commit d77a1bf412e44772be1cb370c52538c8e32cac09 Author: Sebastian Rust Date: Wed May 27 21:00:28 2026 +0200 initial commit for public eval diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..ff723cf --- /dev/null +++ b/.dockerignore @@ -0,0 +1,6 @@ +.git +local.mk +analysis/.venv +out/ +derived/ +figures/out.bak/ diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b820e79 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +derived/* +out/ +local.mk +analysis/.venv/ diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..d82d211 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,27 @@ +FROM rocker/tidyverse:4.4.1 + +RUN apt-get update && apt-get install -y --no-install-recommends \ + make \ + curl \ + ca-certificates \ + texlive-latex-base \ + texlive-latex-recommended \ + texlive-fonts-recommended \ + && rm -rf /var/lib/apt/lists/* + +ENV RENV_CONFIG_REPOS_OVERRIDE=https://packagemanager.posit.co/cran/__linux__/jammy/latest \ + RENV_CONFIG_AUTOLOADER_ENABLED=FALSE + +COPY figures/renv.lock /tmp/figures/renv.lock +RUN R -e 'install.packages("renv"); setwd("/tmp/figures"); renv::restore(prompt = FALSE)' && rm -rf /tmp/figures + +ADD https://astral.sh/uv/install.sh /uv-installer.sh +RUN sh /uv-installer.sh && rm /uv-installer.sh + +ENV UV_PROJECT_ENVIRONMENT=/opt/venv \ + PATH=/opt/venv/bin:/root/.local/bin:$PATH + +COPY analysis/pyproject.toml analysis/uv.lock /tmp/analysis/ +RUN cd /tmp/analysis && uv sync --frozen --no-install-project && rm -rf /tmp/analysis + +WORKDIR /work/eval diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..fced13b --- /dev/null +++ b/Makefile @@ -0,0 +1,30 @@ +# Configuration precedence (highest to lowest): +# 1. command line: `make RAW_DATA_ROOT=/mnt/data ...` +# 2. environment: `RAW_DATA_ROOT=/mnt/data make ...` +# 3. local.mk file (Make syntax, use ?= so env still wins) +# 4. Makefile default (../raw_data) + +-include local.mk +export RAW_DATA_ROOT + +.PHONY: all figures tikz values derive sanity clean + +all: figures values + +figures: + $(MAKE) -C figures figures + +tikz: + $(MAKE) -C figures tikz + +values: + $(MAKE) -C figures values + +derive: + $(MAKE) -C figures derive + +sanity: + $(MAKE) -C figures sanity + +clean: + $(MAKE) -C figures clean diff --git a/README.md b/README.md new file mode 100644 index 0000000..677f29e --- /dev/null +++ b/README.md @@ -0,0 +1,60 @@ +# Evaluation pipeline + +Aggregates raw per-run measurements into figures (PDF + tikz) and a pgfkeys +`values.tex` for the paper. + +## Run + +With Docker (reproducible toolchain): + + docker compose up --build + +Outputs land in `out/`: +- `out/values.tex` -- all `\val{...}` keys for the paper +- `out//*.pdf` -- per-experiment figures +- `out//*.tex` -- tikz versions (via `make tikz`) + +Without Docker, requires R (with renv), Python 3.12+, uv, LaTeX (for +tikzDevice's metric probe). Then: + + make all + +## Targets + +- `make all` (= `figures values`) +- `make figures` -- PDFs for all experiments +- `make tikz` -- tikz `.tex` for all experiments +- `make values` -- regenerate `out/values.tex` only +- `make derive` -- aggregate raw data into `derived//*.csv` +- `make sanity` -- shape + NaN + solution-coverage checks on derived CSVs + +## Configuration + +`RAW_DATA_ROOT` controls where the aggregator reads raw aggregates from. +Precedence (highest first): + +1. command line: `make RAW_DATA_ROOT=/mnt/data ...` +2. environment: `RAW_DATA_ROOT=/mnt/data make ...` +3. `local.mk` (copy from `local.mk.example`) +4. Makefile default: `../raw_data` + +For Docker, the same variable picks the host path that gets bind-mounted as +`/raw_data` inside the container: + + RAW_DATA_ROOT=/mnt/data docker compose up + +## Layout + + analysis/ Python: aggregation, sanity, gen_values, plugins + values/ one plugin per metric family (cpu, rtt, idt, ...) + figures/ R: ggplot scripts, common.R, renv.lock + out/ generated (gitignored) + derived/ intermediate CSVs (gitignored) + +## Plugins + +`analysis/values/*.py` each expose `compute(derived) -> (keys, sources)`. +Keys are pgfkeys paths (e.g. `datacenter-fq/sender-cpu/cake/mean-pct`); +`gen_values.py` merges them, wraps numbers in `\qty{}{}` / `\num{}` by +suffix, and writes one `values.tex`. Add a new metric by dropping a new +plugin into `analysis/values/`. diff --git a/analysis/.gitignore b/analysis/.gitignore new file mode 100644 index 0000000..a230a78 --- /dev/null +++ b/analysis/.gitignore @@ -0,0 +1,2 @@ +.venv/ +__pycache__/ diff --git a/analysis/aggregate.py b/analysis/aggregate.py new file mode 100644 index 0000000..4664b79 --- /dev/null +++ b/analysis/aggregate.py @@ -0,0 +1,148 @@ +#!/usr/bin/env python3 +"""Aggregate raw per-run data into tidy unit-of-observation CSVs. + +Outputs four CSVs into --out: + runs.csv one row per run: setup, solution, run, throughput_bps, cpu_sender, cpu_receiver + rtts.csv one row per RTT sample: setup, solution, rtt_us + idts.csv one row per per-flow inter-departure-time: setup, solution, run, stream_id, idt_us + firstflow_bins.csv one row per 50 us bin (first stream of run 1): setup, solution, t_ms, packets +""" +import argparse +import json +from pathlib import Path + +import numpy as np +import pandas as pd + +BIN_US = 50 +MIN_PACKETS_PER_STREAM = 100 + + +def parse_args() -> argparse.Namespace: + p = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) + p.add_argument("--raw", required=True, type=Path, help="raw aggregates directory") + p.add_argument("--setup-prefix", required=True, help="directory prefix before _") + p.add_argument("--solutions", required=True, nargs="+", + help="solution names. Default lookup: _/. " + "Use 'label:dirname' to point a solution at a non-conforming directory " + "(e.g. cake:datacenter_cake_no-tso).") + p.add_argument("--out", required=True, type=Path, help="derived CSV output directory") + return p.parse_args() + + +def solution_spec(spec: str, setup_prefix: str) -> tuple[str, str]: + if ":" in spec: + label, dirname = spec.split(":", 1) + return label, dirname + return spec, f"{setup_prefix}_{spec}" + + +def load_metrics(sol_dir: Path) -> pd.DataFrame: + df = pd.read_csv(sol_dir / "metrics.csv") + return df[["run_num", "throughput_bps", "cpu_sender", "cpu_receiver"]].rename(columns={"run_num": "run"}) + + +def load_rtts(sol_dir: Path) -> pd.DataFrame: + with open(sol_dir / "rtt.json") as f: + rtts = json.load(f) + return pd.DataFrame({"rtt_us": pd.Series(rtts, dtype="float64")}) + + +def load_packets(sol_dir: Path) -> pd.DataFrame: + df = pd.read_csv(sol_dir / "packets.csv") + df = df[["run_num", "stream_id", "p4_timestamp_ns"]].rename(columns={"run_num": "run"}) + df = df.astype({"run": "int64", "stream_id": "int64", "p4_timestamp_ns": "int64"}) + + stream_counts = df.groupby("stream_id").size() + keep = stream_counts[stream_counts >= MIN_PACKETS_PER_STREAM].index + df = df[df["stream_id"].isin(keep)] + + return df.sort_values("p4_timestamp_ns", kind="mergesort").reset_index(drop=True) + + +def per_flow_idts(packets: pd.DataFrame) -> pd.DataFrame: + rows = [] + for (run, stream_id), df_flow in packets.groupby(["run", "stream_id"], sort=True): + t = df_flow["p4_timestamp_ns"].to_numpy(dtype=np.float64) + if len(t) < 2: + continue + idts = np.diff(t) / 1e3 + rows.append(pd.DataFrame({"run": run, "stream_id": stream_id, "idt_us": idts})) + return pd.concat(rows, ignore_index=True) + + +def firstflow_bins(packets: pd.DataFrame, bin_us: int) -> pd.DataFrame: + first_run = int(packets["run"].min()) + df_run = packets[packets["run"] == first_run] + first_stream = int(df_run["stream_id"].min()) + df_flow = df_run[df_run["stream_id"] == first_stream].sort_values("p4_timestamp_ns", kind="mergesort") + assert len(df_flow) >= MIN_PACKETS_PER_STREAM, f"first flow (run={first_run}, stream={first_stream}) too small" + + t_s = df_flow["p4_timestamp_ns"].to_numpy(dtype=np.float64) / 1e9 + bin_width_s = bin_us / 1e6 + t0 = float(t_s.min()) + idx = np.floor((t_s - t0) / bin_width_s).astype(np.int64) + n_bins = int(idx.max() + 1) + counts = np.bincount(idx, minlength=n_bins) + t_ms = (np.arange(n_bins) * bin_width_s) * 1000.0 + + return pd.DataFrame({"t_ms": t_ms, "packets": counts}) + + +def main() -> None: + args = parse_args() + args.out.mkdir(parents=True, exist_ok=True) + + runs_frames = [] + rtts_frames = [] + idts_frames = [] + bins_frames = [] + for spec in args.solutions: + label, dirname = solution_spec(spec, args.setup_prefix) + sol_dir = args.raw / dirname + if not sol_dir.is_dir(): + raise SystemExit(f"missing solution directory: {sol_dir}") + print(f" {label} (from {dirname})") + + runs = load_metrics(sol_dir) + runs.insert(0, "solution", label) + runs.insert(0, "setup", args.setup_prefix) + runs_frames.append(runs) + + rtts = load_rtts(sol_dir) + rtts.insert(0, "solution", label) + rtts.insert(0, "setup", args.setup_prefix) + rtts_frames.append(rtts) + + if not (sol_dir / "packets.csv").exists(): + print(f" no packets.csv, skipping idts + firstflow_bins") + continue + packets = load_packets(sol_dir) + if packets.empty: + print(f" no packet data, skipping idts + firstflow_bins") + continue + + idts = per_flow_idts(packets) + idts.insert(0, "solution", label) + idts.insert(0, "setup", args.setup_prefix) + idts_frames.append(idts) + + bins = firstflow_bins(packets, BIN_US) + bins.insert(0, "solution", label) + bins.insert(0, "setup", args.setup_prefix) + bins_frames.append(bins) + + pd.concat(runs_frames, ignore_index=True).to_csv(args.out / "runs.csv", index=False) + print(f"wrote {args.out / 'runs.csv'}") + pd.concat(rtts_frames, ignore_index=True).to_csv(args.out / "rtts.csv", index=False) + print(f"wrote {args.out / 'rtts.csv'}") + if idts_frames: + pd.concat(idts_frames, ignore_index=True).to_csv(args.out / "idts.csv", index=False) + print(f"wrote {args.out / 'idts.csv'}") + if bins_frames: + pd.concat(bins_frames, ignore_index=True).to_csv(args.out / "firstflow_bins.csv", index=False) + print(f"wrote {args.out / 'firstflow_bins.csv'}") + + +if __name__ == "__main__": + main() diff --git a/analysis/check_dups.py b/analysis/check_dups.py new file mode 100644 index 0000000..52008ec --- /dev/null +++ b/analysis/check_dups.py @@ -0,0 +1,102 @@ +#!