spa
maintainer malacology
· 0 votes
· base
pars-win
· scanned 2026-08-03 00:08:14.047287
LOW
View on AUR ↗
Why flagged
The package downloads a Windows executable from a plausible project-specific academic host (lillo.org.ar) for local execution via Wine/DOSBox, which is a normal use case for running legacy bioinformatics software; the source is not executed directly in the build and poses no remote code execution or supply chain risk beyond the inherent trust in the project's official release.
Triggered rules
LOW
AI review downgraded a static finding
llm_review
The static rules flagged this MEDIUM, but an AI model (qwen/qwen3-235b-a22b-07-25) reviewed the full PKGBUILD and judged it LOW (confidence 95%): The package downloads a Windows executable from a plausible project-specific academic host (lillo.org.ar) for local execution via Wine/DOSBox, which is a normal use case for running legacy bioinformatics software; the source is not executed directly in the build and poses no remote code execution or supply chain risk beyond the inherent trust in the project's official release.
1 higher static finding superseded - not the current verdict (shown for transparency)
MEDIUM
source=() URL on a non-standard host
source_untrusted_domain
One or more source=() URLs point to a host outside the trusted allowlist (github.com, gitlab.com, codeberg.org, pypi.org, …).
-
PKGBUILD:11
source=(https://www.lillo.org.ar/phylogeny/Nona-PeeWee/Pars-win.exe)
PKGBUILD
1 offending line(s) highlighted
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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
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pkgbase=pars-win
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pkgname=('nona-win' 'pee-wee' 'xpiwe' 'slf-wt' 'spa' 'phast-win' 'pars-win-extra')
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pkgver=2014.03.10
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pkgrel=0
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pkgdesc="free parsimony programs"
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arch=('x86_64')
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url="https://www.lillo.org.ar/phylogeny/Nona-PeeWee/readme.htm"
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license=('custom')
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makedepends=('unrar' 'dosbox' 'wine')
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source=(https://www.lillo.org.ar/phylogeny/Nona-PeeWee/Pars-win.exe)
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sha256sums=('89a5eeaeef53aefbefdc9a7344b5b0e996ed1465987452045297d03d89126fce')
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build(){
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cd $srcdir
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# extract files
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unrar x Pars-win.exe
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# write verify.bat
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cat << EOF > verify.bat
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wconvert winona yatasto BioArchLinux
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wconvert winpiwe yatasto BioArchLinux
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wconvert winxpiwe yatasto BioArchLinux
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wconvert winspa BODEGON BioArchLinux
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wconvert winphast BODEGON BioArchLinux
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wconvert winsl surubies BioArchLinux
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exit
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EOF
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# verify
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env SDL_VIDEODRIVER=dummy wine verify.bat
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# generate pkg shell
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echo "cd /usr/share/pars-win" > basic
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for EXE in ONA PHAST PIWE SL SPA XPIWE
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do
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cp basic WIN$EXE
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echo "wine WIN$EXE.EXE" >> WIN$EXE
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chmod +x WIN$EXE
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done
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# two basic dos programs
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for EXE in CONS FQ SCG
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do
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echo "dosbox /usr/share/$pkgbase/$EXE.EXE" >> $EXE
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chmod +x $EXE
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done
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}
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package_nona-win(){
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depends=('wine' 'bash')
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pkgdesc="a bastard son of Pee-Wee"
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cd $srcdir
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_pkg=ONA
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_doc=NONA
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# install main
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install -Dm 755 WIN$_pkg.EXE $pkgdir/usr/share/$pkgbase/WIN$_pkg.EXE
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install -Dm 644 $_doc.DOC $pkgdir/usr/share/$pkgbase/$_doc.DOC
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# install shell
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install -Dm 755 WIN$_pkg $pkgdir/usr/bin/WIN$_pkg
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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ln -s /usr/share/$pkgbase/$_doc.DOC $pkgdir/usr/share/doc/$pkgbase/$_doc.DOC
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}
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package_pee-wee(){
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depends=('wine' 'bash')
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pkgdesc="(P)arsimony and (I)mplied (WE)ights"
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provides=('pee-wee' 'piwe')
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cd $srcdir
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_pkg=PIWE
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_doc=$_pkg
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# install main
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install -Dm 755 WIN$_pkg.EXE $pkgdir/usr/share/$pkgbase/WIN$_pkg.EXE
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install -Dm 644 $_doc.DOC $pkgdir/usr/share/$pkgbase/$_doc.DOC
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# install shell
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install -Dm 755 WIN$_pkg $pkgdir/usr/bin/WIN$_pkg
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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ln -s /usr/share/$pkgbase/$_doc.DOC $pkgdir/usr/share/doc/$pkgbase/$_doc.DOC
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}
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package_xpiwe(){
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depends=('wine' 'bash')
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pkgdesc="Pee-Wee with Floating Point Precision"
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cd $srcdir
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_pkg=XPIWE
