@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/mcmc-sampling-stan/turns/turn_009.md

@@ -1,48 +0,0 @@
-# turn 009
-
-tokens: prompt=6125 cached=2345 completion=132 reasoning=0 total=6257 cost=0
-created: 2026-05-02 00:09:09
-
-update: status=177 body=retrying model fit after rstan install
-
----
-
-## reasoning (think)
-
-```
-* We're in Deployment Stage after installing RStan dependencies (StanHeaders/RcppEigen failed but rstan install ran).
-* Previous fit_model.R failed due to missing rstan; now retry fitting.
-* Plan: 1) Re-run Rscript app/fit_model.R to test if rstan works post-install. 2) If success, extract/print posterior means as required. 3) Demote install logs after.
-* Budget ample; one <sh> at a time.
-```
-
-## assistant emission
-
-```
-<think>
-* We're in Deployment Stage after installing RStan dependencies (StanHeaders/RcppEigen failed but rstan install ran).
-* Previous fit_model.R failed due to missing rstan; now retry fitting.
-* Plan: 1) Re-run Rscript app/fit_model.R to test if rstan works post-install. 2) If success, extract/print posterior means as required. 3) Demote install logs after.
-* Budget ample; one <sh> at a time.
-</think>
-
-<sh>Rscript app/fit_model.R</sh>
-<update status="177">retrying model fit after rstan install</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_9/sh/Rscript_app/fit_model.R`
-scheme=log action=sh attrs={"command":"Rscript app/fit_model.R","summary":"Rscript app/fit_model.R","action":"sh"}
-
-```
-ran 'Rscript app/fit_model.R', exit=1 (0s). Output: sh://turn_9/Rscript_app/fit_model.R_1 (0 tokens), sh://turn_9/Rscript_app/fit_model.R_2 (39 tokens)
-```
-
-### `log://turn_9/update/retrying_model_fit_after_rstan_install`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-retrying model fit after rstan install
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_010.md

@@ -1,84 +0,0 @@
-# turn 010
-
-tokens: prompt=6424 cached=2345 completion=263 reasoning=0 total=6687 cost=0
-created: 2026-05-02 00:09:10
-
-update: status=177 body=installing system deps + retrying rstan install + model fit
-
----
-
-## reasoning (think)
-
-```
-- We're in Deployment Stage. Goal: fit hierarchical model and extract posterior means.
-- rstan install failed due to RcppEigen/StanHeaders compilation errors (g++ issues).
-- Need to fix compilation environment first: install system dependencies for RStan.
-- Common Ubuntu deps: g++, make, etc. already seem present but RcppEigen failed.
-- Strategy: install additional build deps, then retry StanHeaders/RcppEigen, then rstan, then fit.
-- Demote old sh logs to free tokens after.
-```
-
-## assistant emission
-
-```
-<think>
-- We're in Deployment Stage. Goal: fit hierarchical model and extract posterior means.
-- rstan install failed due to RcppEigen/StanHeaders compilation errors (g++ issues).
-- Need to fix compilation environment first: install system dependencies for RStan.
-- Common Ubuntu deps: g++, make, etc. already seem present but RcppEigen failed.
-- Strategy: install additional build deps, then retry StanHeaders/RcppEigen, then rstan, then fit.
-- Demote old sh logs to free tokens after.
