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Bioconductor 側の release ブランチを checkout」から始める完全手順**として再構成します。\n\n今回の対象は、Bioconductor check report 上では `TDbasedUFEadv 1.12.0`、branch は `RELEASE_3_23` です。Linux 側の check で `Enrichment.Rmd` の再ビルドが失敗しており、途中で STRING の `protein.aliases` 20.7 MB と `protein.info` 1.8 MB を取得した後、`gson` が無いため `DOSE::enrichDGN()` で落ちています。citeturn729198view0\n\n---\n\n# 0. Bioconductor 側の release ブランチを checkout\n\nBioconductor 公式 repository から作業する場合：\n\n```bash\ngit clone git@git.bioconductor.org:packages/TDbasedUFEadv.git\ncd TDbasedUFEadv\n\ngit checkout RELEASE_3_23\ngit pull\ngit status\n```\n\nBioconductor の git では、開発者が書き込み権限を得るには SSH 形式の remote を使う必要があります。公式手順でも `git@git.bioconductor.org:packages/.git` を remote に追加する形式が示されています。citeturn168697view2\n\nすでに GitHub clone で作業している場合は、Bioconductor remote を追加します。\n\n```bash\ngit remote -v\n\ngit remote add upstream git@git.bioconductor.org:packages/TDbasedUFEadv.git\ngit fetch upstream\n\ngit checkout -B RELEASE_3_23 upstream/RELEASE_3_23\ngit status\n```\n\nこの時点で、\n\n```text\nnothing to commit, working tree clean\n```\n\nになっていることを確認してください。\n\n---\n\n# 1. 作業前バックアップを作る\n\n失敗時に戻せるように、まず現在位置を保存します。\n\n```bash\ngit branch backup-before-suggests-fix\ngit rev-parse HEAD\n```\n\n`git rev-parse HEAD` の出力例：\n\n```text\n0a335d4xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\n```\n\nこの hash をメモしておきます。\n\nさらにログも確認します。\n\n```bash\ngit log --oneline -5\n```\n\n---\n\n# 2. 使用箇所を確認する\n\nまず、問題になっている依存パッケージがどこで使われているか確認します。\n\n```bash\ngrep -R \"STRINGdb\\|enrichDGN\\|enrichr\\|plotEnrich\\|dotplot\\|ggtitle\" R vignettes tests\n```\n\n主に見るべき場所は次の2つです。\n\n```text\nR/TDbasedUFEadv-package.R\nvignettes/Enrichment.Rmd\n```\n\n---\n\n# 3. DESCRIPTION を修正する\n\n`DESCRIPTION` を開きます。\n\n```bash\nnano DESCRIPTION\n```\n\nまたは VS Code などで編集して構いません。\n\n---\n\n## 3-1. Version を上げる\n\n修正前：\n\n```text\nVersion: 1.12.0\n```\n\n修正後：\n\n```text\nVersion: 1.12.1\n```\n\nBioconductor では、変更を build/report やユーザー側へ伝播させるために version bump が必要です。公式ドキュメントでも、変更の反映には valid version bump が必要とされています。citeturn168697view4\n\n---\n\n## 3-2. Imports から外す\n\n`Imports:` に以下が入っていたら削除します。\n\n```text\nSTRINGdb\nDOSE\nenrichR\nenrichplot\n```\n\n修正後の `Imports:` は、例えば次のようにします。\n\n```text\nImports:\n TDbasedUFE,\n Biobase,\n GenomicRanges,\n utils,\n rTensor,\n methods,\n graphics,\n RTCGA,\n stats,\n hash,\n shiny\n```\n\n---\n\n## 3-3. Suggests に追加する\n\n`Suggests:` に以下を追加します。\n\n```text\nSTRINGdb,\nenrichR,\nenrichplot,\nDOSE,\ngson,\nggplot2\n```\n\n修正後の例：\n\n```text\nSuggests:\n knitr,\n rmarkdown,\n testthat (>= 3.0.0),\n RTCGA.rnaseq,\n RTCGA.clinical,\n BiocStyle,\n MOFAdata,\n STRINGdb,\n enrichR,\n enrichplot,\n DOSE,\n gson,\n ggplot2\n```\n\n`gson` を追加するのは、今回の check error が `DOSE::enrichDGN()` から `gson` を要求して失敗しているためです。