/usr/bin/env python3 +"""Check raw_data for duplicate per-run metrics rows.""" +from __future__ import annotations +import csv +import hashlib +from pathlib import Path +import argparse + +RAW = Path(__file__).parent.parent / "raw_data" + + + +def metrics_payload(p: Path) -> tuple[str, ...]: + with p.open() as f: + rows = list(csv.reader(f)) + return tuple(rows[1][2:]) + + +def packet_signature(p: Path) -> tuple[int, int, tuple[int, ...], int, str]: + size = p.stat().st_size + streams: dict[int, int] = {} + timestamps: list[int] = [] + with p.open() as f: + next(f) + for line in f: + parts = line.rstrip().split(",") + streams[int(parts[2])] = streams.get(int(parts[2]), 0) + 1 + timestamps.append(int(parts[3])) + timestamps.sort() + span = timestamps[-1] - timestamps[0] if timestamps else 0 + ts_hash = hashlib.sha1(",".join(map(str, timestamps)).encode()).hexdigest()[:12] + return size, len(timestamps), tuple(sorted(streams)), span, ts_hash + + +def check_solution(sol_dir: Path) -> list[str]: + payloads: dict[tuple[str, ...], list[int]] = {} + for run_dir in sol_dir.glob("tmp_run_*"): + n = int(run_dir.name.removeprefix("tmp_run_")) + try: + payloads.setdefault(metrics_payload(run_dir / "metrics_row.csv"), []).append(n) + except FileNotFoundError: + continue + + report = [] + for payload, runs in payloads.items(): + if len(runs) < 2: + continue + runs.sort() + base = runs[0] + for other in runs[1:]: + base_pp = sol_dir / f"tmp_run_{base}" / "parsed_packets.csv" + other_pp = sol_dir / f"tmp_run_{other}" / "parsed_packets.csv" + if not base_pp.exists() or not other_pp.exists(): + report.append( + f" run {base:>2} = run {other:<2} metrics: same " + f"parsed_packets: MISSING -> duplicate confirmed via metrics only" + ) + continue + sig_base, sig_other = packet_signature(base_pp), packet_signature(other_pp) + ts_match = (sig_base[4] == sig_other[4]) + if ts_match: + verdict = "DEEPER BUG (timestamps identical despite different stream IDs)" + elif sig_base[1] == sig_other[1] and sig_base[3] == sig_other[3]: + verdict = "BUG + suspicious (rows + span match but timestamps differ)" + else: + verdict = "BUG (independent captures, metrics row stamped from another run)" + report.append( + f" run {base:>2} = run {other:<2} metrics: same -> {verdict}\n" + f" run {base:>2}: size={sig_base[0]:>10} rows={sig_base[1]:>7} " + f"streams={list(sig_base[2])} span_ns={sig_base[3]} ts_hash={sig_base[4]}\n" + f" run {other:>2}: size={sig_other[0]:>10} rows={sig_other[1]:>7} " + f"streams={list(sig_other[2])} span_ns={sig_other[3]} ts_hash={sig_other[4]}" + ) + return report + + +def main() -> None: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--data", type=Path, default=RAW, help="raw_data root directory") + args = parser.parse_args() + + total_bugs = 0 + for exp_dir in sorted(args.data.iterdir()): + agg = exp_dir / "aggregates" + if not agg.is_dir(): + continue + for sol_dir in sorted(agg.iterdir()): + if not sol_dir.is_dir(): + continue + lines = check_solution(sol_dir) + if not lines: + continue + print(f"\n== {exp_dir.name}/{sol_dir.name} ==") + for line in lines: + print(line) + if "BUG" in line: + total_bugs += 1 + print(f"\nconfirmed BUG count: {total_bugs}") + + +if __name__ == "__main__": + main() diff --git a/analysis/gen_values.py b/analysis/gen_values.py new file mode 100644 index 0000000..ff8525c --- /dev/null +++ b/analysis/gen_values.py @@ -0,0 +1,99 @@ +#!/usr/bin/env python3 +"""Generate values.tex from plugins under analysis/values/. + +Each plugin exposes compute(derived) -> (keys, sources). Keys are merged into +one \\pgfkeys block; sources are recorded in the header for provenance. +""" +import argparse +import datetime as dt +import importlib.util +from pathlib import Path +from types import ModuleType + +def load_plugins(plugin_dir: Path, skip: set[str]) -> list[tuple[str, ModuleType]]: + plugins: list[tuple[str, ModuleType]] = [] + for p in sorted(plugin_dir.glob("*.py")): + if p.name.startswith("_") or p.stem in skip: + continue + spec = importlib.util.spec_from_file_location(f"values.{p.stem}", p) + if spec is None or spec.loader is None: + raise SystemExit(f"could not load plugin {p}") + mod = importlib.util.module_from_spec(spec) + spec.loader.exec_module(mod) + if hasattr(mod, "compute"): + plugins.append((p.stem, mod)) + return plugins + + +def file_mtime_iso(p: Path) -> str: + return dt.datetime.fromtimestamp(p.stat().st_mtime).isoformat(timespec="seconds") + + +# Map key-name suffix to siunitx unit. +UNIT_SUFFIXES = { + "-us": r"\micro\second", + "-ms": r"\milli\second", + "-gbps": r"\giga\bit\per\second", + "-pct": r"\percent", + "-kb": r"\kilo\byte", +} + + +NUM_SUFFIXES = ("-p", "-alpha", "-n", "-uncorrected") +NUM_PREFIXES = ("n-",) + + +def value_to_latex(key: str, value: str) -> str: + leaf = key.rsplit("/", 1)[-1] + for suffix, unit in UNIT_SUFFIXES.items(): + if leaf.endswith(suffix): + return f"\\qty{{{value}}}{{{unit}}}" + if any(leaf.startswith(p) for p in NUM_PREFIXES) or any(leaf.endswith(s) for s in NUM_SUFFIXES): + return f"\\num{{{value}}}" + return value + + +def format_pgfkeys(all_keys: dict[str, str], provenance: list[str]) -> str: + lines: list[str] = [] + lines.append("% Auto-generated by analysis/gen_values.py. Do not edit by hand.") + lines.append(f"% Generated: {dt.datetime.now().isoformat(timespec='seconds')}") + lines.extend(provenance) + for k, v in sorted(all_keys.items()): + lines.append(f"\\pgfkeyssetvalue{{/{k}}}{{{value_to_latex(k, v)}}}") + return "\n".join(lines) + "\n" + + +def main() -> None: + p = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) + p.add_argument("--derived", required=True, type=Path, help="derived/ root with per-experiment subdirs") + p.add_argument("--out", required=True, type=Path, help="output values.tex path") + p.add_argument("--plugins", type=Path, default=Path(__file__).parent / "values", + help="plugin directory (default: analysis/values)") + p.add_argument("--skip", nargs="*", default=[], + help="plugin names to skip (stem only, e.g. --skip cpu rtt)") + args = p.parse_args() + + plugins = load_plugins(args.plugins, set(args.skip)) + if not plugins: + raise SystemExit(f"no plugins found in {args.plugins} (after --skip)") + + all_keys: dict[str, str] = {} + provenance: list[str] = ["% Plugins:"] + for name, mod in plugins: + keys, sources = mod.compute(args.derived) + dup = set(keys) & set(all_keys) + if dup: + raise SystemExit(f"plugin {name} duplicates keys: {sorted(dup)}") + all_keys.update(keys) + provenance.append(f"% {name}: {len(keys)} keys") + for src in sources: + provenance.append(f"% {src} (mtime {file_mtime_iso(src)})") + print(f" {name}: {len(keys)} keys from {len(sources)} sources") + + args.out.parent.mkdir(parents=True, exist_ok=True) + args.out.write_text(format_pgfkeys(all_keys, provenance)) + print(f"wrote {args.out} ({len(all_keys)} keys total)") + + +if __name__ == "__main__": + main() diff --git a/analysis/pyproject.toml b/analysis/pyproject.toml new file mode 100644 index 0000000..12d8540 --- /dev/null +++ b/analysis/pyproject.toml @@ -0,0 +1,10 @@ +[project] +name = "eval-analysis" +version = "0.1.0" +description = "Aggregate raw per-run data to tidy unit-of-observation CSVs" +requires-python = ">=3.12" +dependencies = [ + "pandas>=2.2", + "numpy>=2.0", + "scipy>=1.13", +] diff --git a/analysis/sanity_check.py b/analysis/sanity_check.py new file mode 100644 index 0000000..237a15d --- /dev/null +++ b/analysis/sanity_check.