From 487b711e464644f708a3f614df23ae1f28ee4228 Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu, 27 Nov 2025 16:35:01 +0100 Subject: [PATCH] Roll back mrcieu.R Fixes #318 --- CHANGELOG.md | 5 +++ docker/dockerfiles/python3/Dockerfile | 4 +- docker/dockerfiles/r/Dockerfile | 4 -- docker/scripts/R/github.R | 61 +++++++++++++++++---------- docker/scripts/R/mrcieu.R | 33 --------------- version/version.py | 2 +- 6 files changed, 47 insertions(+), 62 deletions(-) delete mode 100644 docker/scripts/R/mrcieu.R diff --git a/CHANGELOG.md b/CHANGELOG.md index 820ea763..083c10ed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,11 @@ Removed features goes here Miscellaneous goes here +## 1.13.1 - 2025-11-27 + +### +* Removed mrcieu.R installer script, prefer installation from GitHub repos. + ## 1.13.0 - 2025-11-27 ### Added diff --git a/docker/dockerfiles/python3/Dockerfile b/docker/dockerfiles/python3/Dockerfile index ebd02488..ed23eadb 100644 --- a/docker/dockerfiles/python3/Dockerfile +++ b/docker/dockerfiles/python3/Dockerfile @@ -41,7 +41,7 @@ RUN mamba install python=3.10.6 \ openpyxl=3.1.5 \ pandas=2.2.3 \ pandas-plink=2.2.9 \ - paramiko \ + paramiko=4.0.0 \ psutil=5.9.3 \ pyarrow=19.0.1 \ pydot=3.0.4 \ @@ -72,7 +72,7 @@ RUN pip install --no-cache-dir --no-deps cbgen==1.0.2 \ LDpred==1.0.11 \ Pgenlib==0.93.0 \ plinkio==0.9.8 \ - plinkliftover \ + plinkliftover==0.5.2 \ poetry==2.2.1 \ pooch==1.8.2 \ pycap==2.1.0 \ diff --git a/docker/dockerfiles/r/Dockerfile b/docker/dockerfiles/r/Dockerfile index 10612775..28ac1279 100644 --- a/docker/dockerfiles/r/Dockerfile +++ b/docker/dockerfiles/r/Dockerfile @@ -43,10 +43,6 @@ RUN Rscript cran.R COPY /scripts/R/bioconductor.R . RUN Rscript bioconductor.R -# MRCIEU packages: -COPY /scripts/R/mrcieu.R . -RUN Rscript mrcieu.R - # GitHub distributed packages: COPY /scripts/R/github.R . RUN --mount=type=secret,id=github_pat \ diff --git a/docker/scripts/R/github.R b/docker/scripts/R/github.R index da7a96a6..6d762fdc 100644 --- a/docker/scripts/R/github.R +++ b/docker/scripts/R/github.R @@ -1,27 +1,44 @@ url <- "https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01" -dependencies <- c('Depends', 'Imports', 'LinkingTo') -# upgrade <- 'default' -upgrade <- 'never' +dependencies <- c("Depends", "Imports", "LinkingTo") +# upgrade <- "default" +upgrade <- "never" +upgrade_dependencies <- FALSE auth_token <- Sys.getenv("github_pat") cat("GitHub PAT length: ", nchar(auth_token), "\n") # GitHub packages w. Git SHA packages <- list( - 'alexploner/cfdr.pleio' = '76d5085e6d3f3ca9576d5d7564d2acf11bcfd021', - 'amslala/regtools' = 'v0.2.0', - 'dajiangliu/rareGWAMA' = '72e962dae19dc07251244f6c33275ada189c2126', - 'deepchocolate/glm-extras' = 'ecba68c0378fc953edf8fe594ce914aff8ada6fa', - 'jamesliley/cfdr' = 'ec5fddbd27c746a470eb827dc249a80194b231e8', - 'jamesliley/cFDR-common-controls' = '9b923fea283e2373ee8effa2909620a1930004bd', - 'norment/normentR' = 'dfa1fbae9587db6c3613b0405df4f9cfa98ee0e1', - 'psychgen/phenotools' = '62dd11e111d8d952837c9f207557e9b297ba56bc', - 'wouterpeyrot/CCGWAS' = 'ce9764da946189623a0164f156ad119773bc32f5', - 'xiashen/MultiABEL' = '7067fe6753c74f6580029abc82bce914472b4b16', - 'amorris28/hazrd' = 'ff9f1690e930792f29e1fd87e25c0dc8632339d5', - 'cnfoley/hyprcoloc' = '26ea5953a46b3e204dfa8eadd202f746244afa13', - 'zhenin/HDL/HDL' = '551a8864c5ed3389a6892743ff059357735dc195', - 'JBPG/Gsens' = '6cac02ba1ccaf38870e2526076f0306c0cf0dc0a' -) + "alexploner/cfdr.pleio" = "76d5085e6d3f3ca9576d5d7564d2acf11bcfd021", + "amslala/regtools" = "v0.2.0", + "dajiangliu/rareGWAMA" = "72e962dae19dc07251244f6c33275ada189c2126", + "deepchocolate/glm-extras" = "ecba68c0378fc953edf8fe594ce914aff8ada6fa", + "GenomicSEM/GenomicSEM" = "8e0ef594e95885b1f734f1dfcfe668b16ada2880", + "jamesliley/cfdr" = "ec5fddbd27c746a470eb827dc249a80194b231e8", + "jamesliley/cFDR-common-controls" = "9b923fea283e2373ee8effa2909620a1930004bd", + # gwasvcf deps: + "MRCIEU/genetics.binaRies" = "b0324f180476d80c43bba2ab026b72c5be426a92", + "MRCIEU/gwasglue2" = "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", + "MRCIEU/gwasvcf" = "477b365da8522e9a47f3bce51993d5f36df49ceb", + # gwasglue/TwoSampleMR deps: + "rondolab/MR-PRESSO" = "3e3c92d7eda6dce0d1d66077373ec0f7ff4f7e87", + "gqi/MRMix"="56afdb2bc96760842405396f5d3f02e60e305039", + "WSpiller/RadialMR" = "0ed91f83aebf265a09482561c128c830e58ed697", + "qingyuanzhao/mr.raps" = "27b96f31e26ae97a395422bd757f514a7f96cc85", + "MRCIEU/TwoSampleMR" = "578c68fa754c57d764553812bf85d69ecf43b011", + "MRCIEU/gwasglue" = "c2d5660eed389e1a9b3e04406b88731d642243f1", + "noahlorinczcomi/MRBEE" = "6295549a1f5a158c6701eb793646d60c8aef11ca", + "norment/normentR" = "dfa1fbae9587db6c3613b0405df4f9cfa98ee0e1", + "psychgen/phenotools" = "62dd11e111d8d952837c9f207557e9b297ba56bc", + "wouterpeyrot/CCGWAS" = "ce9764da946189623a0164f156ad119773bc32f5", + "WSpiller/MVMR" = "65705da9421b6235c7458dba6f01cddfebfe96f5", + "xiashen/MultiABEL" = "7067fe6753c74f6580029abc82bce914472b4b16", + "amorris28/hazrd" = "ff9f1690e930792f29e1fd87e25c0dc8632339d5", + "cnfoley/hyprcoloc" = "26ea5953a46b3e204dfa8eadd202f746244afa13", + "zhenin/HDL/HDL" = "551a8864c5ed3389a6892743ff059357735dc195", + "JBPG/Gsens" = "6cac02ba1ccaf38870e2526076f0306c0cf0dc0a", + "MRCIEU/genetics.binaRies" = "2fcd3ee3088b729c7eb34cf2aac9dc2e04fe4412", + "mrcieu/gwasglue2" = "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", + "gqi/MRMix" = "56afdb2bc96760842405396f5d3f02e60e305039") # install package from GitHub and quit with error if installation fails for (package in names(packages)) { @@ -29,12 +46,12 @@ for (package in names(packages)) { cat("Installing package ", package, " from GitHub with ref ", ref, "\n") tryCatch( { - devtools::install_github(package, ref=ref, repos=url, dependencies=dependencies, upgrade=upgrade, auth_token=auth_token) + devtools::install_github(package, ref=ref, repos=url, dependencies=dependencies, upgrade_dependencies=upgrade_dependencies, upgrade=upgrade, auth_token=auth_token) }, error = function(e) { cat("Error occurred during package installation:\n") print(e) - quit(status=1, save='no') + quit(status=1, save="no") }, finally = { } @@ -44,5 +61,5 @@ for (package in names(packages)) { # misc. packages library(remotes) -remotes::install_version('RcppEigen', version = '0.3.3.9.3') -remotes::install_github('jrs95/hyprcoloc', build_opts = c('--resave-data', '--no-manual'), upgrade = 'never') \ No newline at end of file +remotes::install_version("RcppEigen", version = "0.3.3.9.3") +remotes::install_github("jrs95/hyprcoloc", build_opts = c("--resave-data", "--no-manual"), upgrade = "never") \ No newline at end of file diff --git a/docker/scripts/R/mrcieu.R b/docker/scripts/R/mrcieu.R deleted file mode 100644 index 5e04ba37..00000000 --- a/docker/scripts/R/mrcieu.R +++ /dev/null @@ -1,33 +0,0 @@ -require(devtools) -repos <- c("https://mrcieu.r-universe.dev", "https://cloud.r-project.org") - -packages <- list( - "GenomicSEM" = "0.0.5", - "genetics.binaRies" = "0.1.2", - "gwasglue2" = "0.0.0.9000", - "gwasvcf" = "0.1.5", - "MRPRESSO" = "1.0", - "MRMix" = "0.1.0", - "RadialMR" = "1.2.1", - "mr.raps" = "0.4.3", - "TwoSampleMR" = "0.6.24", - "gwasglue" = "0.0.0.9001", - "MRBEE" = "0.1.0", - "MVMR" = "0.4.2") - -for (package in names(packages)) { - version <- packages[[package]] - cat("Installing package ", package, " from MRCIEU with version ", version, "\n") - tryCatch( - { - devtools::install_version(package, version=version, repos=repos) - }, - error = function(e) { - cat("Error occurred during package installation:\n") - print(e) - quit(status=1, save="no") - }, - finally = { - } - ) -} diff --git a/version/version.py b/version/version.py index c4a1e1db..be6b93fa 100644 --- a/version/version.py +++ b/version/version.py @@ -2,7 +2,7 @@ _MINOR = "13" # On main and in a nightly release the patch should be one ahead of the last # released build. -_PATCH = "0" +_PATCH = "1" # This is mainly for nightly builds which have the suffix ".dev$DATE". See # https://semver.org/#is-v123-a-semantic-version for the semantics. _SUFFIX = ""