check report でも `there is no package called 'gson'` と出ています。citeturn729198view0\n\n---\n\n# 4. R/TDbasedUFEadv-package.R を修正する\n\n次に roxygen の import 指定を削除します。\n\n```bash\nnano R/TDbasedUFEadv-package.R\n```\n\n以下の行を削除します。\n\n```r\n#' @importFrom enrichR setEnrichrSite enrichr plotEnrich\n#' @import STRINGdb\n#' @importFrom enrichplot dotplot\n#' @importFrom DOSE enrichDGN\n```\n\n削除後、残っていないか確認します。\n\n```bash\ngrep -n \"STRINGdb\\|DOSE\\|enrichR\\|enrichplot\" R/TDbasedUFEadv-package.R\n```\n\n何も出なければ OK です。\n\n---\n\n# 5. vignettes/Enrichment.Rmd を修正する\n\n```bash\nnano vignettes/Enrichment.Rmd\n```\n\n---\n\n## 5-1. setup chunk から任意依存を外す\n\nもし setup chunk に以下があれば削除します。\n\n```r\nlibrary(DOSE)\nlibrary(enrichplot)\nlibrary(enrichR)\nlibrary(STRINGdb)\n```\n\nsetup chunk は例えば次のようにします。\n\n````markdown\n```{r setup}\nlibrary(TDbasedUFE)\nlibrary(TDbasedUFEadv)\nlibrary(RTCGA.rnaseq)\nlibrary(RTCGA.clinical)\n```\n````\n\n---\n\n## 5-2. Enrichr の chunk を `eval=FALSE` にする\n\nEnrichr は外部サービスにアクセスする可能性があるので、Bioconductor check 中には実行しない方が安全です。\n\n該当 chunk を、例えば次のようにします。\n\n````markdown\n```{r enrichr-example, eval=FALSE}\nif (!requireNamespace(\"enrichR\", quietly = TRUE)) {\n stop(\"The enrichR package is required to run this example.\")\n}\n\nenrichR::setEnrichrSite(\"Enrichr\")\n\ndbs <- c(\n \"GO_Molecular_Function_2015\",\n \"GO_Cellular_Component_2015\",\n \"GO_Biological_Process_2015\"\n)\n\nenriched <- enrichR::enrichr(genes, dbs)\n\nenrichR::plotEnrich(\n enriched$GO_Biological_Process_2015,\n showTerms = 20,\n numChar = 40,\n y = \"Count\",\n orderBy = \"P.value\"\n)\n```\n````\n\n---\n\n## 5-3. STRINGdb の chunk を `eval=FALSE` にする\n\nここが最重要です。\n\ncheck report では、`Enrichment.Rmd` の再ビルド中に `protein.aliases.v11.5` と `protein.info.v11.5` が実際にダウンロードされています。citeturn729198view0 \nしたがって `STRINGdb::STRINGdb$new()` を vignette build 中に実行させないようにします。\n\n該当 chunk を次のようにします。\n\n````markdown\n```{r stringdb-example, eval=FALSE}\nif (!requireNamespace(\"STRINGdb\", quietly = TRUE)) {\n stop(\"The STRINGdb package is required to run this example.\")\n}\n\nstring_cache <- tools::R_user_dir(\"TDbasedUFEadv\", which = \"cache\")\ndir.create(string_cache, recursive = TRUE, showWarnings = FALSE)\n\nstring_db <- STRINGdb::STRINGdb$new(\n version = \"11.5\",\n species = 9606,\n score_threshold = 200,\n network_type = \"full\",\n input_directory = string_cache\n)\n\nexample1_mapped <- string_db$map(\n data.frame(genes = genes),\n \"genes\",\n removeUnmappedRows = TRUE\n)\n\nhits <- example1_mapped$STRING_id\nstring_db$plot_network(hits)\n```\n````\n\n重要なのはこの2点です。\n\n```r\neval=FALSE\n```\n\nと\n\n```r\ninput_directory = string_cache\n```\n\n`eval=FALSE` により、Bioconductor check 時には STRING の大きなファイルを取りに行きません。 \n`input_directory = string_cache` により、ユーザーが自分で実行する場合にはローカル cache が使われます。