⚡ Bolt: [performance improvement] Cache inverted matrices in vuongtest#28
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seonghobae wants to merge 4 commits into
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⚡ Bolt: [performance improvement] Cache inverted matrices in vuongtest#28seonghobae wants to merge 4 commits into
seonghobae wants to merge 4 commits into
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Extracted and cached the matrix inversion for AB1 and AB2 into local variables before constructing the block matrix W in calcLambda to prevent redundant O(n^3) computation.
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Pull request overview
OpenCode cannot approve yet because required coverage evidence did not pass.
Review outcome
1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence
-
Problem: The required coverage-evidence job result was
failure, so OpenCode cannot establish approval sufficiency for this head. -
Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.
-
Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports
successwith required evidence or explicit no-source not-applicable evidence. -
Regression test: Keep the approval branch checking
needs.coverage-evidence.result == successbefore posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present. -
Result: REQUEST_CHANGES
-
Reason: coverage-evidence result was
failure, so required test/docstring evidence was not proven for current head16d17e1d238b54994b4d8be9135952520a3bff0a. -
Head SHA:
16d17e1d238b54994b4d8be9135952520a3bff0a -
Workflow run: 28728609984
-
Workflow attempt: 1
Coverage evidence
Coverage Evidence
- Head SHA:
16d17e1d238b54994b4d8be9135952520a3bff0a - Required test evidence: supported repository test suites must pass.
- Required docstring evidence: repository-owned docstring gates must pass when configured; otherwise docstring coverage is advisory.
R runtime install (r-base and package headers)
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libssl-dev is already the newest version (3.0.13-0ubuntu3.11).
libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.8).
libxml2-dev set to manually installed.
The following additional packages will be installed:
build-essential bzip2-doc curl libblas-dev libblas3 libbz2-dev
libcurl3t64-gnutls libcurl4t64 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base-core r-base-dev r-base-html r-cran-boot
r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
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r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
Suggested packages:
liblapack-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev liblzma-doc readline-doc elpa-ess r-doc-info | r-doc-pdf
r-mathlib texlive-base texlive-latex-base texlive-plain-generic
texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
texlive-latex-recommended texlive-latex-extra
The following NEW packages will be installed:
build-essential bzip2-doc libblas-dev libblas3 libbz2-dev
libcurl4-openssl-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base r-base-core r-base-dev r-base-html
r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
The following packages will be upgraded:
curl libcurl3t64-gnutls libcurl4t64
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- Result: PASS
R coverage tooling (covr/testthat)
also installing the dependencies ‘sys’, ‘askpass’, ‘curl’, ‘mime’, ‘openssl’, ‘R6’, ‘digest’, ‘jsonlite’, ‘rex’, ‘httr’, ‘cli’, ‘withr’, ‘yaml’
trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.3.tar.gz'
Content type 'application/x-gzip' length 19936 bytes (19 KB)
## Changed-File Evidence Map
```mermaid
flowchart LR
PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
Evidence --> S1["Changed file (2 files)"]
S1 --> I1["repository behavior"]
I1 --> R1["Review risk: Changed file (2 files)"]
R1 --> V1["required checks"]
OpenCode Review Overview
Pull request overviewOpenCode cannot approve yet because required coverage evidence did not pass. Review outcome1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence
Coverage evidenceCoverage Evidence
R runtime install (r-base and package headers)
R coverage tooling (covr/testthat) |
Extracted and cached the matrix inversion for AB1 and AB2 into local variables before constructing the block matrix W in calcLambda to prevent redundant O(n^3) computation.
There was a problem hiding this comment.
Pull request overview
OpenCode cannot approve yet because required coverage evidence did not pass.
Review outcome
1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence
-
Problem: The required coverage-evidence job result was
failure, so OpenCode cannot establish approval sufficiency for this head. -
Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.
