject: [PATCH 6/6] core 2.17.0-rc0 -> 2.17.0 --- apis/r/tools/get_tarball.R | 4 +-- .../cmake/Modules/FindTileDB_EP.cmake | 28 +++++++++---------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/apis/r/tools/get_tarball.R b/apis/r/tools/get_tarball.R index daaea5c3ab..97ad341e2e 100644 --- a/apis/r/tools/get_tarball.R +++ b/apis/r/tools/get_tarball.R @@ -1,8 +1,8 @@ #!/usr/bin/env Rscript ## version pinning info -tiledb_core_version <- "2.17.0-rc0" -tiledb_core_sha1 <- "46b9ca5" +tiledb_core_version <- "2.17.0" +tiledb_core_sha1 <- "93c173d" if ( ! dir.exists("inst/") ) { stop("No 'inst/' directory. Exiting.", call. = FALSE) diff --git a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake index c973a109de..f689401ad6 100644 --- a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake +++ b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake @@ -58,8 +58,8 @@ else() # NB When updating the pinned URLs here, please also update in file apis/r/tools/get_tarball.R if(DOWNLOAD_TILEDB_PREBUILT) if (WIN32) # Windows - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-windows-x86_64-2.17.0-rc0-46b9ca5.zip") - SET(DOWNLOAD_SHA1 "740c7885b5191a467cb742b3420a51ae7b2a0a99") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-windows-x86_64-2.17.0-93c173d.zip") + SET(DOWNLOAD_SHA1 "d43589b22de95d45b40de9918d105a6174ec352e") elseif(APPLE) # OSX # Status quo as of 2023-05-18: @@ -76,22 +76,22 @@ else() # o CMAKE_SYSTEM_PROCESSOR is x86_64 if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64) - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-x86_64-2.17.0-rc0-46b9ca5.tar.gz") - SET(DOWNLOAD_SHA1 "a3280bfaad8697080f9804b2d0756887962bdaa5") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-x86_64-2.17.0-93c173d.tar.gz") + SET(DOWNLOAD_SHA1 "9a232015cbf09c5bd37375537cef80a382e1ffa4") elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64) - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-arm64-2.17.0-rc0-46b9ca5.tar.gz") - SET(DOWNLOAD_SHA1 "1b15a9aad373d491224f586fcbd677d47c2b86e8") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-arm64-2.17.0-93c173d.tar.gz") + SET(DOWNLOAD_SHA1 "b861b90b462963db44fe0217087fac3510fd6293") elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)") - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-x86_64-2.17.0-rc0-46b9ca5.tar.gz") - SET(DOWNLOAD_SHA1 "a3280bfaad8697080f9804b2d0756887962bdaa5") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-x86_64-2.17.0-93c173d.tar.gz") + SET(DOWNLOAD_SHA1 "9a232015cbf09c5bd37375537cef80a382e1ffa4") elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm") - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-macos-arm64-2.17.0-rc0-46b9ca5.tar.gz") - SET(DOWNLOAD_SHA1 "1b15a9aad373d491224f586fcbd677d47c2b86e8") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-arm64-2.17.0-93c173d.tar.gz") + SET(DOWNLOAD_SHA1 "b861b90b462963db44fe0217087fac3510fd6293") endif() else() # Linux - SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0-rc0/tiledb-linux-x86_64-2.17.0-rc0-46b9ca5.tar.gz") - SET(DOWNLOAD_SHA1 "f7fe14f444ab3ea9799844ebed247f18f6e40a90") + SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-linux-x86_64-2.17.0-93c173d.tar.gz") + SET(DOWNLOAD_SHA1 "5c04c07a73d3fe48a9ba8f3ad8af5e1912a39ce8") endif() ExternalProject_Add(ep_tiledb @@ -113,8 +113,8 @@ else() else() # Build from source ExternalProject_Add(ep_tiledb PREFIX "externals" - URL "https://github.com/TileDB-Inc/TileDB/archive/2.17.0-rc0.zip" - URL_HASH SHA1=54c229897ead5fb578d28ba3c134e7f17a95c3a3 + URL "https://github.com/TileDB-Inc/TileDB/archive/2.17.0.zip" + URL_HASH SHA1=bbf5b34fec1c729f048f48bf1a0f03abb447d7de DOWNLOAD_NAME "tiledb.zip" CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}