\n\n---\n\n## 5-4. DOSE / enrichplot の chunk を安全化する\n\n修正前が例えば次のようなコードなら：\n\n```r\nedo <- enrichDGN(entrez)\ndotplot(edo, showCategory=30) + ggtitle(\"dotplot for ORA\")\n```\n\n次のように置き換えます。\n\n````markdown\n```{r dose-example}\nif (\n requireNamespace(\"DOSE\", quietly = TRUE) &&\n requireNamespace(\"enrichplot\", quietly = TRUE) &&\n requireNamespace(\"gson\", quietly = TRUE) &&\n requireNamespace(\"ggplot2\", quietly = TRUE)\n) {\n edo <- DOSE::enrichDGN(entrez)\n\n enrichplot::dotplot(edo, showCategory = 30) +\n ggplot2::ggtitle(\"dotplot for ORA\")\n} else {\n message(\n \"Skipping DOSE/enrichplot example because one or more optional packages \",\n \"are not installed: DOSE, enrichplot, gson, ggplot2.\"\n )\n}\n```\n````\n\nこれで `gson` が無い環境でも vignette 全体が ERROR で停止しにくくなります。\n\n---\n\n# 6. NAMESPACE を再生成する\n\n`NAMESPACE` は手で直接編集せず、roxygen で再生成します。\n\n```bash\nRscript -e 'roxygen2::roxygenise(\".\")'\n```\n\n確認します。\n\n```bash\ngrep -n \"STRINGdb\\|DOSE\\|enrichR\\|enrichplot\" NAMESPACE\n```\n\n何も出なければ OK です。\n\nもし以下のような行が残っていれば、`R/` 以下のどこかに roxygen import 指定が残っています。\n\n```r\nimport(STRINGdb)\nimportFrom(DOSE,enrichDGN)\nimportFrom(enrichR,enrichr)\nimportFrom(enrichR,plotEnrich)\nimportFrom(enrichR,setEnrichrSite)\nimportFrom(enrichplot,dotplot)\n```\n\nその場合は次で探します。\n\n```bash\ngrep -R \"@import.*STRINGdb\\|@import.*DOSE\\|@import.*enrichR\\|@import.*enrichplot\" R\n```\n\n見つかった行を削除して、もう一度：\n\n```bash\nRscript -e 'roxygen2::roxygenise(\".\")'\n```\n\nを実行します。\n\n---\n\n# 7. 修正内容を確認する\n\n```bash\ngit diff\n```\n\n変更対象は基本的に次の4ファイルです。\n\n```text\nDESCRIPTION\nR/TDbasedUFEadv-package.R\nNAMESPACE\nvignettes/Enrichment.Rmd\n```\n\n`DESCRIPTION` の確認：\n\n```bash\ngrep -n \"Version\\|Imports\\|Suggests\\|STRINGdb\\|DOSE\\|enrichR\\|enrichplot\\|gson\\|ggplot2\" DESCRIPTION\n```\n\n`NAMESPACE` の確認：\n\n```bash\ngrep -n \"STRINGdb\\|DOSE\\|enrichR\\|enrichplot\" NAMESPACE\n```\n\n`NAMESPACE` の grep で何も出ないのが望ましいです。\n\n---\n\n# 8. build / check する\n\nまず build します。\n\n```bash\nR CMD build .\n```\n\n生成物を確認します。\n\n```bash\nls -lh TDbasedUFEadv_*.tar.gz\n```\n\n例えば：\n\n```text\nTDbasedUFEadv_1.12.1.tar.gz\n```\n\nができていれば、check します。\n\n```bash\nR CMD check TDbasedUFEadv_1.12.1.tar.gz\n```\n\n可能なら BiocCheck も実行します。\n\n```bash\nRscript -e 'BiocCheck::BiocCheck(\"TDbasedUFEadv_1.12.1.tar.gz\")'\n```\n\n---\n\n# 9. 成功したら commit する\n\n```bash\ngit status\n```\n\n想定外のファイルが入っていないことを確認します。\n\n```bash\ngit add DESCRIPTION R/TDbasedUFEadv-package.R NAMESPACE vignettes/Enrichment.Rmd\n\ngit commit -m \"Move enrichment packages to Suggests and avoid STRING download in vignette\"\n```\n\n---\n\n# 10. Bioconductor 側へ push する\n\nremote 名を確認します。\n\n```bash\ngit remote -v\n```\n\nBioconductor repository が `origin` の場合：\n\n```bash\ngit push origin RELEASE_3_23\n```\n\nBioconductor repository が `upstream` の場合：\n\n```bash\ngit push upstream RELEASE_3_23\n```\n\nBioconductor の build report は push 直後に即時反映されるとは限りません。