-
Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports
successwith required evidence or explicit no-source not-applicable evidence. -
Regression test: Keep the approval branch checking
needs.coverage-evidence.result == successbefore posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present. -
Result: REQUEST_CHANGES
-
Reason: coverage-evidence result was
failure, so required test/docstring evidence was not proven for current head7a6f5335e486f3a4f407275d2f48cc4c6018d11e. -
Head SHA:
7a6f5335e486f3a4f407275d2f48cc4c6018d11e -
Workflow run: 28728978360
-
Workflow attempt: 1
Coverage evidence
Coverage Evidence
- Head SHA:
7a6f5335e486f3a4f407275d2f48cc4c6018d11e - Required test evidence: supported repository test suites must pass.
- Required docstring evidence: repository-owned docstring gates must pass when configured; otherwise docstring coverage is advisory.
R runtime install (r-base and package headers)
Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
Get:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease [126 kB]
Get:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease [126 kB]
Get:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease [126 kB]
Get:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease [3600 B]
Get:8 https://dl.google.com/linux/chrome-stable/deb stable InRelease [1825 B]
Get:9 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 Packages [1077 kB]
Get:10 http://azure.archive.ubuntu.com/ubuntu noble-updates/main Translation-en [267 kB]
Get:11 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 Components [181 kB]
Get:12 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 c-n-f Metadata [17.7 kB]
Get:13 http://azure.archive.ubuntu.com/ubuntu noble-updates/universe amd64 Packages [1658 kB]
Get:14 http://azure.archive.ubuntu.com/ubuntu noble-updates/universe Translation-en [327 kB]
Get:15 http://azure.archive.ubuntu.com/ubuntu noble-updates/universe amd64 Components [388 kB]
Get:16 http://azure.archive.ubuntu.com/ubuntu noble-updates/universe amd64 c-n-f Metadata [34.9 kB]
Get:17 http://azure.archive.ubuntu.com/ubuntu noble-updates/restricted amd64 Packages [1196 kB]
Get:18 http://azure.archive.ubuntu.com/ubuntu noble-updates/restricted Translation-en [271 kB]
Get:19 http://azure.archive.ubuntu.com/ubuntu noble-updates/multiverse Translation-en [11.8 kB]
Get:20 http://azure.archive.ubuntu.com/ubuntu noble-updates/multiverse amd64 Components [940 B]
Get:21 http://azure.archive.ubuntu.com/ubuntu noble-backports/main amd64 Components [5776 B]
Get:22 http://azure.archive.ubuntu.com/ubuntu noble-backports/universe amd64 Components [10.6 kB]
Get:23 http://azure.archive.ubuntu.com/ubuntu noble-security/main amd64 Packages [825 kB]
Get:24 http://azure.archive.ubuntu.com/ubuntu noble-security/main Translation-en [186 kB]
Get:25 http://azure.archive.ubuntu.com/ubuntu noble-security/main amd64 Components [44.9 kB]
Get:26 http://azure.archive.ubuntu.com/ubuntu noble-security/main amd64 c-n-f Metadata [11.8 kB]
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Get:29 http://azure.archive.ubuntu.com/ubuntu noble-security/universe amd64 Components [76.2 kB]
Get:30 http://azure.archive.ubuntu.com/ubuntu noble-security/universe amd64 c-n-f Metadata [24.2 kB]
Get:31 http://azure.archive.ubuntu.com/ubuntu noble-security/restricted amd64 Packages [1133 kB]
Get:32 http://azure.archive.ubuntu.com/ubuntu noble-security/restricted Translation-en [259 kB]
Get:34 https://packages.microsoft.com/ubuntu/24.04/prod noble/main amd64 Packages [199 kB]
Get:35 https://packages.microsoft.com/ubuntu/24.04/prod noble/main arm64 Packages [165 kB]
Get:36 https://packages.microsoft.com/ubuntu/24.04/prod noble/main armhf Packages [11.6 kB]
Get:33 http://azure.archive.ubuntu.com/ubuntu noble-security/multiverse Translation-en [10.1 kB]
Get:37 https://dl.google.com/linux/chrome-stable/deb stable/main amd64 Packages [1214 B]
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
libssl-dev is already the newest version (3.0.13-0ubuntu3.11).
libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.8).
libxml2-dev set to manually installed.