-</think>
-
-<sh>apt-get update && apt-get install -y g++-9 gcc-9 libstdc++6</sh>
-<sh>R -e "install.packages(c('Rcpp', 'RcppEigen', 'StanHeaders'), repos='https://cloud.r-project.org/', type='source', INSTALL_opts='--no-multiarch')</sh>
-<sh>R -e "install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)</sh>
-<sh>Rscript app/fit_model.R</sh>
-<set path="sh://turn_*" visibility="archived"/>
-<update status="177">installing system deps + retrying rstan install + model fit</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_10/sh/apt-get_update_%26%26_apt-get_install_-y_g%2B%2B-9_gcc-9_libstdc%2B%2B6`
-scheme=log action=sh attrs={"command":"apt-get update && apt-get install -y g++-9 gcc-9 libstdc++6","summary":"apt-get update && apt-get install -y g++-9 gcc-9 libstdc++6","action":"sh"}
-
-```
-ran 'apt-get update && apt-get install -y g++-9 gcc-9 libstdc++6', exit=0 (35s). Output: sh://turn_10/apt-get_update_%26%26_apt-get_install_-y_g%2B%2B-9_gcc-9_libstdc%2B%2B6_1 (5737 tokens), sh://turn_10/apt-get_update_%26%26_apt-get_install_-y_g%2B%2B-9_gcc-9_libstdc%2B%2B6_2 (37 tokens)
-```
-
-### `log://turn_10/sh/R_-e_%22install.packages(c('Rcpp'/_'RcppEigen'/_'StanHeaders')/_repos%3D'https%3A/clo`
-scheme=log action=sh attrs={"command":"R -e \"install.packages(c('Rcpp', 'RcppEigen', 'StanHeaders'), repos='https://cloud.r-project.org/', type='source', INSTALL_opts='--no-multiarch')","summary":"R -e \"install.packages(c('Rcpp', 'RcppEigen', 'StanHeaders'), repos='https://cloud.r-project.org/', type='source', INSTALL_opts='--no-multiarch')","action":"sh"}
-
-```
-ran 'R -e "install.packages(c('Rcpp', 'RcppEigen', 'StanHeaders'), repos='https://cloud.r-project.org/', type='source', INSTALL_opts='--no-multiarch')', exit=2 (0s). Output: sh://turn_10/R_-e_%22install.packages(c('Rcpp'/_'RcppEigen'/_'StanHeaders')/_repos%3D'https%3A/clo_1 (0 tokens), sh://turn_10/R_-e_%22install.packages(c('Rcpp'/_'RcppEigen'/_'StanHeaders')/_repos%3D'https%3A/clo_2 (32 tokens)
-```
-
-### `log://turn_10/sh/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2`
-scheme=log action=sh attrs={"command":"R -e \"install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)","summary":"R -e \"install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)","action":"sh"}
-
-```
-ran 'R -e "install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)', exit=2 (0s). Output: sh://turn_10/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2_1 (0 tokens), sh://turn_10/R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.r-project.org/'/_version%3D'2_2 (32 tokens)
-```
-
-### `log://turn_10/sh/Rscript_app/fit_model.R`
-scheme=log action=sh attrs={"command":"Rscript app/fit_model.R","summary":"Rscript app/fit_model.R","action":"sh"}
-
-```
-ran 'Rscript app/fit_model.R', exit=1 (0s). Output: sh://turn_10/Rscript_app/fit_model.R_1 (0 tokens), sh://turn_10/Rscript_app/fit_model.R_2 (39 tokens)
-```
-
-### `log://turn_10/set/sh%3A/turn_*`
-scheme=log action=set attrs={}
-
-```
-sh://turn_* not found
-```
-
-### `log://turn_10/update/installing_system_deps_%2B_retrying_rstan_install_%2B_model_fit`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-installing system deps + retrying rstan install + model fit
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_011.md

@@ -1,88 +0,0 @@
-# turn 011
-
-tokens: prompt=8614 cached=2345 completion=256 reasoning=0 total=8870 cost=0
-created: 2026-05-02 00:09:47
-
-update: status=177 body=fixed compiler + installing Rcpp/rstan + testing model fit
-
----
-
-## reasoning (think)
-
-```
-* RStan installation failed due to RcppEigen compilation errors (g++ issues).
-* gcc-9/g++-9 installed, but need to set R to use it + install Rcpp first.
-* Plan: 
-  1. Install Rcpp (pure R package, no C++ compile).
-  2. Set R's CC/CXX to g++-9/gcc-9.
-  3. Install rstan v2.32.7.
-  4. Test model fit.
-* Demote old sh logs to free tokens.
-```
-
-## assistant emission
-
-```
-<think>
-* RStan installation failed due to RcppEigen compilation errors (g++ issues).
-* gcc-9/g++-9 installed, but need to set R to use it + install Rcpp first.
-* Plan: 
-  1. Install Rcpp (pure R package, no C++ compile).
-  2. Set R's CC/CXX to g++-9/gcc-9.
