diff options
| -rw-r--r-- | contrib/patches/edirect-xml-bounds-check.patch | 36 | ||||
| -rw-r--r-- | guix.scm | 6 |
2 files changed, 40 insertions, 2 deletions
diff --git a/contrib/patches/edirect-xml-bounds-check.patch b/contrib/patches/edirect-xml-bounds-check.patch new file mode 100644 index 0000000..7e369ca --- /dev/null +++ b/contrib/patches/edirect-xml-bounds-check.patch @@ -0,0 +1,36 @@ +--- a/eutils/xml.go 2026-01-08 20:01:51.000000000 +0000 ++++ b/eutils/xml.go 2026-04-03 06:53:30.494928480 +0000 +@@ -1791,14 +1791,23 @@ + + // at start of end tag + idx++ ++ if idx >= txtlen { ++ return NOTAG, NONE, "", "", idx ++ } + start = idx + ch = text[idx] + // expect legal first character of element + if inFirst[ch] { + idx++ ++ if idx >= txtlen { ++ return NOTAG, NONE, "", "", idx ++ } + ch = text[idx] + for inElement[ch] { + idx++ ++ if idx >= txtlen { ++ return NOTAG, NONE, "", "", idx ++ } + ch = text[idx] + } + str := text[start:idx] +@@ -1806,6 +1815,9 @@ + // skip past unexpected blanks + for inBlank[ch] { + idx++ ++ if idx >= txtlen { ++ return NOTAG, NONE, "", "", idx ++ } + ch = text[idx] + } + if ch != '>' { diff --git a/guix.scm b/guix.scm index 5530c24..43c3f77 100644 --- a/guix.scm +++ b/guix.scm @@ -141,7 +141,9 @@ GeneCup with four gene symbols (gria1, crhr1, drd2, and penk).") (snippet '(begin (delete-file "Mozilla-CA.tar.gz") - (delete-file "cacert.pem"))))) + (delete-file "cacert.pem"))) + (patches + (list (local-file "contrib/patches/edirect-xml-bounds-check.patch"))))) (build-system gnu-build-system) (arguments (list @@ -276,7 +278,7 @@ GeneCup with four gene symbols (gria1, crhr1, drd2, and penk).") go-github-com-surgebase-porter2 go-golang-org-x-sys go-golang-org-x-text)) - (propagated-inputs (list curl wget grep sed gawk coreutils)) + (propagated-inputs (list curl wget grep sed gawk coreutils findutils gzip unzip)) (inputs (list bash-minimal coreutils perl perl-xml-simple python)) (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") |