The following additional packages will be installed:
build-essential bzip2-doc curl libblas-dev libblas3 libbz2-dev
libcurl3t64-gnutls libcurl4t64 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base-core r-base-dev r-base-html r-cran-boot
r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
Suggested packages:
liblapack-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev liblzma-doc readline-doc elpa-ess r-doc-info | r-doc-pdf
r-mathlib texlive-base texlive-latex-base texlive-plain-generic
texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
texlive-latex-recommended texlive-latex-extra
The following NEW packages will be installed:
build-essential bzip2-doc libblas-dev libblas3 libbz2-dev
libcurl4-openssl-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base r-base-core r-base-dev r-base-html
r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
The following packages will be upgraded:
curl libcurl3t64-gnutls libcurl4t64
3 upgraded, 38 newly installed, 0 to remove and 32 not upgraded.
Need to get 59.3 MB of archives.
After this operation, 118 MB of additional disk space will be used.
Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
Get:2 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
Get:3 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 bzip2-doc all 1.0.8-5.1build0.1 [499 kB]
Get:4 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 curl amd64 8.5.0-2ubuntu10.10 [227 kB]
Get:5 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libcurl4t64 amd64 8.5.0-2ubuntu10.10 [343 kB]
Get:6 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libblas3 amd64 3.12.0-3build1.1 [238 kB]
Get:7 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libblas-dev amd64 3.12.0-3build1.1 [170 kB]
Get:8 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libbz2-dev amd64 1.0.8-5.1build0.1 [33.6 kB]
Get:9 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libcurl3t64-gnutls amd64 8.5.0-2ubuntu10.10 [335 kB]
Get:10 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libcurl4-openssl-dev amd64 8.5.0-2ubuntu10.10 [446 kB]
Get:11 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu2 [295 kB]
Get:12 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
Get:13 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
Get:14 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 liblapack3 amd64 3.12.0-3build1.1 [2646 kB]
Get:15 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 liblapack-dev amd64 3.12.0-3build1.1 [5196 kB]
Get:16 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB]
Get:17 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B]
Get:18 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libpng-dev amd64 1.6.43-5ubuntu0.6 [265 kB]
Get:19 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 libpng-tools amd64 1.6.43-5ubuntu0.6 [28.5 kB]
Get:20 http://azure.archive.ubuntu.com/ubuntu noble/main amd64 libreadline-dev amd64 8.2-4build1 [167 kB]
Get:21 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base-core amd64 4.3.3-2build2 [27.1 MB]
Get:22 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-boot all 1.3-30-1 [619 kB]
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Get:24 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-foreign amd64 0.8.86-1build1 [242 kB]
Get:25 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB]
Get:26 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-kernsmooth amd64 2.23-22-1build1 [91.8 kB]
Get:27 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1build1 [1341 kB]
Get:28 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1build1 [2261 kB]
Get:29 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB]
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Get:31 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB]
Get:32 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-rpart amd64 4.1.23-1build1 [661 kB]
Get:33 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-class amd64 7.3-22-2build1 [88.2 kB]
Get:34 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-nnet amd64 7.3-19-2build1 [112 kB]
Get:35 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-spatial amd64 7.3-17-1build1 [132 kB]
Get:36 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB]
Get:37 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-recommended all 4.3.3-2build2 [2636 B]
Get:38 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base all 4.3.3-2build2 [9304 B]
Get:39 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1ubuntu0.3 [176 kB]
Get:40 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base-dev all 4.3.3-2build2 [4334 B]
Get:41 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-doc-html all 4.3.3-2build2 [587 kB]
Get:42 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base-html all 4.3.3-2build2 [58.1 kB]
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- Result: PASS
R coverage tooling (covr/testthat)
also installing the dependencies ‘sys’, ‘askpass’, ‘curl’, ‘mime’, ‘openssl’, ‘R6’, ‘digest’, ‘jsonlite’, ‘rex’, ‘httr’, ‘cli’, ‘withr’, ‘yaml’
trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.3.tar.gz'
Content type 'application/x-gzip' length 19936 bytes (19 KB)
## Changed-File Evidence Map
```mermaid
flowchart LR
PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
Evidence --> S1["Changed file (2 files)"]
S1 --> I1["repository behavior"]
I1 --> R1["Review risk: Changed file (2 files)"]
R1 --> V1["required checks"]
Extracted and cached the matrix inversion for AB1 and AB2 into local variables before constructing the block matrix W in calcLambda to prevent redundant O(n^3) computation.