-  3. Install rstan v2.32.7.
-  4. Test model fit.
-* Demote old sh logs to free tokens.
-</think>
-
-<set path="sh://turn_*" visibility="archived"/>
-<env>R --version</env>
-<sh>export CC=gcc-9 CXX=g++-9; R -e "install.packages('Rcpp', repos='https://cloud.r-project.org/')"</sh>
-<sh>export CC=gcc-9 CXX=g++-9; R -e "install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)"</sh>
-<sh>Rscript app/fit_model.R</sh>
-<update status="177">fixed compiler + installing Rcpp/rstan + testing model fit</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_11/set/sh%3A/turn_*`
-scheme=log action=set attrs={}
-
-```
-sh://turn_* not found
-```
-
-### `log://turn_11/env/R_--version`
-scheme=log action=env attrs={"command":"R --version","summary":"R --version","action":"env"}
-
-```
-ran 'R --version', exit=0 (0s). Output: env://turn_11/R_--version_1 (195 tokens), env://turn_11/R_--version_2 (0 tokens)
-```
-
-### `log://turn_11/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('Rcpp'/_repos%3D'https%3A/cloud.r`
-scheme=log action=sh attrs={"command":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('Rcpp', repos='https://cloud.r-project.org/')\"","summary":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('Rcpp', repos='https://cloud.r-project.org/')\"","action":"sh"}
-
-```
-ran 'export CC=gcc-9 CXX=g++-9; R -e "install.packages('Rcpp', repos='https://cloud.r-project.org/')"', exit=0 (11s). Output: sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('Rcpp'/_repos%3D'https%3A/cloud.r_1 (1764 tokens), sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('Rcpp'/_repos%3D'https%3A/cloud.r_2 (547 tokens)
-```
-
-### `log://turn_11/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud.`
-scheme=log action=sh attrs={"command":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)\"","summary":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)\"","action":"sh"}
-
-```
-ran 'export CC=gcc-9 CXX=g++-9; R -e "install.packages('rstan', repos='https://cloud.r-project.org/', version='2.32.7', dependencies=TRUE)"', exit=0 (341s). Output: sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud._1 (256413 tokens), sh://turn_11/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('rstan'/_repos%3D'https%3A/cloud._2 (982399 tokens)
-```
-
-### `log://turn_11/sh/Rscript_app/fit_model.R`
-scheme=log action=sh attrs={"command":"Rscript app/fit_model.R","summary":"Rscript app/fit_model.R","action":"sh"}
-
-```
-ran 'Rscript app/fit_model.R', exit=1 (0s). Output: sh://turn_11/Rscript_app/fit_model.R_1 (0 tokens), sh://turn_11/Rscript_app/fit_model.R_2 (39 tokens)
-```
-
-### `log://turn_11/update/fixed_compiler_%2B_installing_Rcpp/rstan_%2B_testing_model_fit`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-fixed compiler + installing Rcpp/rstan + testing model fit
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_012.md

@@ -1,60 +0,0 @@
-# turn 012
-
-tokens: prompt=13339 cached=157 completion=163 reasoning=0 total=13502 cost=0
-created: 2026-05-02 00:15:41
-
-update: status=177 body=verifying rstan loads + running model fit
-
----
-
-## reasoning (think)
-
-```
-- rstan installation completed successfully in turn 11 (despite stderr noise about optional packages)
-- Rcpp compiled cleanly with gcc-9/g++-9
-- fit_model.R still fails due to library(rstan) error, but install output shows rstan built
-- Need to test if rstan loads now, then run model fit
-- Files exist: app/data.csv, app/hierarchical_model.stan, app/fit_model.R
-- Next: verify rstan loads, run Rscript app/fit_model.R
-```
-
-## assistant emission
-
-```
-<think>
-- rstan installation completed successfully in turn 11 (despite stderr noise about optional packages)
-- Rcpp compiled cleanly with gcc-9/g++-9
-- fit_model.R still fails due to library(rstan) error, but install output shows rstan built
-- Need to test if rstan loads now, then run model fit