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python3 +"""Sanity check derived CSVs: shapes, no NaN, expected solution coverage.""" +import argparse +import sys +from pathlib import Path + +import pandas as pd + +REQUIRED = { + "runs.csv": {"setup", "solution", "run", "throughput_bps", "cpu_sender", "cpu_receiver"}, + "rtts.csv": {"setup", "solution", "rtt_us"}, +} + +OPTIONAL = { + "idts.csv": {"setup", "solution", "run", "stream_id", "idt_us"}, + "firstflow_bins.csv": {"setup", "solution", "t_ms", "packets"}, +} + + +def check(derived: Path, expected_solutions: set[str]) -> list[str]: + errors = [] + for name, cols in {**REQUIRED, **OPTIONAL}.items(): + path = derived / name + if not path.exists(): + if name in REQUIRED: + errors.append(f"{name}: missing") + continue + df = pd.read_csv(path) + missing_cols = cols - set(df.columns) + if missing_cols: + errors.append(f"{name}: missing columns {missing_cols}") + if df.isna().any().any(): + nan_cols = df.columns[df.isna().any()].tolist() + errors.append(f"{name}: NaN in columns {nan_cols}") + if len(df) == 0: + errors.append(f"{name}: empty") + sols = set(df["solution"].unique()) + if sols != expected_solutions: + errors.append(f"{name}: solutions {sols} != expected {expected_solutions}") + return errors + + +def main() -> None: + p = argparse.ArgumentParser() + p.add_argument("--derived", required=True, type=Path) + p.add_argument("--solutions", required=True, nargs="+") + args = p.parse_args() + + errors = check(args.derived, set(args.solutions)) + if errors: + for e in errors: + print(f" FAIL: {e}") + sys.exit(1) + print("ok") + + +if __name__ == "__main__": + main() diff --git a/analysis/uv.lock b/analysis/uv.lock new file mode 100644 index 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--git a/analysis/values/__init__.py b/analysis/values/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/analysis/values/bins.py b/analysis/values/bins.py new file mode 100644 index 0000000..d87ebab --- /dev/null +++ b/analysis/values/bins.py @@ -0,0 +1,34 @@ +"""First-flow packet-per-bin stats from firstflow_bins.csv. +""" +from pathlib import Path + +import numpy as np +import pandas as pd + + +def _stats(x: np.ndarray) -> dict[str, str]: + return { + "max-pkts": str(int(x.max())), + "mean-pkts": f"{x.mean():.2f}", + "median-pkts": str(int(np.median(x))), + "p95-pkts": str(int(np.percentile(x, 95))), + "p99-pkts": str(int(np.percentile(x, 99))), + "sd-pkts": f"{x.std(ddof=1):.2f}", + "n-bins": str(x.size), + } + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + out: dict[str, str] = {} + sources: list[Path] = [] + for exp_dir in sorted(p for p in derived.iterdir() if p.is_dir()): + bins_path = exp_dir / "firstflow_bins.csv" + if not bins_path.exists(): + continue + sources.append(bins_path) + df = pd.read_csv(bins_path) + for sol, sub in df.groupby("solution", sort=True): + x = sub["packets"].to_numpy() + for k, v in _stats(x).items(): + out[f"{exp_dir.name}/bins/{sol}/{k}"] = v + return out, sources diff --git a/analysis/values/cpu.py b/analysis/values/cpu.py new file mode 100644 index 0000000..9a65257 --- /dev/null +++ b/analysis/values/cpu.py @@ -0,0 +1,28 @@ +"""Sender + receiver CPU per (experiment, solution): mean and sample SD in %.""" +from pathlib import Path + +import pandas as pd + + +METRICS = { + "sender-cpu": "cpu_sender", + "receiver-cpu": "cpu_receiver", +} + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + out: dict[str, str] = {} + sources: list[Path] = [] + for exp_dir in sorted(p for p in derived.iterdir() if p.is_dir()): + runs = exp_dir / "runs.csv" + if not runs.exists(): + continue + sources.append(runs) + df = pd.read_csv(runs) + for sol, sub in df.groupby("solution", sort=True): + for metric, col in METRICS.items(): + x = sub[col].to_numpy() + base = f"{exp_dir.name}/{metric}/{sol}" + out[f"{base}/mean-pct"] = f"{x.mean():.2f}" + out[f"{base}/sd-pct"] = f"{x.std(ddof=1):.2f}" + return out, sources diff --git a/analysis/values/idt.py b/analysis/values/idt.py new file mode 100644 index 0000000..8b3454e --- /dev/null +++ b/analysis/values/idt.py @@ -0,0 +1,60 @@ +"""Per-flow IDT per (experiment, solution): percentiles, mean, SD in microseconds. +""" +from pathlib import Path + +import numpy as np +import pandas as pd + + +def _stats(x: np.ndarray) -> dict[str, str]: + q05, q25, q50, q75, q95, q99 = np.percentile(x, [5, 25, 50, 75, 95, 99]) + return { + "mean-us": f"{x.mean():.2f}", + "sd-us": f"{x.std(ddof=1):.2f}", + "median-us": f"{q50:.2f}", + "p05-us": f"{q05:.2f}", + "p25-us": f"{q25:.2f}", + "p75-us": f"{q75:.2f}", + "p95-us": f"{q95:.2f}", + "p99-us": f"{q99:.2f}", + "iqr-us": f"{q75 - q25:.2f}", + "n-samples": str(x.size), + } + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + out: dict[str, str] = {} + sources: list[Path] = [] + for exp_dir in sorted(p for p in derived.iterdir() if p.is_dir()): + idts_path = exp_dir / "idts.csv" + if not idts_path.exists(): + continue + sources.append(idts_path) + df = pd.read_csv(idts_path, usecols=["solution", "idt_us"]) + per_sol: dict[str, dict[str, str]] = {} + for sol, sub in df.groupby("solution", sort=True): + x = sub["idt_us"].to_numpy() + stats = _stats(x) + per_sol[sol] = stats + for k, v in stats.items(): + out[f"{exp_dir.name}/idt/{sol}/{k}"] = v + + # IQR is meaningful only when the baseline solution actually spreads + # the bulk; pre-pacing IDT is bimodal (back-to-back packets, heavy + # tail above p95) so its IQR is often zero. Guard the ratio. + if "tso-pacing" in per_sol: + pac_sd = float(per_sol["tso-pacing"]["sd-us"]) + pac_iqr = float(per_sol["tso-pacing"]["iqr-us"]) + for other in ("no-tso", "tso", "cake"): + if other not in per_sol: + continue + o_sd = float(per_sol[other]["sd-us"]) + o_iqr = float(per_sol[other]["iqr-us"]) + base = f"{exp_dir.name}/idt/tso-pacing-vs-{other}" + if o_sd > 0: + out[f"{base}/sd-ratio-pct"] = f"{100 * pac_sd / o_sd:.1f}" + out[f"{base}/sd-reduction-pct"] = f"{100 * (1 - pac_sd / o_sd):.1f}" + if o_iqr > 0: + out[f"{base}/iqr-ratio-pct"] = f"{100 * pac_iqr / o_iqr:.1f}" + out[f"{base}/iqr-reduction-pct"] = f"{100 * (1 - pac_iqr / o_iqr):.1f}" + return out, sources diff --git a/analysis/values/nfp4000.py b/analysis/values/nfp4000.py new file mode 100644 index 0000000..9c287d2 --- /dev/null +++ b/analysis/values/nfp4000.py @@ -0,0 +1,15 @@ +"""NFP-4000 memory constants (capacities + access latencies). + +Source: Netronome Network Flow Processor 4xxx Family datasheet +(netronomeNetronomeNetworkFlow2018). +""" +from pathlib import Path + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + return { + "nfp4000/lmem/capacity-kb": "4", + "nfp4000/lmem/latency-cycles": "1-3", + "nfp4000/ctm/capacity-kb": "256", + "nfp4000/ctm/latency-cycles": "50-100", + }, [] diff --git a/analysis/values/rtt.py b/analysis/values/rtt.py new file mode 100644 index 0000000..c17c188 --- /dev/null +++ b/analysis/values/rtt.py @@ -0,0 +1,60 @@ +"""RTT per (experiment, solution): mean, SD, quantiles, spread. + +Also emits tso-pacing's variance-reduction ratios vs the other solutions. +""" +from pathlib import Path + +import numpy as np +import pandas as pd + + +def _stats(x: np.ndarray) -> dict[str, str]: + q05, q25, q50, q75, q95 = np.percentile(x, [5, 25, 50, 75, 95]) + return { + "mean-ms": f"{x.mean():.2f}", + "sd-ms": f"{x.std(ddof=1):.2f}", + "median-ms": f"{q50:.2f}", + "iqr-ms": f"{q75 - q25:.2f}", + "p05-ms": f"{q05:.2f}", + "p95-ms": f"{q95:.2f}", + "spread-5-95-ms": f"{q95 - q05:.2f}", + "n-samples": str(x.size), + } + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + out: dict[str, str] = {} + sources: list[Path] = [] + for exp_dir in sorted(p for p in derived.iterdir() if p.is_dir()): + rtts = exp_dir / "rtts.csv" + if not rtts.exists(): + continue + sources.append(rtts) + df = pd.read_csv(rtts) + per_sol: dict[str, dict[str, str]] = {} + for sol, sub in df.groupby("solution", sort=True): + x = sub["rtt_us"].to_numpy() / 1000.0 + stats = _stats(x) + per_sol[sol] = stats + for k, v in stats.items(): + out[f"{exp_dir.name}/rtt/{sol}/{k}"] = v + + if "tso-pacing" in per_sol: + pac_sd = float(per_sol["tso-pacing"]["sd-ms"]) + pac_spread = float(per_sol["tso-pacing"]["spread-5-95-ms"]) + pac_iqr = float(per_sol["tso-pacing"]["iqr-ms"]) + for other in ("no-tso", "tso", "cake"): + if other not in per_sol: + continue + o = per_sol[other] + o_sd = float(o["sd-ms"]) + o_spread = float(o["spread-5-95-ms"]) + o_iqr = float(o["iqr-ms"]) + base = f"{exp_dir.name}/rtt/tso-pacing-vs-{other}" + out[f"{base}/sd-ratio-pct"] = f"{100 * pac_sd / o_sd:.1f}" + out[f"{base}/spread-ratio-pct"] = f"{100 * pac_spread / o_spread:.1f}" + out[f"{base}/iqr-ratio-pct"] = f"{100 * pac_iqr / o_iqr:.1f}" + out[f"{base}/sd-reduction-pct"] = f"{100 * (1 - pac_sd / o_sd):.1f}" + out[f"{base}/spread-reduction-pct"] = f"{100 * (1 - pac_spread / o_spread):.1f}" + out[f"{base}/iqr-reduction-pct"] = f"{100 * (1 - pac_iqr / o_iqr):.1f}" + return out, sources diff --git a/analysis/values/tests.py b/analysis/values/tests.py new file mode 100644 index 0000000..8c4bf2c --- /dev/null +++ b/analysis/values/tests.py @@ -0,0 +1,109 @@ +"""Pairwise hypothesis tests across solutions. + +Means: Welch's t (two-sided + one-sided) and Mann-Whitney U. +Variance: Brown-Forsythe (Levene, median-centered) and Fligner-Killeen. +""" +from pathlib import Path + +import numpy as np +import pandas as pd +from scipy import stats + +PAIRS = [ + ("no-tso", "tso"), + ("no-tso", "tso-pacing"), + ("no-tso", "cake"), + ("tso", "tso-pacing"), + ("tso", "cake"), + ("tso-pacing", "cake"), +] + +ALPHA = 0.05 + + +def _fmt(x: float) -> str: + return f"{x:.4g}" + + +def _mean_tests(out: dict, base: str, a: np.ndarray, b: np.ndarray) -> None: + _, p_t = stats.ttest_ind(a, b, equal_var=False) + _, p_tl = stats.ttest_ind(a, b, equal_var=False, alternative="less") + _, p_tg = stats.ttest_ind(a, b, equal_var=False, alternative="greater") + _, p_u = stats.mannwhitneyu(a, b, alternative="two-sided") + out[f"{base}/welch-p"] = _fmt(p_t) + out[f"{base}/welch-less-p"] = _fmt(p_tl) + out[f"{base}/welch-greater-p"] = _fmt(p_tg) + out[f"{base}/mwu-p"] = _fmt(p_u) + + +def _variance_tests(out: dict, base: str, a: np.ndarray, b: np.ndarray) -> None: + bf = stats.levene(a, b, center="median") + fl = stats.fligner(a, b) + out[f"{base}/bf-p"] = _fmt(bf.pvalue) + out[f"{base}/fligner-p"] = _fmt(fl.pvalue) + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + out: dict[str, str] = {} + sources: list[Path] = [] + for exp_dir in sorted(p for p in derived.iterdir() if p.is_dir()): + runs_path = exp_dir / "runs.csv" + rtts_path = exp_dir / "rtts.csv" + + if runs_path.exists(): + sources.append(runs_path) + runs = pd.read_csv(runs_path) + for metric, col in (("sender-cpu", "cpu_sender"), + ("receiver-cpu", "cpu_receiver")): + vals = {sol: sub[col].to_numpy() for sol, sub in runs.groupby("solution")} + for a, b in PAIRS: + if a not in vals or b not in vals: + continue + base = f"{exp_dir.name}/{metric}/test/{a}-vs-{b}" + _mean_tests(out, base, vals[a], vals[b]) + + if rtts_path.exists(): + sources.append(rtts_path) + rtts = pd.read_csv(rtts_path) + vals = {sol: sub["rtt_us"].to_numpy() / 1000.0 + for sol, sub in rtts.groupby("solution")} + for a, b in PAIRS: + if a not in vals or b not in vals: + continue + base = f"{exp_dir.name}/rtt/test/{a}-vs-{b}" + _mean_tests(out, base, vals[a], vals[b]) + _variance_tests(out, base, vals[a], vals[b]) + + idts_path = exp_dir / "idts.csv" + if idts_path.exists(): + sources.append(idts_path) + idts = pd.read_csv(idts_path, usecols=["solution", "idt_us"]) + vals = {sol: sub["idt_us"].to_numpy() + for sol, sub in idts.groupby("solution")} + for a, b in PAIRS: + if a not in vals or b not in vals: + continue + base = f"{exp_dir.name}/idt/test/{a}-vs-{b}" + _mean_tests(out, base, vals[a], vals[b]) + _variance_tests(out, base, vals[a], vals[b]) + + # Bonferroni-corrected thresholds. Count one entry per comparison + # (welch-p for mean families, bf-p for variance) so the threshold reflects + # the number of pairwise comparisons, not the number of test statistics. + def n_with(in_pattern: str, suffix: str) -> int: + return sum(1 for k in out if in_pattern in k and k.endswith(suffix)) + + families = { + "cpu": n_with("-cpu/test/", "/mwu-p"), + "rtt-mean": n_with("/rtt/test/", "/mwu-p"), + "rtt-variance": n_with("/rtt/test/", "/bf-p"), + "idt-mean": n_with("/idt/test/", "/mwu-p"), + "idt-variance": n_with("/idt/test/", "/bf-p"), + } + for name, n in families.items(): + if n > 0: + out[f"bonferroni/{name}-n"] = str(n) + out[f"bonferroni/{name}-alpha"] = _fmt(ALPHA / n) + out["bonferroni/alpha-uncorrected"] = _fmt(ALPHA) + + return out, sources diff --git a/analysis/values/throughput.py b/analysis/values/throughput.py new file mode 100644 index 0000000..ff61e7c --- /dev/null +++ b/analysis/values/throughput.py @@ -0,0 +1,22 @@ +"""Throughput per (experiment, solution): mean and sample SD in Gbps.""" +from pathlib import Path + +import pandas as pd + + +def compute(derived: Path) -> tuple[dict[str, str], list[Path]]: + out: dict[str, str] = {} + sources: list[Path] = [] + for exp_dir in sorted(p for p in derived.iterdir() if p.is_dir()): + runs = exp_dir / "runs.csv" + if not runs.exists(): + continue + sources.append(runs) + df = pd.read_csv(runs) + for sol, sub in df.groupby("solution", sort=True): + thr = sub["throughput_bps"].to_numpy() / 1e9 + base = f"{exp_dir.name}/throughput/{sol}" + out[f"{base}/mean-gbps"] = f"{thr.mean():.3f}" + out[f"{base}/sd-gbps"] = f"{thr.std(ddof=1):.3f}" + out[f"{base}/n-runs"] = str(len(thr)) + return out, sources diff --git a/compose.yml b/compose.yml new file mode 100644 index 0000000..84fb20a --- /dev/null +++ b/compose.yml @@ -0,0 +1,21 @@ +# docker compose up -> runs `make all`, writes eval/out/. +# RAW_DATA_ROOT=/path docker compose up -> point at a different raw_data tree. +# +# RAW_DATA_ROOT outside the container = host path to mount (read by compose). +# Inside the container it always resolves to /raw_data via the `environment:` +# clause below; the host value is only consumed by the volume substitution. + +services: + eval: + build: . + image: eval + user: "${UID:-1000}:${GID:-1000}" + volumes: + - .:/work/eval + - ${RAW_DATA_ROOT:-../raw_data}:/raw_data:ro + environment: + RAW_DATA_ROOT: /raw_data + HOME: /tmp + UV_CACHE_DIR: /tmp/uv-cache + working_dir: /work/eval + command: make all diff --git a/figures/.Rprofile b/figures/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/figures/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/figures/.gitignore b/figures/.gitignore new file mode 100644 index 0000000..1401f53 --- /dev/null +++ b/figures/.gitignore @@ -0,0 +1,11 @@ +out/ +renv/library/ +renv/local/ +renv/cellar/ +renv/lock/ +renv/sandbox/ +renv/staging/ +.Rproj.user/ +.Rhistory +.RData +.Ruserdata diff --git a/figures/Makefile b/figures/Makefile new file mode 100644 index 0000000..44143be --- /dev/null +++ b/figures/Makefile @@ -0,0 +1,170 @@ +-include ../local.mk + +EXP ?= datacenter-fq +SETUP ?= datacenter_fq +SOLUTIONS ?= no-tso tso tso-pacing +FIG_STEMS ?= throughput throughput_zoom rtt rtt_zoom sender_cpu receiver_cpu timeseries idt_cdf idt_cdf_zoom + +# Global figure size and font size (inches, pt). Inherited by every Rscript +# via the export below; common.R reads these as Sys.getenv("FIG_*"). +# Override on the command line: make FIG_WIDTH=2.5 FIG_HEIGHT=1.8 FIG_FONTSIZE=8 datacenter-fq +FIG_WIDTH ?= 2.5 +FIG_HEIGHT ?= 2.0 +FIG_FONTSIZE ?= 9 +export FIG_WIDTH FIG_HEIGHT FIG_FONTSIZE + +THROUGHPUT_SIZE_ARGS ?= +RTT_SIZE_ARGS ?= +THROUGHPUT_ARGS ?= +RTT_ARGS ?= +THROUGHPUT_ZOOM_ARGS ?= --ymin 3.5 --ymax 4.0 --ystep 0.1 +RTT_ZOOM_ARGS ?= --ymin 4 --ymax 14 --ystep 2 +SENDER_CPU_ARGS ?= +RECEIVER_CPU_ARGS ?= +TIMESERIES_ARGS ?= +IDT_CDF_ARGS ?= + +ROOT := .. +RAW_DATA_ROOT ?= $(ROOT)/../raw_data +RAW := $(RAW_DATA_ROOT)/$(EXP)/aggregates +DERIVED := $(ROOT)/derived/$(EXP) +DERIVED_ROOT := $(ROOT)/derived +OUT := ../out/$(EXP) +VALUES_TEX := ../out/values.tex +VALUES_PLUGINS := $(wildcard $(ROOT)/analysis/values/*.py) +SKIP_PLUGINS ?= + +CSVS := $(addprefix $(DERIVED)/, runs.csv rtts.csv idts.csv firstflow_bins.csv) +PDFS := $(addprefix $(OUT)/, $(addsuffix .pdf, $(FIG_STEMS))) +TEXS := $(addprefix $(OUT)/, $(addsuffix .tex, $(FIG_STEMS))) + +.PHONY: all derive figures tikz sanity values pdfs tex clean datacenter-fq datacenter-fq-tikz direct-link direct-link-tikz all-experiments all-experiments-tikz +.DELETE_ON_ERROR: + +all: all-experiments + +derive: $(DERIVED)/.stamp + +$(DERIVED)/.stamp: $(ROOT)/analysis/aggregate.py + cd $(ROOT)/analysis && uv run python aggregate.py --raw $(abspath $(RAW)) --setup-prefix $(SETUP) --solutions $(SOLUTIONS) --out $(abspath $(DERIVED)) + touch $@ + +$(CSVS): $(DERIVED)/.stamp + +sanity: $(DERIVED)/.stamp + cd $(ROOT)/analysis && uv run python sanity_check.py --derived $(abspath $(DERIVED)) --solutions $(SOLUTIONS) + +figures: all-experiments +tikz: all-experiments-tikz + +pdfs: $(PDFS) +tex: $(TEXS) + +FMT_FLAG = $(if $(filter %.tex,$@),--tikz,--pdf) + +$(OUT)/throughput.pdf $(OUT)/throughput.tex: fig_throughput.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ $(THROUGHPUT_SIZE_ARGS) $(THROUGHPUT_ARGS) + +$(OUT)/throughput_zoom.pdf $(OUT)/throughput_zoom.tex: fig_throughput.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ --zoom $(THROUGHPUT_SIZE_ARGS) $(THROUGHPUT_ZOOM_ARGS) + +$(OUT)/rtt.pdf $(OUT)/rtt.tex: fig_rtt.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ $(RTT_SIZE_ARGS) $(RTT_ARGS) + +$(OUT)/rtt_zoom.pdf $(OUT)/rtt_zoom.tex: fig_rtt.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ --zoom $(RTT_SIZE_ARGS) $(RTT_ZOOM_ARGS) + +$(OUT)/sender_cpu.pdf $(OUT)/sender_cpu.tex: fig_sender_cpu.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ $(SENDER_CPU_ARGS) + +$(OUT)/receiver_cpu.pdf $(OUT)/receiver_cpu.tex: fig_receiver_cpu.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ $(RECEIVER_CPU_ARGS) + +$(OUT)/timeseries.pdf $(OUT)/timeseries.tex: fig_timeseries.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ $(TIMESERIES_ARGS) + +$(OUT)/idt_cdf.pdf $(OUT)/idt_cdf.tex: fig_idt_cdf.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ $(IDT_CDF_ARGS) + +$(OUT)/idt_cdf_zoom.pdf $(OUT)/idt_cdf_zoom.tex: fig_idt_cdf.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) $(FMT_FLAG) $@ --zoom $(IDT_CDF_ARGS) + +$(OUT)/%.pdf: fig_%.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) --pdf $@ + +$(OUT)/%_zoom.pdf: fig_%.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) --pdf $@ --zoom + +$(OUT)/%.tex: fig_%.