There was a problem hiding this comment.
Pull request overview
OpenCode cannot approve yet because required coverage evidence did not pass.
Review outcome
1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence
-
Problem: The required coverage-evidence job result was
failure, so OpenCode cannot establish approval sufficiency for this head. -
Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.
-
Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports
successwith required evidence or explicit no-source not-applicable evidence. -
Regression test: Keep the approval branch checking
needs.coverage-evidence.result == successbefore posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present. -
Result: REQUEST_CHANGES
-
Reason: coverage-evidence result was
failure, so required test/docstring evidence was not proven for current heada8429a2878201fc07cddff33e435d245ccd4f832. -
Head SHA:
a8429a2878201fc07cddff33e435d245ccd4f832 -
Workflow run: 28729336853
-
Workflow attempt: 1
Coverage evidence
Coverage Evidence
- Head SHA:
a8429a2878201fc07cddff33e435d245ccd4f832 - Required test evidence: supported repository test suites must pass.
- Required docstring evidence: repository-owned docstring gates must pass when configured; otherwise docstring coverage is advisory.
R runtime install (r-base and package headers)
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Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
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libssl-dev is already the newest version (3.0.13-0ubuntu3.11).
libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.8).
libxml2-dev set to manually installed.
The following additional packages will be installed:
build-essential bzip2-doc curl libblas-dev libblas3 libbz2-dev
libcurl3t64-gnutls libcurl4t64 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base-core r-base-dev r-base-html r-cran-boot
r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
Suggested packages:
liblapack-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev liblzma-doc readline-doc elpa-ess r-doc-info | r-doc-pdf
r-mathlib texlive-base texlive-latex-base texlive-plain-generic
texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
texlive-latex-recommended texlive-latex-extra
The following NEW packages will be installed:
build-essential bzip2-doc libblas-dev libblas3 libbz2-dev
libcurl4-openssl-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base r-base-core r-base-dev r-base-html
r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
The following packages will be upgraded:
curl libcurl3t64-gnutls libcurl4t64
3 upgraded, 38 newly installed, 0 to remove and 32 not upgraded.
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- Result: PASS
R coverage tooling (covr/testthat)
also installing the dependencies ‘sys’, ‘askpass’, ‘curl’, ‘mime’, ‘openssl’, ‘R6’, ‘digest’, ‘jsonlite’, ‘rex’, ‘httr’, ‘cli’, ‘withr’, ‘yaml’
trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.3.tar.gz'
Content type 'application/x-gzip' length 19936 bytes (19 KB)
## Changed-File Evidence Map
```mermaid
flowchart LR
PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
Evidence --> S1["Changed file (2 files)"]
S1 --> I1["repository behavior"]
I1 --> R1["Review risk: Changed file (2 files)"]
R1 --> V1["required checks"]
Extracted and cached the matrix inversion for AB1 and AB2 into local variables before constructing the block matrix W in calcLambda to prevent redundant O(n^3) computation.
There was a problem hiding this comment.
Pull request overview
OpenCode cannot approve yet because required coverage evidence did not pass.
Review outcome
1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence
-
Problem: The required coverage-evidence job result was
failure, so OpenCode cannot establish approval sufficiency for this head. -
Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.