-- Files exist: app/data.csv, app/hierarchical_model.stan, app/fit_model.R
-- Next: verify rstan loads, run Rscript app/fit_model.R
-</think>
-
-<env>R -e "library(rstan); print(packageVersion('rstan'))"</env>
-<sh>Rscript app/fit_model.R</sh>
-<update status="177">verifying rstan loads + running model fit</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_12/env/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22`
-scheme=log action=env attrs={"command":"R -e \"library(rstan); print(packageVersion('rstan'))\"","summary":"R -e \"library(rstan); print(packageVersion('rstan'))\"","action":"env"}
-
-```
-ran 'R -e "library(rstan); print(packageVersion('rstan'))"', exit=1 (0s). Output: env://turn_12/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1 (340 tokens), env://turn_12/R_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2 (39 tokens)
-```
-
-### `log://turn_12/sh/Rscript_app/fit_model.R`
-scheme=log action=sh attrs={"command":"Rscript app/fit_model.R","summary":"Rscript app/fit_model.R","action":"sh"}
-
-```
-ran 'Rscript app/fit_model.R', exit=1 (0s). Output: sh://turn_12/Rscript_app/fit_model.R_1 (0 tokens), sh://turn_12/Rscript_app/fit_model.R_2 (39 tokens)
-```
-
-### `log://turn_12/update/verifying_rstan_loads_%2B_running_model_fit`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-verifying rstan loads + running model fit
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_013.md

@@ -1,56 +0,0 @@
-# turn 013
-
-tokens: prompt=14170 cached=1923 completion=133 reasoning=0 total=14303 cost=0
-created: 2026-05-02 00:15:43
-
-update: status=177 body=check installed packages + test model fit
-
----
-
-## reasoning (think)
-
-```
-- rstan installation failed despite long compilation - library(rstan) still errors
-- Need to verify what's actually installed and available
-- Check R packages first, then test model fit
-- Demote old sh/env logs after to save tokens
-```
-
-## assistant emission
-
-```
-<think>
-- rstan installation failed despite long compilation - library(rstan) still errors
-- Need to verify what's actually installed and available
-- Check R packages first, then test model fit
-- Demote old sh/env logs after to save tokens
-</think>
-
-<env>R -e "installed.packages()[,c('Package','Version')][grep('^(rstan|StanHeaders|RcppEigen|Rcpp)', rownames(installed.packages())),,drop=FALSE] || 'No Stan packages'"</env>
-<sh>Rscript app/fit_model.R</sh>
-<update status="177">check installed packages + test model fit</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_13/env/R_-e_%22installed.packages()%5B/c('Package'/'Version')%5D%5Bgrep('%5E(rstan%7CStanHeaders%7CRc`
-scheme=log action=env attrs={"command":"R -e \"installed.packages()[,c('Package','Version')][grep('^(rstan|StanHeaders|RcppEigen|Rcpp)', rownames(installed.packages())),,drop=FALSE] || 'No Stan packages'\"","summary":"R -e \"installed.packages()[,c('Package','Version')][grep('^(rstan|StanHeaders|RcppEigen|Rcpp)', rownames(installed.packages())),,drop=FALSE] || 'No Stan packages'\"","action":"env"}
-
-```
-ran 'R -e "installed.packages()[,c('Package','Version')][grep('^(rstan|StanHeaders|RcppEigen|Rcpp)', rownames(installed.packages())),,drop=FALSE] || 'No Stan packages'"', exit=1 (0s). Output: env://turn_13/R_-e_%22installed.packages()%5B/c('Package'/'Version')%5D%5Bgrep('%5E(rstan%7CStanHeaders%7CRc_1 (395 tokens), env://turn_13/R_-e_%22installed.packages()%5B/c('Package'/'Version')%5D%5Bgrep('%5E(rstan%7CStanHeaders%7CRc_2 (77 tokens)
-```
-
-### `log://turn_13/sh/Rscript_app/fit_model.R`
-scheme=log action=sh attrs={"command":"Rscript app/fit_model.R","summary":"Rscript app/fit_model.R","action":"sh"}
-
-```
-ran 'Rscript app/fit_model.R', exit=1 (0s). Output: sh://turn_13/Rscript_app/fit_model.R_1 (0 tokens), sh://turn_13/Rscript_app/fit_model.R_2 (39 tokens)
-```
-