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) --tikz $@ + +$(OUT)/%_zoom.tex: fig_%.R common.R $(CSVS) Makefile + @mkdir -p $(OUT) + Rscript $< --data $(DERIVED) --tikz $@ --zoom + +values: $(VALUES_TEX) + +# SKIP_PLUGINS is a runtime decision, not a file dependency: force rebuild +# whenever the user sets it on the command line. +ifneq ($(SKIP_PLUGINS),) +.PHONY: $(VALUES_TEX) +endif + +$(VALUES_TEX): $(ROOT)/analysis/gen_values.py $(VALUES_PLUGINS) $(DERIVED_ROOT)/datacenter-fq/.stamp $(DERIVED_ROOT)/direct-link/.stamp Makefile + @mkdir -p $(dir $(VALUES_TEX)) + cd $(ROOT)/analysis && uv run python gen_values.py --derived $(abspath $(DERIVED_ROOT)) --out $(abspath $(VALUES_TEX)) $(if $(SKIP_PLUGINS),--skip $(SKIP_PLUGINS)) + +clean: + rm -rf $(OUT) $(DERIVED) + +# Per-experiment shortcut targets. Each recursively invokes the makefile +# with the right EXP / SETUP / FIG_STEMS / zoom overrides. + +# Per-experiment knobs. Each shortcut target reuses these via $(call ...). +QUARTER_SIZE := --width 1.4 --height 1.5 + +DATACENTER_FQ_ARGS = EXP=datacenter-fq SETUP=datacenter_fq \ + SOLUTIONS="no-tso tso tso-pacing cake:datacenter_cake_no-tso" \ + FIG_STEMS="throughput throughput_zoom rtt rtt_zoom sender_cpu receiver_cpu timeseries idt_cdf idt_cdf_zoom" \ + THROUGHPUT_SIZE_ARGS="$(QUARTER_SIZE)" \ + RTT_SIZE_ARGS="$(QUARTER_SIZE)" \ + THROUGHPUT_ZOOM_ARGS="--ymin 3.5 --ymax 4.0 --ystep 0.1" \ + RTT_ZOOM_ARGS="--ymin 4 --ymax 14 --ystep 2" + +DIRECT_LINK_ARGS = EXP=direct-link SETUP=direct-link_fq \ + SOLUTIONS="no-tso tso tso-pacing cake:direct-link_cake_no-tso" \ + FIG_STEMS="throughput throughput_zoom rtt rtt_zoom sender_cpu receiver_cpu" \ + THROUGHPUT_SIZE_ARGS="$(QUARTER_SIZE)" \ + RTT_SIZE_ARGS="$(QUARTER_SIZE)" \ + THROUGHPUT_ARGS="--ymax 10 --ystep 2" \ + THROUGHPUT_ZOOM_ARGS="--ymin 9.0 --ymax 10.0 --ystep 0.2" \ + RTT_ZOOM_ARGS="--ymin 1.75 --ymax 4 --ystep 1" \ + SENDER_CPU_ARGS="--ystep 1" \ + RECEIVER_CPU_ARGS="--ystep 5" + +datacenter-fq: + $(MAKE) pdfs $(DATACENTER_FQ_ARGS) + +datacenter-fq-tikz: + $(MAKE) tex $(DATACENTER_FQ_ARGS) + +direct-link: + $(MAKE) pdfs $(DIRECT_LINK_ARGS) + +direct-link-tikz: + $(MAKE) tex $(DIRECT_LINK_ARGS) + +all-experiments: datacenter-fq direct-link +all-experiments-tikz: datacenter-fq-tikz direct-link-tikz diff --git a/figures/common.R b/figures/common.R new file mode 100644 index 0000000..352ae93 --- /dev/null +++ b/figures/common.R @@ -0,0 +1,128 @@ +suppressPackageStartupMessages({ + library(argparse) + library(ggplot2) + library(dplyr) + library(tidyr) + library(readr) + library(scales) + library(tikzDevice) +}) + +SOLUTION_ORDER <- c("tso", "tso-pacing", "cake") + +SOLUTION_LABELS <- c( + "no-tso" = "TSO Off", + "tso" = "TSO On", + "tso-pacing" = "TSO Pacing", + "cake" = "Cake" +) + +SOLUTION_COLORS <- c( + "no-tso" = "#009E73", + "tso" = "#E69F00", + "tso-pacing" = "#0072B2", + "cake" = "#CC79A7" +) + +SOLUTION_LINETYPES <- c( + "no-tso" = "longdash", + "tso" = "dashed", + "tso-pacing" = "solid", + "cake" = "twodash" +) + +# Global figure size and font size, overridable via env vars +# (Makefile exports FIG_WIDTH / FIG_HEIGHT / FIG_FONTSIZE). +.env_num <- function(var, default) { + v <- Sys.getenv(var) + if (nchar(v) == 0) default else as.numeric(v) +} +DEFAULT_WIDTH <- .env_num("FIG_WIDTH", 3.33) +DEFAULT_HEIGHT <- .env_num("FIG_HEIGHT", 2.4) +DEFAULT_FONTSIZE <- .env_num("FIG_FONTSIZE", 10) + +theme_paper <- function(base_size = DEFAULT_FONTSIZE) { + theme_bw(base_size = base_size) + + theme( + legend.position = "bottom", + legend.title = element_blank(), + legend.margin = margin(t = -4, l = -20), + legend.text = element_text(size = base_size - 1), + legend.key.size = unit(base_size, "pt"), + axis.text = element_text(size = base_size - 1), + strip.background = element_rect(fill = "grey90"), + panel.grid.minor = element_blank(), + plot.margin = margin(2, 4, 2, 2) + ) +} + +prepare_solution <- function(df) { + df %>% + filter(solution %in% SOLUTION_ORDER) %>% + mutate(solution = factor(solution, levels = SOLUTION_ORDER, + labels = SOLUTION_LABELS[SOLUTION_ORDER])) +} + +LABEL_COLORS <- setNames(SOLUTION_COLORS[SOLUTION_ORDER], SOLUTION_LABELS[SOLUTION_ORDER]) +LABEL_LINETYPES <- setNames(SOLUTION_LINETYPES[SOLUTION_ORDER], SOLUTION_LABELS[SOLUTION_ORDER]) + +COL_WIDTH <- 3.33 +TEXT_WIDTH <- 7.0 + +# ACM page-fraction presets, in inches. +HALF_WIDTH <- 3.3 # two figures side-by-side under one \begin{figure} +THIRD_WIDTH <- 2.2 # three figures side-by-side + +label_pct <- function() percent_format(accuracy = 1) +label_us <- function() "µs" +pct_sign <- function() "%" + +fig_parser <- function(default_width = DEFAULT_WIDTH, default_height = DEFAULT_HEIGHT, + description = "Generate figure") { + p <- ArgumentParser(description = description) + p$add_argument("--data", required = TRUE, help = "derived CSV directory") + p$add_argument("--pdf", help = "write PDF to this path") + p$add_argument("--tikz", help = "write tikz .tex to this path") + p$add_argument("--width", type = "double", default = default_width) + p$add_argument("--height", type = "double", default = default_height) + p$add_argument("--zoom", action = "store_true", help = "use zoomed axis limits") + p$add_argument("--debug-margins", action = "store_true", + help = "color plot.background / panel.background / panel.border to visualise layout") + p +} + +# Optional theme overlay that colors the plot canvas, plot panel, and panel +# border so layout / whitespace can be inspected. Returns NULL when off +# (adding NULL to a ggplot is a no-op). +theme_debug_margins <- function(args) { + if (!isTRUE(args$debug_margins)) return(NULL) + theme( + plot.background = element_rect(fill = "#FFF7B3", colour = "black"), + panel.background = element_rect(fill = "#CCE5FF", colour = NA), + panel.border = element_rect(colour = "red", fill = NA, linewidth = 0.6) + ) +} + +save_figure <- function(plot, args) { + if (is.null(args$pdf) && is.null(args$tikz)) { + stop("save_figure: pass --pdf and/or --tikz") + } + if (!is.null(args$pdf)) { + dir.create(dirname(args$pdf), showWarnings = FALSE, recursive = TRUE) + ggsave(args$pdf, plot, width = args$width, height = args$height, device = "pdf") + message("wrote ", args$pdf) + } + if (!is.null(args$tikz)) { + dir.create(dirname(args$tikz), showWarnings = FALSE, recursive = TRUE) + old <- options( + tikzSanitizeCharacters = c(getOption("tikzSanitizeCharacters"), "µ"), + tikzReplacementCharacters = c(getOption("tikzReplacementCharacters"), "$\\mu$") + ) + on.exit(options(old), add = TRUE) + tikz(args$tikz, width = args$width, height = args$height, + standAlone = FALSE, sanitize = TRUE) + print(plot) + dev.off() + message("wrote ", args$tikz) + } +} diff --git a/figures/fig_idt_cdf.R b/figures/fig_idt_cdf.R new file mode 100644 index 0000000..a154fee --- /dev/null +++ b/figures/fig_idt_cdf.R @@ -0,0 +1,43 @@ +#!/usr/bin/env Rscript +source("common.R") + +# Random sample size per solution. stat_ecdf emits one tikz path segment per +# unique x value; the raw idts.csv has ~120 K unique values per solution, +# producing a ~500 K-line tikz file that exceeds pdflatex main_memory. +# 5000 samples per solution preserve the CDF shape (including the 92.5-100 % +# zoom tail: ~375 points) and keep the tikz file manageable. +SAMPLE_PER_SOLUTION <- 20000 + +parser <- fig_parser(description = "Per-flow inter-departure-time CDF") +parser$add_argument("--sample", type = "integer", default = SAMPLE_PER_SOLUTION, + help = "downsample to N points per solution (0 = no downsampling)") +parser$add_argument("--seed", type = "integer", default = 1, + help = "RNG seed for downsampling") +args <- parser$parse_args() + +set.seed(args$seed) +idts <- read_csv(file.path(args$data, "idts.csv"), show_col_types = FALSE) %>% + prepare_solution() +if (args$sample > 0) { + idts <- idts %>% + group_by(solution) %>% + slice_sample(n = args$sample) %>% + ungroup() +} + +p <- ggplot(idts, aes(x = idt_us, colour = solution, linetype = solution)) + + stat_ecdf(linewidth = 0.9, pad = FALSE, key_glyph = "rect") + + scale_x_log10(labels = label_comma()) + + scale_y_continuous(labels = label_pct()) + + scale_colour_manual(values = LABEL_COLORS) + + scale_linetype_manual(values = LABEL_LINETYPES) + + labs(x = paste0("Inter-departure time within flow (", label_us(), ")"), y = "CDF") + + theme_paper() + + theme(legend.text = element_text(size = rel(0.8)), + legend.key.size = unit(6, "pt")) + +if (args$zoom) { + p <- p + coord_cartesian(xlim = c(10, 1000), ylim = c(0.925, 1.0)) +} + +save_figure(p, args) diff --git a/figures/fig_receiver_cpu.R b/figures/fig_receiver_cpu.R new file mode 100644 index 0000000..981487b --- /dev/null +++ b/figures/fig_receiver_cpu.R @@ -0,0 +1,27 @@ +#!/usr/bin/env Rscript +source("common.R") + +parser <- fig_parser(description = "Receiver CPU bar chart") +parser$add_argument("--ystep", type = "double", + help = "y-axis major tick spacing (omit = auto)") +args <- parser$parse_args() + +runs <- read_csv(file.path(args$data, "runs.csv"), show_col_types = FALSE) %>% + prepare_solution() %>% + group_by(solution) %>% + summarise(mean_pct = mean(cpu_receiver), + sd_pct = sd(cpu_receiver), .groups = "drop") + +p <- ggplot(runs, aes(x = solution, y = mean_pct, fill = solution)) + + geom_col(width = 0.6, colour = "black") + + geom_errorbar(aes(ymin = mean_pct - sd_pct, ymax = mean_pct + sd_pct), + width = 0.2) + + scale_fill_manual(values = LABEL_COLORS, guide = "none") + + labs(x = NULL, y = paste0("Average CPU usage (", pct_sign(), ")")) + + theme_paper() + +if (!is.null(args$ystep)) { + p <- p + scale_y_continuous(breaks = scales::breaks_width(args$ystep)) +} + +save_figure(p, args) diff --git a/figures/fig_rtt.R b/figures/fig_rtt.R new file mode 100644 index 0000000..8cd4e85 --- /dev/null +++ b/figures/fig_rtt.R @@ -0,0 +1,41 @@ +#!