update

davidycliao · Jan 30, 2025 · 7e0558d · 7e0558d
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commit 7e0558d
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diff --git a/Dockerfile b/Dockerfile
@@ -2,37 +2,53 @@ FROM rocker/r-ver:latest
 
 # 系統依賴
 RUN apt-get update && apt-get install -y \
-    python3-minimal \
-    python3-pip \
-    python3-venv \
-    libssl-dev \
-    gdebi-core \
-    wget \
-    sudo \
-    curl \
-    pkg-config \
-    git \
-    cmake \
-    build-essential \
-    g++
+   python3-minimal \
+   python3-pip \
+   python3-venv \
+   libssl-dev \
+   gdebi-core \
+   wget \
+   sudo \
+   curl \
+   pkg-config \
+   git \
+   cmake \
+   build-essential \
+   g++ \
+   protobuf-compiler \
+   libprotobuf-dev \
+   autoconf \
+   automake \
+   libtool \
+   # R 相關套件編譯依賴
+   libxml2-dev \
+   libcurl4-openssl-dev \
+   libssl-dev \
+   libfontconfig1-dev \
+   libharfbuzz-dev \
+   libfribidi-dev \
+   libfreetype6-dev \
+   libpng-dev \
+   libtiff5-dev \
+   libjpeg-dev
 
 # 創建 rstudio 用戶
 ARG USER=rstudio
 ARG PASSWORD=rstudio123
 RUN useradd -m $USER && \
-    echo "$USER:$PASSWORD" | chpasswd && \
-    adduser $USER sudo && \
-    echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+   echo "$USER:$PASSWORD" | chpasswd && \
+   adduser $USER sudo && \
+   echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 
 # 安裝 RStudio Server
 RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12.1-402-amd64.deb && \
-    gdebi -n rstudio-server-2023.12.1-402-amd64.deb && \
-    rm rstudio-server-*.deb
+   gdebi -n rstudio-server-2023.12.1-402-amd64.deb && \
+   rm rstudio-server-*.deb
 
 # 創建並配置 Python 虛擬環境
 RUN python3 -m venv /opt/venv && \
-    chown -R $USER:$USER /opt/venv && \
-    chmod -R 775 /opt/venv
+   chown -R $USER:$USER /opt/venv && \
+   chmod -R 775 /opt/venv
 
 # 設置環境變量
 ENV PATH="/opt/venv/bin:$PATH"
@@ -41,36 +57,33 @@ ENV PYTHONPATH="/opt/venv/lib/python3.12/site-packages"
 
 # 設置 R 環境配置
 RUN mkdir -p /usr/local/lib/R/etc && \
-    echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
-    echo "options(reticulate.prompt = FALSE)" >> /usr/local/lib/R/etc/Rprofile.site
+   echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
+   echo "options(reticulate.prompt = FALSE)" >> /usr/local/lib/R/etc/Rprofile.site
 
 # 創建並設置 R 庫目錄權限
 RUN mkdir -p /usr/local/lib/R/site-library && \
-    chown -R $USER:$USER /usr/local/lib/R/site-library && \
-    chmod -R 775 /usr/local/lib/R/site-library
+   chown -R $USER:$USER /usr/local/lib/R/site-library && \
+   chmod -R 775 /usr/local/lib/R/site-library
+
+# 安裝基本的 R 套件
+RUN R -e 'install.packages(c("remotes", "reticulate", "devtools"), repos="https://cloud.r-project.org/", dependencies=TRUE)'
 
 # 切換到 root 用戶安裝 Python 包
 RUN /opt/venv/bin/pip install --no-cache-dir \
-    numpy==1.26.4 \
-    scipy==1.12.0 \
-    torch>=2.0.0 \
-    transformers>=4.30.0 \
-    flair>=0.11.3 \
-    sentencepiece>=0.1.99
+   'numpy==1.26.4' \
+   'scipy==1.12.0' \
+   'torch>=2.0.0' \
+   'transformers[sentencepiece]>=4.25.0,<5.0.0' \
+   'flair>=0.11.3'
 
-# 切換到 rstudio 用戶安裝 R 包
+# 切換到 rstudio 用戶
 USER $USER
-RUN R -e 'install.packages("reticulate", repos="https://cloud.r-project.org/", dependencies=TRUE)' && \
-    R -e 'if(require(reticulate)) { \
-          Sys.setenv(RETICULATE_PYTHON="/opt/venv/bin/python"); \
-          reticulate::use_python("/opt/venv/bin/python", required=TRUE); \
-          install.packages("remotes", repos="https://cloud.r-project.org/", dependencies=TRUE); \
-          remotes::install_github("davidycliao/flaiR", dependencies=TRUE) \
-        }'
-
-# 設置工作目錄
 WORKDIR /home/$USER
 