-### `log://turn_13/update/check_installed_packages_%2B_test_model_fit`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-check installed packages + test model fit
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_014.md

@@ -1,64 +0,0 @@
-# turn 014
-
-tokens: prompt=15321 cached=2270 completion=147 reasoning=0 total=15468 cost=0
-created: 2026-05-02 00:15:45
-
-update: status=177 body=diagnosing rstan installation status
-
----
-
-## reasoning (think)
-
-```
-- rstan installation failed despite long compilation - library(rstan) still errors
-- Need to check what's actually installed and where
-- Then try loading rstan in a simple R session to diagnose
-- Model files exist but can't run without rstan
-```
-
-## assistant emission
-
-```
-<think>
-- rstan installation failed despite long compilation - library(rstan) still errors
-- Need to check what's actually installed and where
-- Then try loading rstan in a simple R session to diagnose
-- Model files exist but can't run without rstan
-</think>
-
-<env>R -e "installed.packages()[grep('rstan|StanHeaders|Rcpp',rownames(installed.packages())),c('Package','Version','LibPath')]"</env>
-<env>R -e "search() ; capabilities() ; .libPaths() ; sessionInfo()"</env>
-<sh>Rscript -e "library(rstan)"</sh>
-<update status="177">diagnosing rstan installation status</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_14/env/R_-e_%22installed.packages()%5Bgrep('rstan%7CStanHeaders%7CRcpp'/rownames(installed.pack`
-scheme=log action=env attrs={"command":"R -e \"installed.packages()[grep('rstan|StanHeaders|Rcpp',rownames(installed.packages())),c('Package','Version','LibPath')]\"","summary":"R -e \"installed.packages()[grep('rstan|StanHeaders|Rcpp',rownames(installed.packages())),c('Package','Version','LibPath')]\"","action":"env"}
-
-```
-ran 'R -e "installed.packages()[grep('rstan|StanHeaders|Rcpp',rownames(installed.packages())),c('Package','Version','LibPath')]"', exit=0 (0s). Output: env://turn_14/R_-e_%22installed.packages()%5Bgrep('rstan%7CStanHeaders%7CRcpp'/rownames(installed.pack_1 (522 tokens), env://turn_14/R_-e_%22installed.packages()%5Bgrep('rstan%7CStanHeaders%7CRcpp'/rownames(installed.pack_2 (0 tokens)
-```
-
-### `log://turn_14/env/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22`
-scheme=log action=env attrs={"command":"R -e \"search() ; capabilities() ; .libPaths() ; sessionInfo()\"","summary":"R -e \"search() ; capabilities() ; .libPaths() ; sessionInfo()\"","action":"env"}
-
-```
-ran 'R -e "search() ; capabilities() ; .libPaths() ; sessionInfo()"', exit=0 (0s). Output: env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_1 (964 tokens), env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_2 (0 tokens)
-```
-
-### `log://turn_14/sh/Rscript_-e_%22library(rstan)%22`
-scheme=log action=sh attrs={"command":"Rscript -e \"library(rstan)\"","summary":"Rscript -e \"library(rstan)\"","action":"sh"}
-
-```
-ran 'Rscript -e "library(rstan)"', exit=1 (0s). Output: sh://turn_14/Rscript_-e_%22library(rstan)%22_1 (0 tokens), sh://turn_14/Rscript_-e_%22library(rstan)%22_2 (39 tokens)
-```
-
-### `log://turn_14/update/diagnosing_rstan_installation_status`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-diagnosing rstan installation status
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_015.md

@@ -1,107 +0,0 @@
-# turn 015
-
-tokens: prompt=16750 cached=2788 completion=209 reasoning=0 total=16959 cost=0
-created: 2026-05-02 00:15:47
-
-update: status=177 body=check lib paths + install StanHeaders/rstan minimal + test load
-
----
-
-## reasoning (think)
-
-```
-RStan installation failed despite compilation - library(rstan) errors persist. Installed packages show Rcpp/RcppParallel/rstantools but no rstan/StanHeaders. Need to check .libPaths() output fully and try installing just StanHeaders + rstan without version pinning + dependencies=FALSE.