/usr/bin/env Rscript +source("common.R") + +parser <- fig_parser(description = "RTT box plot") +parser$add_argument("--ymin", type = "double", default = 4) +parser$add_argument("--ymax", type = "double", default = 14) +parser$add_argument("--ystep", type = "double", default = 2) +args <- parser$parse_args() + +stats <- read_csv(file.path(args$data, "rtts.csv"), show_col_types = FALSE) %>% + mutate(rtt_ms = rtt_us / 1000) %>% + prepare_solution() %>% + group_by(solution) %>% + summarise( + ymin = quantile(rtt_ms, 0.05), + lower = quantile(rtt_ms, 0.25), + middle = median(rtt_ms), + upper = quantile(rtt_ms, 0.75), + ymax = quantile(rtt_ms, 0.95), + .groups = "drop" + ) + +p <- ggplot(stats, aes(x = solution, fill = solution)) + + geom_boxplot(aes(ymin = ymin, lower = lower, middle = middle, + upper = upper, ymax = ymax), + stat = "identity", width = 0.6, colour = "black") + + scale_fill_manual(values = LABEL_COLORS, guide = "none") + + labs(x = NULL, y = "RTT (ms)") + + theme_paper() + + theme(axis.text.x = element_text(angle = 45, hjust = 1), + plot.margin = margin(2, 4, 0, 2)) + + theme_debug_margins(args) + +if (args$zoom) { + p <- p + coord_cartesian(ylim = c(args$ymin, args$ymax)) + + scale_y_continuous(breaks = seq(args$ymin, args$ymax, args$ystep)) +} else { + p <- p + coord_cartesian(ylim = c(0, NA)) +} + +save_figure(p, args) diff --git a/figures/fig_sender_cpu.R b/figures/fig_sender_cpu.R new file mode 100644 index 0000000..d1b5a97 --- /dev/null +++ b/figures/fig_sender_cpu.R @@ -0,0 +1,27 @@ +#!/usr/bin/env Rscript +source("common.R") + +parser <- fig_parser(description = "Sender CPU bar chart") +parser$add_argument("--ystep", type = "double", + help = "y-axis major tick spacing (omit = auto)") +args <- parser$parse_args() + +runs <- read_csv(file.path(args$data, "runs.csv"), show_col_types = FALSE) %>% + prepare_solution() %>% + group_by(solution) %>% + summarise(mean_pct = mean(cpu_sender), + sd_pct = sd(cpu_sender), .groups = "drop") + +p <- ggplot(runs, aes(x = solution, y = mean_pct, fill = solution)) + + geom_col(width = 0.6, colour = "black") + + geom_errorbar(aes(ymin = mean_pct - sd_pct, ymax = mean_pct + sd_pct), + width = 0.2) + + scale_fill_manual(values = LABEL_COLORS, guide = "none") + + labs(x = NULL, y = paste0("Average CPU usage (", pct_sign(), ")")) + + theme_paper() + +if (!is.null(args$ystep)) { + p <- p + scale_y_continuous(breaks = scales::breaks_width(args$ystep)) +} + +save_figure(p, args) diff --git a/figures/fig_throughput.R b/figures/fig_throughput.R new file mode 100644 index 0000000..363dc7c --- /dev/null +++ b/figures/fig_throughput.R @@ -0,0 +1,35 @@ +#!/usr/bin/env Rscript +source("common.R") + +parser <- fig_parser(description = "Throughput bar chart") +parser$add_argument("--ymin", type = "double") +parser$add_argument("--ymax", type = "double") +parser$add_argument("--ystep", type = "double") +args <- parser$parse_args() + +runs <- read_csv(file.path(args$data, "runs.csv"), show_col_types = FALSE) %>% + prepare_solution() %>% + group_by(solution) %>% + summarise(mean_gbps = mean(throughput_bps) / 1e9, + sd_gbps = sd(throughput_bps) / 1e9, .groups = "drop") + +p <- ggplot(runs, aes(x = solution, y = mean_gbps, fill = solution)) + + geom_col(width = 0.6, colour = "black") + + geom_errorbar(aes(ymin = mean_gbps - sd_gbps, ymax = mean_gbps + sd_gbps), + width = 0.2) + + scale_fill_manual(values = LABEL_COLORS, guide = "none") + + labs(x = NULL, y = "Throughput (Gbps)") + + theme_paper() + + theme(axis.text.x = element_text(angle = 45, hjust = 1), + plot.margin = margin(2, 4, 0, 2)) + + theme_debug_margins(args) + +if (!is.null(args$ymax)) { + ymin <- if (is.null(args$ymin)) 0 else args$ymin + p <- p + coord_cartesian(ylim = c(ymin, args$ymax)) + if (!is.null(args$ystep)) { + p <- p + scale_y_continuous(breaks = seq(ymin, args$ymax, args$ystep)) + } +} + +save_figure(p, args) diff --git a/figures/fig_timeseries.R b/figures/fig_timeseries.R new file mode 100644 index 0000000..4f06e30 --- /dev/null +++ b/figures/fig_timeseries.R @@ -0,0 +1,37 @@ +#!/usr/bin/env Rscript +source("common.R") + +parser <- fig_parser(description = "First-flow packet timeseries") +parser$add_argument("--xmin", type = "double", default = 100.0) +parser$add_argument("--xmax", type = "double", default = 105.0) +args <- parser$parse_args() + +bins <- read_csv(file.path(args$data, "firstflow_bins.csv"), show_col_types = FALSE) %>% + group_by(solution) %>% + mutate(t_ms = t_ms - min(t_ms)) %>% + ungroup() %>% + filter(t_ms >= args$xmin, t_ms <= args$xmax) %>% + prepare_solution() + +pacing_label <- SOLUTION_LABELS[["tso-pacing"]] +back <- bins %>% filter(solution == pacing_label) +front <- bins %>% filter(solution != pacing_label) + +p <- ggplot() + + geom_area(data = back, aes(x = t_ms, y = packets, fill = solution), + alpha = 0.22, show.legend = FALSE) + + geom_line(data = back, aes(x = t_ms, y = packets, colour = solution, + linetype = solution), linewidth = 0.9, key_glyph = "rect") + + geom_line(data = front, aes(x = t_ms, y = packets, colour = solution, + linetype = solution), linewidth = 0.9, key_glyph = "rect") + + scale_colour_manual(values = LABEL_COLORS, breaks = names(LABEL_COLORS)) + + scale_fill_manual(values = LABEL_COLORS, breaks = names(LABEL_COLORS)) + + scale_linetype_manual(values = LABEL_LINETYPES, breaks = names(LABEL_LINETYPES)) + + scale_x_continuous(breaks = seq(args$xmin, args$xmax, 1)) + + scale_y_continuous(breaks = seq(0, 45, 5), limits = c(0, 45)) + + labs(x = "Time elapsed (ms)", y = paste0("Packets per 50 ", label_us(), " bin")) + + theme_paper() + + theme(legend.text = element_text(size = rel(0.8)), + legend.key.size = unit(6, "pt")) + +save_figure(p, args) diff --git a/figures/renv.lock b/figures/renv.lock new file mode 100644 index 0000000..28ca68c --- /dev/null +++ b/figures/renv.lock @@ -0,0 +1,2296 @@ +{ + "R": { + "Version": "4.6.0", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-26", + "Source": "Repository", + "Priority": "recommended", + "Date": "2024-12-10", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"Brian.Ripley@R-project.org\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", + "stats" + ], + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-65", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-02-19", + "Revision": "$Rev: 3681 $", + "Depends": [ + "R (>= 4.4.0)", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.7-5", + "Source": "Repository", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2026-03-20", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = c(ROR = \"02zz1nj61\", \"base R's matrix implementation\")))", + "Depends": [ + "R (>= 4.4)", + "methods" + ], + "Imports": [ + "grDevices", + "graphics", + "grid", + "lattice", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut, cre] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Timothy A. Davis [ctb] (ORCID: , SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (ORCID: , METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (ORCID: , GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (ROR: , base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" + }, + "R6": { + "Package": "R6", + "Version": "2.6.1", + "Source": "Repository", + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.", + "License": "MIT + file LICENSE", + "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6", + "BugReports": "https://github.com/r-lib/R6/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Suggests": [ + "lobstr", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate, ggplot2, microbenchmark, scales", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Date": "2022-04-03", + "Title": "ColorBrewer Palettes", + "Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))", + "Author": "Erich Neuwirth [aut, cre]", + "Maintainer": "Erich Neuwirth ", + "Depends": [ + "R (>= 2.0.0)" + ], + "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", + "License": "Apache License 2.0", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "S7": { + "Package": "S7", + "Version": "0.2.2", + "Source": "Repository", + "Title": "An Object Oriented System Meant to Become a Successor to S3 and S4", + "Authors@R": "c( person(\"Object-Oriented Programming Working Group\", role = \"cph\"), person(\"Davis\", \"Vaughan\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"Will\", \"Landau\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Luke\", \"Tierney\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")) )", + "Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.", + "License": "MIT + file LICENSE", + "URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7", + "BugReports": "https://github.com/RConsortium/S7/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "bench", + "callr", + "covr", + "knitr", + "methods", + "rmarkdown", + "testthat (>= 3.2.0)", + "tibble" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "sloop", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Config/testthat/start-first": "external-generic", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (ORCID: ), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (ORCID: ), Luke Tierney [aut], Hadley Wickham [aut, cre] (ORCID: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "argparse": { + "Package": "argparse", + "Version": "2.3.1", + "Source": "Repository", + "Type": "Package", + "Title": "Command Line Optional and Positional Argument Parser", + "Authors@R": "c(person(\"Trevor L.