-
Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports
successwith required evidence or explicit no-source not-applicable evidence. -
Regression test: Keep the approval branch checking
needs.coverage-evidence.result == successbefore posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present. -
Result: REQUEST_CHANGES
-
Reason: coverage-evidence result was
failure, so required test/docstring evidence was not proven for current head30acd371aa5acf9b890c73128a1c0e5fa933557b. -
Head SHA:
30acd371aa5acf9b890c73128a1c0e5fa933557b -
Workflow run: 28729682170
-
Workflow attempt: 1
Coverage evidence
Coverage Evidence
- Head SHA:
30acd371aa5acf9b890c73128a1c0e5fa933557b - Required test evidence: supported repository test suites must pass.
- Required docstring evidence: repository-owned docstring gates must pass when configured; otherwise docstring coverage is advisory.
R runtime install (r-base and package headers)
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
libssl-dev is already the newest version (3.0.13-0ubuntu3.11).
libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.8).
libxml2-dev set to manually installed.
The following additional packages will be installed:
build-essential bzip2-doc curl libblas-dev libblas3 libbz2-dev
libcurl3t64-gnutls libcurl4t64 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base-core r-base-dev r-base-html r-cran-boot
r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
Suggested packages:
liblapack-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev liblzma-doc readline-doc elpa-ess r-doc-info | r-doc-pdf
r-mathlib texlive-base texlive-latex-base texlive-plain-generic
texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
texlive-latex-recommended texlive-latex-extra
The following NEW packages will be installed:
build-essential bzip2-doc libblas-dev libblas3 libbz2-dev
libcurl4-openssl-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libpaper-utils libpaper1 libpng-dev
libpng-tools libreadline-dev r-base r-base-core r-base-dev r-base-html
r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
r-doc-html r-recommended
The following packages will be upgraded:
curl libcurl3t64-gnutls libcurl4t64
3 upgraded, 38 newly installed, 0 to remove and 32 not upgraded.
Need to get 59.3 MB of archives.
After this operation, 118 MB of additional disk space will be used.
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Get:25 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB]
Get:26 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-kernsmooth amd64 2.23-22-1build1 [91.8 kB]
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Get:32 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-rpart amd64 4.1.23-1build1 [661 kB]
Get:33 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-class amd64 7.3-22-2build1 [88.2 kB]
Get:34 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-nnet amd64 7.3-19-2build1 [112 kB]
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Get:36 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB]
Get:37 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-recommended all 4.3.3-2build2 [2636 B]
Get:38 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base all 4.3.3-2build2 [9304 B]
Get:39 http://azure.archive.ubuntu.com/ubuntu noble-updates/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1ubuntu0.3 [176 kB]
Get:40 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base-dev all 4.3.3-2build2 [4334 B]
Get:41 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-doc-html all 4.3.3-2build2 [587 kB]
Get:42 http://azure.archive.ubuntu.com/ubuntu noble/universe amd64 r-base-html all 4.3.3-2build2 [58.1 kB]
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- Result: PASS
R coverage tooling (covr/testthat)
also installing the dependencies ‘sys’, ‘askpass’, ‘curl’, ‘mime’, ‘openssl’, ‘R6’, ‘digest’, ‘jsonlite’, ‘rex’, ‘httr’, ‘cli’, ‘withr’, ‘yaml’
trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.3.tar.gz'
Content type 'application/x-gzip' length 19936 bytes (19 KB)
## Changed-File Evidence Map
```mermaid
flowchart LR
PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
Evidence --> S1["Changed file (2 files)"]
S1 --> I1["repository behavior"]
I1 --> R1["Review risk: Changed file (2 files)"]
R1 --> V1["required checks"]
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💡 What: Extracted and cached the matrix inversion for AB1 and AB2 into local variables before constructing the block matrix W in calcLambda.
🎯 Why: Matrix inversion is an expensive operation. The previous implementation recalculated the exact same inverse twice for each model during the construction of the block matrix W, leading to redundant computation time.
📊 Impact: Reduces the number of matrix inversions by 50 percent during the calculation of W, which should noticeably speed up the vuongtest function, especially for models with a large number of parameters.
🔬 Measurement: Run a vuongtest on models with a large number of parameters and benchmark execution time using standard system time functions. Both the old and new code should produce identical W matrices.
PR created automatically by Jules for task 2734951907052995651 started by @seonghobae