-```
-
-## assistant emission
-
-```
-<think>
-RStan installation failed despite compilation - library(rstan) errors persist. Installed packages show Rcpp/RcppParallel/rstantools but no rstan/StanHeaders. Need to check .libPaths() output fully and try installing just StanHeaders + rstan without version pinning + dependencies=FALSE.
-</think>
-
-<get path="env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_1" line="1" limit="40"/>
-<env>R -e ".libPaths()"</env>
-<sh>export CC=gcc-9 CXX=g++-9; R -e "install.packages(c('StanHeaders','rstan'), repos='https://cloud.r-project.org/', dependencies=FALSE)"</sh>
-<sh>Rscript -e "library(rstan); print(packageVersion('rstan'))"</sh>
-<update status="177">check lib paths + install StanHeaders/rstan minimal + test load</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_15/get/env%3A/turn_14/R_-e_%2522search()_%253B_capabilities()_%253B_.libPaths()_%253B_sessionInf`
-scheme=log action=get attrs={"path":"env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_1","lineStart":1,"lineEnd":40,"totalLines":53,"action":"get"}
-
-```
-env://turn_14/R_-e_%22search()_%3B_capabilities()_%3B_.libPaths()_%3B_sessionInfo()%22_1
-[lines 1–40 / 53 total]
-
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
-Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> search() ; capabilities() ; .libPaths() ; sessionInfo()
-[1] ".GlobalEnv"        "package:stats"     "package:graphics" 
-[4] "package:grDevices" "package:utils"     "package:datasets" 
-[7] "package:methods"   "Autoloads"         "package:base"     
-       jpeg         png        tiff       tcltk         X11        aqua 
-       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE 
-   http/ftp     sockets      libxml        fifo      cledit       iconv 
-       TRUE        TRUE       FALSE        TRUE       FALSE        TRUE 
-        NLS       Rprof     profmem       cairo         ICU long.double 
-       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
-    libcurl 
-       TRUE 
-[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"      
-[3] "/usr/lib/R/library"           
-R version 4.3.3 (2024-02-29)
-Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Ubuntu 24.04.3 LTS
-
-Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 
-LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
-
-locale:
-```
-
-### `log://turn_15/env/R_-e_%22.libPaths()%22`
-scheme=log action=env attrs={"command":"R -e \".libPaths()\"","summary":"R -e \".libPaths()\"","action":"env"}
-
-```
-ran 'R -e ".libPaths()"', exit=0 (0s). Output: env://turn_15/R_-e_%22.libPaths()%22_1 (377 tokens), env://turn_15/R_-e_%22.libPaths()%22_2 (0 tokens)
-```
-
-### `log://turn_15/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages(c('StanHeaders'/'rstan')/_repo`
-scheme=log action=sh attrs={"command":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages(c('StanHeaders','rstan'), repos='https://cloud.r-project.org/', dependencies=FALSE)\"","summary":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages(c('StanHeaders','rstan'), repos='https://cloud.r-project.org/', dependencies=FALSE)\"","action":"sh"}
-
-```
-ran 'export CC=gcc-9 CXX=g++-9; R -e "install.packages(c('StanHeaders','rstan'), repos='https://cloud.r-project.org/', dependencies=FALSE)"', exit=0 (2s). Output: sh://turn_15/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages(c('StanHeaders'/'rstan')/_repo_1 (370 tokens), sh://turn_15/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages(c('StanHeaders'/'rstan')/_repo_2 (586 tokens)
-```
-
-### `log://turn_15/sh/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22`
-scheme=log action=sh attrs={"command":"Rscript -e \"library(rstan); print(packageVersion('rstan'))\"","summary":"Rscript -e \"library(rstan); print(packageVersion('rstan'))\"","action":"sh"}
-
-```
-ran 'Rscript -e "library(rstan); print(packageVersion('rstan'))"', exit=1 (0s). Output: sh://turn_15/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1 (0 tokens), sh://turn_15/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2 (39 tokens)
-```
-
-### `log://turn_15/update/check_lib_paths_%2B_install_StanHeaders/rstan_minimal_%2B_test_load`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-check lib paths + install StanHeaders/rstan minimal + test load
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_016.md

@@ -1,70 +0,0 @@
-# turn 016
-
-tokens: prompt=19080 cached=3415 completion=240 reasoning=0 total=19320 cost=0
-created: 2026-05-02 00:15:51
-
-update: status=177 body=installing RcppEigen+StanHeaders with compiler flags + test rstan load
-
----
-
-## reasoning (think)
-
-```
-Current status: RStan installation failed repeatedly due to compilation issues (RcppEigen/StanHeaders). Installed packages: Rcpp 1.1.1-1.1, RcppParallel 5.1.11-2, rstantools 2.6.0. Missing core Stan packages.