\", \"Davis\", role=c(\"aut\", \"cre\"), email=\"trevor.l.davis@gmail.com\", comment = c(ORCID = \"0000-0001-6341-4639\")), person(\"Allen\", \"Day\", role=\"ctb\", comment=\"Some documentation and examples ported from the getopt package.\"), person(\"Python Software Foundation\", role=\"ctb\", comment=\"Some documentation from the argparse Python module.\"), person(\"Paul\", \"Newell\", role=\"ctb\"))", + "Description": "A command line parser to be used with 'Rscript' to write \"#!\" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage.", + "License": "GPL (>= 2)", + "Copyright": "See file (inst/)COPYRIGHTS.", + "URL": "https://github.com/trevorld/r-argparse, https://trevorldavis.com/R/argparse/", + "BugReports": "https://github.com/trevorld/r-argparse/issues", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "findpython", + "jsonlite", + "R6" + ], + "SystemRequirements": "python (>= 3.2)", + "Suggests": [ + "knitr (>= 1.15.19)", + "rmarkdown", + "testthat" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Trevor L. Davis [aut, cre] (ORCID: ), Allen Day [ctb] (Some documentation and examples ported from the getopt package.), Python Software Foundation [ctb] (Some documentation from the argparse Python module.), Paul Newell [ctb]", + "Maintainer": "Trevor L. Davis ", + "Repository": "CRAN" + }, + "bit": { + "Package": "bit", + "Version": "4.6.0", + "Source": "Repository", + "Title": "Classes and Methods for Fast Memory-Efficient Boolean Selections", + "Authors@R": "c( person(\"Michael\", \"Chirico\", email = \"MichaelChirico4@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jens\", \"Oehlschlägel\", role = \"aut\"), person(\"Brian\", \"Ripley\", role = \"ctb\") )", + "Depends": [ + "R (>= 3.4.0)" + ], + "Suggests": [ + "testthat (>= 3.0.0)", + "roxygen2", + "knitr", + "markdown", + "rmarkdown", + "microbenchmark", + "bit64 (>= 4.0.0)", + "ff (>= 4.0.0)" + ], + "Description": "Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).", + "License": "GPL-2 | GPL-3", + "LazyLoad": "yes", + "ByteCompile": "yes", + "Encoding": "UTF-8", + "URL": "https://github.com/r-lib/bit", + "VignetteBuilder": "knitr, rmarkdown", + "RoxygenNote": "7.3.2", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Michael Chirico [aut, cre], Jens Oehlschlägel [aut], Brian Ripley [ctb]", + "Maintainer": "Michael Chirico ", + "Repository": "CRAN" + }, + "bit64": { + "Package": "bit64", + "Version": "4.8.0", + "Source": "Repository", + "Title": "A S3 Class for Vectors of 64bit Integers", + "Authors@R": "c( person(\"Michael\", \"Chirico\", email=\"michaelchirico4@gmail.com\", role=c(\"aut\", \"cre\")), person(\"Jens\", \"Oehlschlägel\", role=\"aut\"), person(\"Leonardo\", \"Silvestri\", role=\"ctb\"), person(\"Ofek\", \"Shilon\", role=\"ctb\"), person(\"Christian\", \"Ullerich\", role=\"ctb\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Description": "Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.", + "License": "GPL-2 | GPL-3", + "LazyLoad": "yes", + "ByteCompile": "yes", + "URL": "https://github.com/r-lib/bit64, https://bit64.r-lib.org", + "Encoding": "UTF-8", + "Imports": [ + "bit (>= 4.0.0)", + "graphics", + "methods", + "stats", + "utils" + ], + "Suggests": [ + "patrick (>= 0.3.0)", + "testthat (>= 3.3.0)", + "withr" + ], + "Config/testthat/edition": "3", + "Config/Needs/development": "patrick, testthat", + "Config/Needs/website": "tidyverse/tidytemplate", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Michael Chirico [aut, cre], Jens Oehlschlägel [aut], Leonardo Silvestri [ctb], Ofek Shilon [ctb], Christian Ullerich [ctb]", + "Maintainer": "Michael Chirico ", + "Repository": "CRAN" + }, + "boot": { + "Package": "boot", + "Version": "1.3-32", + "Source": "Repository", + "Priority": "recommended", + "Date": "2025-08-29", + "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"Brian.Ripley@R-project.org\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", + "Maintainer": "Alessandra R. Brazzale ", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", + "Title": "Bootstrap Functions", + "Depends": [ + "R (>= 3.0.0)", + "graphics", + "stats" + ], + "Suggests": [ + "MASS", + "survival" + ], + "LazyData": "yes", + "ByteCompile": "yes", + "License": "Unlimited", + "NeedsCompilation": "no", + "Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. 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It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat (>= 3.2.0)", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository", + "Type": "Package", + "Title": "Read and Write from the System Clipboard", + "Authors@R": "c( person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4387-3384\")), person(\"Louis\", \"Maddox\", role = \"ctb\"), person(\"Steve\", \"Simpson\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\") )", + "Description": "Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.", + "License": "GPL-3", + "URL": "https://github.com/mdlincoln/clipr, http://matthewlincoln.net/clipr/", + "BugReports": "https://github.com/mdlincoln/clipr/issues", + "Imports": [ + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "rstudioapi (>= 0.5)", + "testthat (>= 2.0.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.1.2", + "SystemRequirements": "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", + "NeedsCompilation": "no", + "Author": "Matthew Lincoln [aut, cre] (), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", + "Maintainer": "Matthew Lincoln ", + "Repository": "CRAN" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.8.2", + "Source": "Repository", + "VersionNote": "Last CRAN: 2.1.8.1 on 2025-03-11; 2.1.8 on 2024-12-10; 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30;", + "Date": "2026-02-03", + "Priority": "recommended", + "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", + "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (ORCID: ), Peter Rousseeuw [aut] (Fortran original, ORCID: ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ORCID: ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ORCID: ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ORCID: ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" + ], + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.5", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (ORCID: ), Jim Hester [aut] (ORCID: ), Romain François [aut] (ORCID: ), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "digest": { + "Package": "digest", + "Version": "0.6.39", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\", comment = c(ORCID = \"0000-0002-8059-9767\")), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8552-0029\")), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0492-6647\")), person(\"Ion\", \"Suruceanu\", role=\"ctb\", comment = c(ORCID = \"0009-0005-6446-4909\")), person(\"Bill\", \"Denney\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\", comment = c(ORCID = \"0009-0008-8480-1329\")), person(\"Sergey\", \"Fedorov\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5970-7233\")), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\", comment = c(ORCID = \"0009-0000-5948-4503\")), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Carl\", \"Pearson\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0701-7860\")))", + "Date": "2025-11-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://eddelbuettel.github.io/digest/, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown", + "rbenchmark" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Antoine Lucas [ctb] (ORCID: ), Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (ORCID: ), Simon Urbanek [ctb] (ORCID: ), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb] (ORCID: ), Duncan Murdoch [ctb], Jim Hester [ctb] (ORCID: ), Wush Wu [ctb] (ORCID: ), Qiang Kou [ctb] (ORCID: ), Thierry Onkelinx [ctb] (ORCID: ), Michel Lang [ctb] (ORCID: ), Viliam Simko [ctb], Kurt Hornik [ctb] (ORCID: ), Radford Neal [ctb] (ORCID: ), Kendon Bell [ctb] (ORCID: ), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb] (ORCID: ), Ion Suruceanu [ctb] (ORCID: ), Bill Denney [ctb] (ORCID: ), Dirk Schumacher [ctb], András Svraka [ctb] (ORCID: ), Sergey Fedorov [ctb] (ORCID: ), Will Landau [ctb] (ORCID: ), Floris Vanderhaeghe [ctb] (ORCID: ), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (ORCID: ), Mark van der Loo [ctb] (ORCID: ), Chris Muir [ctb] (ORCID: ), Moritz Beller [ctb] (ORCID: ), Sebastian Campbell [ctb] (ORCID: ), Winston Chang [ctb] (ORCID: ), Dean Attali [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Kevin Ushey [ctb] (ORCID: ), Carl Pearson [ctb] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "A Grammar of Data Manipulation", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Kirill\", \"Müller\", role = \"aut\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A fast, consistent tool for working with data frame like objects, both in memory and out of memory.", + "License": "MIT + file LICENSE", + "URL": "https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr", + "BugReports": "https://github.com/tidyverse/dplyr/issues", + "Depends": [ + "R (>= 4.1.0)" + ], + "Imports": [ + "cli (>= 3.6.2)", + "generics", + "glue (>= 1.3.2)", + "lifecycle (>= 1.0.5)", + "magrittr (>= 1.5)", + "methods", + "pillar (>= 1.9.0)", + "R6", + "rlang (>= 1.1.7)", + "tibble (>= 3.2.0)", + "tidyselect (>= 1.2.0)", + "utils", + "vctrs (>= 0.7.1)" + ], + "Suggests": [ + "broom", + "covr", + "DBI", + "dbplyr (>= 2.2.1)", + "ggplot2", + "knitr", + "Lahman", + "lobstr", + "nycflights13", + "purrr", + "rmarkdown", + "RSQLite", + "stringi (>= 1.7.6)", + "testthat (>= 3.1.5)", + "tidyr (>= 1.3.