check report ページにも、最新 push の反映には最大24時間、場合によって48時間かかることがあると書かれています。citeturn729198view0\n\n---\n\n# 11. GitHub 側にも反映する場合\n\nGitHub remote が `origin`、Bioconductor remote が `upstream` の構成なら、GitHub 側にも push します。\n\n```bash\ngit push origin RELEASE_3_23\n```\n\nただし GitHub 側に `RELEASE_3_23` ブランチを作りたくない場合は省略しても構いません。Bioconductor check に必要なのは Bioconductor repository 側への push です。\n\n---\n\n# 12. devel 側にも同じ修正を入れる\n\nrelease だけでなく devel にも入れておく方が安全です。\n\nまず release 側の commit hash を確認します。\n\n```bash\ngit log --oneline -3\n```\n\n例：\n\n```text\n9f8e7d6 Move enrichment packages to Suggests and avoid STRING download in vignette\n0a335d4 Previous commit\n```\n\ndevel に移動します。\n\n```bash\ngit checkout devel\ngit pull\n```\n\nrelease の修正 commit を取り込みます。\n\n```bash\ngit cherry-pick 9f8e7d6\n```\n\n`DESCRIPTION` の `Version` で conflict する可能性があります。 \nその場合は、devel 側の現在 version に合わせて patch 番号を1つ上げます。\n\n例えば devel が：\n\n```text\nVersion: 1.13.0\n```\n\nなら：\n\n```text\nVersion: 1.13.1\n```\n\nにします。\n\nその後：\n\n```bash\nRscript -e 'roxygen2::roxygenise(\".\")'\n\nR CMD build .\nls -lh TDbasedUFEadv_*.tar.gz\n```\n\ntar.gz が `TDbasedUFEadv_1.13.1.tar.gz` なら：\n\n```bash\nR CMD check TDbasedUFEadv_1.13.1.tar.gz\n```\n\n成功したら：\n\n```bash\ngit status\ngit add DESCRIPTION R/TDbasedUFEadv-package.R NAMESPACE vignettes/Enrichment.Rmd\ngit commit -m \"Move enrichment packages to Suggests and avoid STRING download in vignette\"\ngit push origin devel\n```\n\nすでに `cherry-pick` が commit を作っている場合は、version 修正だけ別 commit にするか、`git commit --amend` でまとめます。\n\nBioconductor 公式手順でも、devel branch へ push する場合や release branch へ cherry-pick する場合に version bump を行う流れが説明されています。citeturn168697view0\n\n---\n\n# 13. 失敗した場合に戻す方法\n\nここからが復旧手順です。\n\n---\n\n## 13-A. commit 前に失敗した場合\n\nまだ commit していないなら、作業変更を全部捨てられます。\n\n```bash\ngit restore DESCRIPTION\ngit restore R/TDbasedUFEadv-package.R\ngit restore NAMESPACE\ngit restore vignettes/Enrichment.Rmd\n```\n\n全部まとめて戻すなら：\n\n```bash\ngit restore .\n```\n\nbuild/check でできたファイルも消します。\n\n```bash\nrm -f TDbasedUFEadv_*.tar.gz\nrm -rf TDbasedUFEadv.Rcheck\n```\n\nWindows PowerShell なら：\n\n```powershell\nRemove-Item TDbasedUFEadv_*.tar.gz\nRemove-Item -Recurse -Force TDbasedUFEadv.Rcheck\n```\n\n---\n\n## 13-B. commit したが、まだ push していない場合\n\ncommit だけ取り消して、編集内容は残す場合：\n\n```bash\ngit reset --soft HEAD~1\n```\n\ncommit も編集内容もすべて捨てて、作業前へ戻す場合：\n\n```bash\ngit reset --hard backup-before-suggests-fix\n```\n\nまたは、最初にメモした hash へ戻します。\n\n```bash\ngit reset --hard 0a335d4\n```\n\nこれは **push 前だけ**にしてください。\n\n---\n\n## 13-C. push 後に失敗した場合\n\nBioconductor に push した後は、`reset --hard` + force push ではなく、`git revert` で取り消すのが安全です。\n\nまず失敗 commit を確認します。