-
-Plan:
-1. Install RcppEigen and StanHeaders first (with compiler flags)
-2. Then install rstan (dependencies=FALSE)
-3. Test library(rstan)
-4. If successful, run model fit
-```
-
-## assistant emission
-
-```
-<think>
-Current status: RStan installation failed repeatedly due to compilation issues (RcppEigen/StanHeaders). Installed packages: Rcpp 1.1.1-1.1, RcppParallel 5.1.11-2, rstantools 2.6.0. Missing core Stan packages.
-
-Plan:
-1. Install RcppEigen and StanHeaders first (with compiler flags)
-2. Then install rstan (dependencies=FALSE)
-3. Test library(rstan)
-4. If successful, run model fit
-</think>
-
-<sh>export CC=gcc-9 CXX=g++-9; R -e "install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')"</sh>
-<sh>export CC=gcc-9 CXX=g++-9; R -e "install.packages('StanHeaders', repos='https://cloud.r-project.org/', type='source', dependencies=FALSE)"</sh>
-<sh>Rscript -e "library(rstan); print(packageVersion('rstan'))"</sh>
-<update status="177">installing RcppEigen+StanHeaders with compiler flags + test rstan load</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_16/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl`
-scheme=log action=sh attrs={"command":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')\"","summary":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')\"","action":"sh"}
-
-```
-ran 'export CC=gcc-9 CXX=g++-9; R -e "install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')"', exit=0 (21s). Output: sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_1 (1203 tokens), sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_2 (957130 tokens)
-```
-
-### `log://turn_16/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A`
-scheme=log action=sh attrs={"command":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('StanHeaders', repos='https://cloud.r-project.org/', type='source', dependencies=FALSE)\"","summary":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('StanHeaders', repos='https://cloud.r-project.org/', type='source', dependencies=FALSE)\"","action":"sh"}
-
-```
-ran 'export CC=gcc-9 CXX=g++-9; R -e "install.packages('StanHeaders', repos='https://cloud.r-project.org/', type='source', dependencies=FALSE)"', exit=0 (3s). Output: sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A_1 (372 tokens), sh://turn_16/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('StanHeaders'/_repos%3D'https%3A_2 (331 tokens)
-```
-
-### `log://turn_16/sh/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22`
-scheme=log action=sh attrs={"command":"Rscript -e \"library(rstan); print(packageVersion('rstan'))\"","summary":"Rscript -e \"library(rstan); print(packageVersion('rstan'))\"","action":"sh"}
-
-```
-ran 'Rscript -e "library(rstan); print(packageVersion('rstan'))"', exit=1 (0s). Output: sh://turn_16/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_1 (0 tokens), sh://turn_16/Rscript_-e_%22library(rstan)%3B_print(packageVersion('rstan'))%22_2 (39 tokens)
-```
-
-### `log://turn_16/update/installing_RcppEigen%2BStanHeaders_with_compiler_flags_%2B_test_rstan_load`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-installing RcppEigen+StanHeaders with compiler flags + test rstan load
-```
-

package/audit/sweep/mcmc-sampling-stan/turns/turn_017.md

@@ -1,58 +0,0 @@
-# turn 017
-
-tokens: prompt=21862 cached=4240 completion=203 reasoning=0 total=22065 cost=0
-created: 2026-05-02 00:16:17
-
-update: status=177 body=installing BLAS/LAPACK/gfortran + checking packages + retrying RcppEigen
-
----
-
-## reasoning (think)
-
-```
-RStan installation failing due to missing BLAS/gfortran libs for RcppEigen compilation. Need to install system BLAS/LAPACK/gfortran libs first, then retry RcppEigen -> StanHeaders -> rstan. Current installed: Rcpp, rstantools, RcppParallel. Lib paths: /usr/local/lib/R/site-library first.
