Roll back mrcieu.R

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

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 \

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 \

docker/scripts/R/github.R

@@ -1,40 +1,57 @@
 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)) {
     ref <- packages[[package]]
     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')
+remotes::install_version("RcppEigen", version = "0.3.3.9.3")
+remotes::install_github("jrs95/hyprcoloc", build_opts = c("--resave-data", "--no-manual"), upgrade = "never")

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 = ""