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_doc=$_pkg
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# install main
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install -Dm 755 WIN$_pkg.EXE $pkgdir/usr/share/$pkgbase/WIN$_pkg.EXE
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install -Dm 644 $_doc.DOC $pkgdir/usr/share/$pkgbase/$_doc.DOC
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# install shell
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install -Dm 755 WIN$_pkg $pkgdir/usr/bin/WIN$_pkg
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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ln -s /usr/share/$pkgbase/$_doc.DOC $pkgdir/usr/share/doc/$pkgbase/$_doc.DOC
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}
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package_slf-wt(){
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depends=('wine' 'bash')
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pkgdesc="A prototype program implementing character state reconstructions under non-lineal functions of the state changes \
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(Pee-Wee with SeLF-WeighTed) \
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https://doi.org/10.1006/clad.1997.0043"
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cd $srcdir
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_pkg=SL
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_doc=$_pkg
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# install main
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install -Dm 755 WIN$_pkg.EXE $pkgdir/usr/share/$pkgbase/WIN$_pkg.EXE
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install -Dm 644 $_doc.DOC $pkgdir/usr/share/$pkgbase/$_doc.DOC
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# install shell
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install -Dm 755 WIN$_pkg $pkgdir/usr/bin/WIN$_pkg
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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ln -s /usr/share/$pkgbase/$_doc.DOC $pkgdir/usr/share/doc/$pkgbase/$_doc.DOC
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}
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package_spa(){
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depends=('wine' 'bash')
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pkgdesc="Sankoff Parsimony Analysis \
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https://doi.org/10.1006/clad.1998.0068"
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cd $srcdir
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_pkg=SPA
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_doc=$_pkg
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# install main
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install -Dm 755 WIN$_pkg.EXE $pkgdir/usr/share/$pkgbase/WIN$_pkg.EXE
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install -Dm 644 $_doc.DOC $pkgdir/usr/share/$pkgbase/$_doc.DOC
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# install shell
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install -Dm 755 WIN$_pkg $pkgdir/usr/bin/WIN$_pkg
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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ln -s /usr/share/$pkgbase/$_doc.DOC $pkgdir/usr/share/doc/$pkgbase/$_doc.DOC
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}
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package_phast-win(){
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depends=('wine' 'bash')
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pkgdesc="PHylogenetic Analysis for Sankoff Transformations \
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https://doi.org/10.1006/clad.1998.0068"
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provides=('phast')
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cd $srcdir
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_pkg=PHAST
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_doc=$_pkg
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# install main
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install -Dm 755 WIN$_pkg.EXE $pkgdir/usr/share/$pkgbase/WIN$_pkg.EXE
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install -Dm 644 $_doc.DOC $pkgdir/usr/share/$pkgbase/$_doc.DOC
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# install shell
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install -Dm 755 WIN$_pkg $pkgdir/usr/bin/WIN$_pkg
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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ln -s /usr/share/$pkgbase/$_doc.DOC $pkgdir/usr/share/doc/$pkgbase/$_doc.DOC
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}
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package_pars-win-extra(){
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depends=('dosbox' 'bash')
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pkgdesc="Parsimony programs extra software from Pablo A. Goloboff"
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cd $srcdir
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# install shell and main
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for EXE in CONS FQ SCG
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do
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install -Dm 755 $EXE $pkgdir/usr/bin/$EXE
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install -Dm 755 $EXE.EXE $pkgdir/usr/share/$pkgbase/$EXE.EXE
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done
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# install doc
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mkdir -p $pkgdir/usr/share/doc/$pkgbase
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for DOC in PROGRAMS.DOC "README_!.DOC"
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do
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install -Dm 644 $DOC $pkgdir/usr/share/$pkgbase/$DOC
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ln -s /usr/share/$pkgbase/$DOC $pkgdir/usr/share/doc/$pkgbase/$DOC
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done
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# run
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for RUN in $(ls *.RUN)
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do
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install -Dm 644 $RUN $pkgdir/usr/share/$pkgbase/scripts/$RUN
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done
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# dat
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for DAT in $(ls *.DAT)
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do
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install -Dm 644 $DAT $pkgdir/usr/share/$pkgbase/data/$DAT
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done
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}
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Scan history
| Scanned at (UTC) | Severity | Rules |
|---|---|---|
| 2026-08-03 00:08:14 | LOW | 2 |
| 2026-08-02 00:16:08 | LOW | 2 |
| 2026-08-01 00:11:18 | LOW | 2 |
| 2026-07-31 00:14:10 | LOW | 2 |
| 2026-07-30 00:17:23 | LOW | 2 |
| 2026-07-29 00:25:53 | LOW | 2 |
| 2026-07-28 00:07:28 | LOW | 2 |
| 2026-07-27 00:24:32 | LOW | 2 |
| 2026-07-26 00:07:32 | LOW | 2 |
| 2026-07-25 00:13:44 | LOW | 2 |
| 2026-07-24 00:02:28 | LOW | 2 |
| 2026-07-23 00:14:47 | LOW | 2 |
| 2026-07-22 00:29:32 | LOW | 2 |
| 2026-07-21 00:24:15 | LOW | 2 |
| 2026-07-20 00:19:49 | LOW | 2 |
| 2026-07-19 00:17:08 | LOW | 2 |
| 2026-07-18 00:14:48 | LOW | 2 |
| 2026-07-17 00:06:16 | LOW | 2 |
| 2026-07-16 00:05:41 | LOW | 2 |
| 2026-07-15 00:09:25 | LOW | 2 |