\n\n```bash\ngit checkout RELEASE_3_23\ngit pull\ngit log --oneline -5\n```\n\n例：\n\n```text\n9f8e7d6 Move enrichment packages to Suggests and avoid STRING download in vignette\n0a335d4 Previous commit\n```\n\n失敗 commit が `9f8e7d6` なら：\n\n```bash\ngit revert 9f8e7d6\n```\n\nエディタが開いたら、そのまま保存して閉じます。\n\n次に `DESCRIPTION` の version をさらに上げます。 \n失敗修正で：\n\n```text\nVersion: 1.12.1\n```\n\nになっていたなら、revert 後は：\n\n```text\nVersion: 1.12.2\n```\n\nにします。\n\n```bash\nnano DESCRIPTION\n```\n\n保存後：\n\n```bash\ngit add DESCRIPTION\ngit commit -m \"Bump version after reverting failed fix\"\ngit push origin RELEASE_3_23\n```\n\nBioconductor remote が `upstream` の場合：\n\n```bash\ngit push upstream RELEASE_3_23\n```\n\n---\n\n# 14. 最初から最後までの実行例\n\nまとめると、release 修正だけなら以下です。\n\n```bash\n# 0. checkout\ngit clone git@git.bioconductor.org:packages/TDbasedUFEadv.git\ncd TDbasedUFEadv\ngit checkout RELEASE_3_23\ngit pull\ngit status\n\n# 1. backup\ngit branch backup-before-suggests-fix\ngit rev-parse HEAD\n\n# 2. 使用箇所確認\ngrep -R \"STRINGdb\\|enrichDGN\\|enrichr\\|plotEnrich\\|dotplot\\|ggtitle\" R vignettes tests\n```\n\nここで次を編集します。\n\n```text\nDESCRIPTION\nR/TDbasedUFEadv-package.R\nvignettes/Enrichment.Rmd\n```\n\n編集後：\n\n```bash\n# 6. NAMESPACE 再生成\nRscript -e 'roxygen2::roxygenise(\".\")'\n\n# 7. 確認\ngrep -n \"STRINGdb\\|DOSE\\|enrichR\\|enrichplot\" NAMESPACE\ngrep -n \"Version\\|Imports\\|Suggests\\|STRINGdb\\|DOSE\\|enrichR\\|enrichplot\\|gson\\|ggplot2\" DESCRIPTION\n\ngit diff\n\n# 8. build/check\nR CMD build .\nR CMD check TDbasedUFEadv_1.12.1.tar.gz\nRscript -e 'BiocCheck::BiocCheck(\"TDbasedUFEadv_1.12.1.tar.gz\")'\n\n# 9. commit\ngit add DESCRIPTION R/TDbasedUFEadv-package.R NAMESPACE vignettes/Enrichment.Rmd\ngit commit -m \"Move enrichment packages to Suggests and avoid STRING download in vignette\"\n\n# 10. push\ngit push origin RELEASE_3_23\n```\n\n失敗して push 前に戻すなら：\n\n```bash\ngit reset --hard backup-before-suggests-fix\nrm -f TDbasedUFEadv_*.tar.gz\nrm -rf TDbasedUFEadv.Rcheck\n```\n\npush 後に戻すなら：\n\n```bash\ngit checkout RELEASE_3_23\ngit pull\ngit log --oneline -5\n\ngit revert <失敗commitのhash>\n\n# DESCRIPTION を編集して Version: 1.12.2 にする\ngit add DESCRIPTION\ngit commit -m \"Bump version after reverting failed fix\"\ngit push origin RELEASE_3_23\n```\n\n---\n\n# 15. 最終確認ポイント\n\n最後に、以下が満たされていれば目的はほぼ達成です。\n\n```bash\ngrep -n \"STRINGdb\\|DOSE\\|enrichR\\|enrichplot\" NAMESPACE\n```\n\n何も出ない。\n\n```bash\ngrep -n \"STRINGdb\\|DOSE\\|enrichR\\|enrichplot\\|gson\\|ggplot2\" DESCRIPTION\n```\n\nこれらが `Suggests:` 側にある。\n\n```bash\ngrep -n \"eval=FALSE\" vignettes/Enrichment.Rmd\n```\n\nSTRINGdb と Enrichr の外部アクセス系 chunk が `eval=FALSE` になっている。\n\n特に重要なのは、`STRINGdb::STRINGdb$new()` が Bioconductor の vignette rebuild 中に実行されないことです。今回の check report では、vignette rebuild 中の STRING ファイル取得と、その後の `gson` 不足が ERROR 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