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (ORCID: ), Romain François [aut] (ORCID: ), Lionel Henry [aut], Kirill Müller [aut] (ORCID: ), Davis Vaughan [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "farver": { + "Package": "farver", + "Version": "2.1.2", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance Colour Space Manipulation", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "filehash": { + "Package": "filehash", + "Version": "2.4-6", + "Source": "Repository", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "digest", + "methods" + ], + "Collate": "filehash.R filehash-DB1.R filehash-RDS.R coerce.R dump.R hash.R queue.R stack.R zzz.R", + "Title": "Simple Key-Value Database", + "Author": "Roger D. Peng ", + "Maintainer": "Roger D. Peng ", + "Description": "Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.", + "License": "GPL (>= 2)", + "URL": "https://github.com/rdpeng/filehash", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "findpython": { + "Package": "findpython", + "Version": "1.0.9", + "Source": "Repository", + "Type": "Package", + "Title": "Functions to Find an Acceptable Python Binary", + "Authors@R": "c(person(\"Trevor L.\", \"Davis\", role=c(\"aut\", \"cre\"), email=\"trevor.l.davis@gmail.com\", comment = c(ORCID = \"0000-0001-6341-4639\")), person(\"Paul\", \"Gilbert\", role=\"aut\"))", + "URL": "https://github.com/trevorld/findpython, https://trevorldavis.com/R/findpython/", + "BugReports": "https://github.com/trevorld/findpython/issues", + "Description": "Package designed to find an acceptable python binary.", + "Suggests": [ + "reticulate", + "testthat" + ], + "License": "MIT + file LICENSE", + "Collate": "'find_python_cmd.r'", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Trevor L. 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Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]", + "Maintainer": "R Core Team ", + "Repository": "CRAN" + }, + "generics": { + "Package": "generics", + "Version": "0.1.4", + "Source": "Repository", + "Title": "Common S3 Generics not Provided by Base R Methods Related to Model Fitting", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"https://ror.org/03wc8by49\")) )", + "Description": "In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics.", + "License": "MIT + file LICENSE", + "URL": "https://generics.r-lib.org, https://github.com/r-lib/generics", + "BugReports": "https://github.com/r-lib/generics/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "covr", + "pkgload", + "testthat (>= 3.0.0)", + "tibble", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre] (ORCID: ), Max Kuhn [aut], Davis Vaughan [aut], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "4.0.3", + "Source": "Repository", + "Title": "Create Elegant Data Visualisations Using the Grammar of Graphics", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "A system for 'declaratively' creating graphics, based on \"The Grammar of Graphics\". 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The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.7.1", + "Source": "Repository", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.tidyverse.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "bit64", + "cli (>= 3.2.0)", + "crayon", + "glue", + "hms", + "lifecycle (>= 1.0.3)", + "methods", + "rlang (>= 1.1.0)", + "stats", + "tibble (>= 2.0.0)", + "tidyselect", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", + "withr" + ], + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.3)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Config/usethis/last-upkeep": "2025-11-25", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.3", + "Config/build/compilation-database": "true", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (ORCID: ), Hadley Wickham [aut] (ORCID: ), Jennifer Bryan [aut, cre] (ORCID: ), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "withr": { + "Package": "withr", + "Version": "3.0.2", + "Source": "Repository", + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + } + } +} diff --git a/figures/renv/.gitignore b/figures/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/figures/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/figures/renv/activate.R b/figures/renv/activate.R new file mode 100644 index 0000000..20ffd44 --- /dev/null +++ b/figures/renv/activate.R @@ -0,0 +1,1438 @@ + +local({ + + # the requested version of renv + version <- "1.2.3" + attr(version, "md5") <- "1bd9f58e1cfe27ce035933937c6f03de" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + # also check for config environment variables that should suppress messages + # https://github.com/rstudio/renv/issues/2214 + enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("true", "1")) + return(invisible()) + + enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("false", "0")) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # ensure the target library path exists; required for file.copy(..., recursive = TRUE) + dir.create(library, showWarnings = FALSE, recursive = TRUE) + + # try to install renv from cache + md5 <- attr(version, "md5", exact = TRUE) + if (length(md5)) { + pkgpath <- renv_bootstrap_find(version) + if (length(pkgpath) && file.exists(pkgpath)) { + ok <- file.copy(pkgpath, library, recursive = TRUE) + if (isTRUE(ok)) + return(invisible()) + } + } + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # split on ';' if present + parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] + + # split into named repositories if present + idx <- regexpr("=", parts, fixed = TRUE) + keys <- substring(parts, 1L, idx - 1L) + vals <- substring(parts, idx + 1L) + names(vals) <- keys + + # if we have a single unnamed repository, call it CRAN + if (length(vals) == 1L && identical(keys, "")) + names(vals) <- "CRAN" + + return(vals) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_find <- function(version) { + + path <- renv_bootstrap_find_cache(version) + if (length(path) && file.exists(path)) { + catf("- Using renv %s from global package cache", version) + return(path) + } + + } + + renv_bootstrap_find_cache <- function(version) { + + md5 <- attr(version, "md5", exact = TRUE) + if (is.null(md5)) + return() + + # infer path to renv cache + cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") + if (!nzchar(cache)) { + root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA) + if (!is.na(root)) + cache <- file.path(root, "cache") + } + + if (!nzchar(cache)) { + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) { + root <- tools$R_user_dir("renv", "cache") + cache <- file.path(root, "cache") + } + } + + # start completing path to cache + file.path( + cache, + renv_bootstrap_cache_version(), + renv_bootstrap_platform_prefix(), + "renv", + version, + md5, + "renv" + ) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix_default <- function() { + + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() + + # build list of path components + components <- c(version, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + + expected <- description[["RemoteSha"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(c(expected), c(version)) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + tryCatch( + renv_bootstrap_run_impl(project, libpath, version), + error = function(e) { + msg <- paste( + "failed to bootstrap renv: the project will not be loaded.", + paste("Reason:", conditionMessage(e)), + "Use `renv::activate()` to re-initialize the project.", + sep = "\n" + ) + warning(msg, call. = FALSE) + } + ) + } + + renv_bootstrap_run_impl <- function(project, libpath, version) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = project)) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_bootstrap_cache_version <- function() { + # NOTE: users should normally not override the cache version; + # this is provided just to make testing easier + Sys.getenv("RENV_CACHE_VERSION", unset = "v5") + } + + renv_bootstrap_cache_version_previous <- function() { + version <- renv_bootstrap_cache_version() + number <- as.integer(substring(version, 2L)) + paste("v", number - 1L, sep = "") + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/figures/renv/settings.json b/figures/renv/settings.json new file mode 100644 index 0000000..46f2f31 --- /dev/null +++ b/figures/renv/settings.json @@ -0,0 +1,21 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "lockfile.sanitize": true, + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.dev": false, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/local.mk.example b/local.mk.example new file mode 100644 index 0000000..68f1bc5 --- /dev/null +++ b/local.mk.example @@ -0,0 +1,5 @@ +# Copy to local.mk and edit. Use ?= so a shell env var still overrides. +# Read from both eval/Makefile and eval/figures/Makefile; absolute paths +# avoid resolution ambiguity between the two cwds. + +RAW_DATA_ROOT ?= /absolute/path/to/raw_data