+# 設置 R 環境
+RUN R -e 'Sys.setenv(RETICULATE_PYTHON="/opt/venv/bin/python")' && \
+   R -e 'reticulate::use_python("/opt/venv/bin/python", required=TRUE)'
+
 # 暴露 RStudio Server 端口
 EXPOSE 8787
 

diff --git a/R/zzz.R b/R/zzz.R
@@ -9,75 +9,30 @@ NULL
 
 
 ### Add Version Constants ------------------------------------------------------
-# .pkgenv$package_constants <- list(
-#   python_min_version = "3.9",
-#   python_max_version = "3.12",
-#   numpy_version = "1.26.4",
-#   scipy_version = "1.12.0",
-#   flair_min_version = "0.11.3",
-#   torch_version = "2.2.0",
-#   transformers_version = "4.37.2",
-#   gensim_version = "4.0.0",
-#   sentencepiece_version = "0.1.97",
-#   install_options = list(
-#     sentencepiece = "--no-deps"
-#   )
-# )
-
 .pkgenv$package_constants <- list(
-  # Python 版本限制
   python_min_version = "3.9",
   python_max_version = "3.12",
 
-  # 核心套件版本
+  # 核心依賴版本
   numpy_version = "1.26.4",
   scipy_version = "1.12.0",
 
-  # Flair 和主要 ML 套件版本
+  # 主要包版本
+  torch_version = "2.2.0",
+  transformers_version = "4.37.2",  # 要改成 transformers[sentencepiece]
   flair_min_version = "0.11.3",
-  torch_version = "2.2.0",                            # 符合 torch>=1.5.0,!=1.8
-  transformers_min_version = "4.25.0",
-  transformers_max_version = "5.0.0",
-
-  # NLP 相關套件
   gensim_version = "4.0.0",
-  sentencepiece_version = "0.1.97",
-  tokenizers_min_version = "0.14.0",
-  tokenizers_max_version = "0.19.0",
-
-  # 其他必要套件最低版本
-  boto3_min_version = "1.20.27",
-  conllu_min_version = "4.0",
-  conllu_max_version = "5.0.0",
-  deprecated_min_version = "1.2.13",
-  ftfy_min_version = "6.1.0",
-  gdown_min_version = "4.4.0",
-  huggingface_hub_min_version = "0.10.0",
-  langdetect_min_version = "1.0.9",
-  lxml_min_version = "4.8.0",
-  matplotlib_min_version = "2.2.3",
-  more_itertools_min_version = "8.13.0",
-  mpld3_min_version = "0.3",
-  pptree_min_version = "3.1",
-  dateutil_min_version = "2.8.2",
-  pytorch_revgrad_min_version = "0.2.0",
-  regex_min_version = "2022.1.18",
-  scikit_learn_min_version = "1.0.2",
-  segtok_min_version = "1.5.11",
-  sqlitedict_min_version = "2.0.0",
-  tabulate_min_version = "0.8.10",
-  tqdm_min_version = "4.63.0",
-  transformer_vocab_min_version = "0.2.3",
-  wikipedia_api_min_version = "0.5.7",
-  bioc_min_version = "2.0.0",
-  bioc_max_version = "3.0.0",
-
-  # 安裝選項
-  install_options = list(
-    sentencepiece = "--no-deps",
-    transformers = "sentencepiece"  # 表示安裝時要包含 sentencepiece
+
+  # 安裝設定
+  install_configs = list(
+    transformers = list(
+      name = "transformers[sentencepiece]",
+      version = "4.37.2",
+      options = "--no-deps"
+    )
   )
 )
+
 ### Add installation state tracking
 .pkgenv$installation_state <- new.env(parent = emptyenv())
 
@@ -725,7 +680,7 @@ install_dependencies <- function(venv = NULL, max_retries = 3, quiet = FALSE) {
         packages = c(
           sprintf("numpy==%s", .pkgenv$package_constants$numpy_version),
           sprintf("scipy==%s", .pkgenv$package_constants$scipy_version),
-          sprintf("transformers==%s", .pkgenv$package_constants$transformers_version)
+          sprintf("transformers[sentencepiece]>=%s,<5.0.0", .pkgenv$package_constants$transformers_version)  # 修改這行
         )
       ),
       flair = list(
@@ -2089,8 +2044,6 @@ initialize_modules <- function() {
 
   invisible(NULL)
 }
-
-
 # .onAttach <- function(libname, pkgname) {
 #   # 儲存原始環境設定
 #   original_python <- Sys.getenv("RETICULATE_PYTHON")