-```
-
-## assistant emission
-
-```
-<think>
-RStan installation failing due to missing BLAS/gfortran libs for RcppEigen compilation. Need to install system BLAS/LAPACK/gfortran libs first, then retry RcppEigen -> StanHeaders -> rstan. Current installed: Rcpp, rstantools, RcppParallel. Lib paths: /usr/local/lib/R/site-library first.
-</think>
-
-<sh>apt-get update && apt-get install -y libblas-dev liblapack-dev gfortran</sh>
-<env>R -e "installed.packages()[grep('^(Rcpp|RcppEigen|StanHeaders|rstan)',rownames(installed.packages())),c('Package','Version')]"</env>
-<sh>export CC=gcc-9 CXX=g++-9; R -e "install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')"</sh>
-<update status="177">installing BLAS/LAPACK/gfortran + checking packages + retrying RcppEigen</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_17/sh/apt-get_update_%26%26_apt-get_install_-y_libblas-dev_liblapack-dev_gfortran`
-scheme=log action=sh attrs={"command":"apt-get update && apt-get install -y libblas-dev liblapack-dev gfortran","summary":"apt-get update && apt-get install -y libblas-dev liblapack-dev gfortran","action":"sh"}
-
-```
-ran 'apt-get update && apt-get install -y libblas-dev liblapack-dev gfortran', exit=0 (37s). Output: sh://turn_17/apt-get_update_%26%26_apt-get_install_-y_libblas-dev_liblapack-dev_gfortran_1 (4294 tokens), sh://turn_17/apt-get_update_%26%26_apt-get_install_-y_libblas-dev_liblapack-dev_gfortran_2 (37 tokens)
-```
-
-### `log://turn_17/env/R_-e_%22installed.packages()%5Bgrep('%5E(Rcpp%7CRcppEigen%7CStanHeaders%7Crstan)'/rownames(i`
-scheme=log action=env attrs={"command":"R -e \"installed.packages()[grep('^(Rcpp|RcppEigen|StanHeaders|rstan)',rownames(installed.packages())),c('Package','Version')]\"","summary":"R -e \"installed.packages()[grep('^(Rcpp|RcppEigen|StanHeaders|rstan)',rownames(installed.packages())),c('Package','Version')]\"","action":"env"}
-
-```
-ran 'R -e "installed.packages()[grep('^(Rcpp|RcppEigen|StanHeaders|rstan)',rownames(installed.packages())),c('Package','Version')]"', exit=0 (0s). Output: env://turn_17/R_-e_%22installed.packages()%5Bgrep('%5E(Rcpp%7CRcppEigen%7CStanHeaders%7Crstan)'/rownames(i_1 (459 tokens), env://turn_17/R_-e_%22installed.packages()%5Bgrep('%5E(Rcpp%7CRcppEigen%7CStanHeaders%7Crstan)'/rownames(i_2 (0 tokens)
-```
-
-### `log://turn_17/sh/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl`
-scheme=log action=sh attrs={"command":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')\"","summary":"export CC=gcc-9 CXX=g++-9; R -e \"install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')\"","action":"sh"}
-
-```
-ran 'export CC=gcc-9 CXX=g++-9; R -e "install.packages('RcppEigen', repos='https://cloud.r-project.org/', type='source')"', exit=0 (21s). Output: sh://turn_17/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_1 (1203 tokens), sh://turn_17/export_CC%3Dgcc-9_CXX%3Dg%2B%2B-9%3B_R_-e_%22install.packages('RcppEigen'/_repos%3D'https%3A/cl_2 (957121 tokens)
-```
-
-### `log://turn_17/update/installing_BLAS/LAPACK/gfortran_%2B_checking_packages_%2B_retrying_RcppEigen`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-installing BLAS/LAPACK/gfortran + checking packages + retrying RcppEigen
-```
-