diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index a85be9b5c1ab..ddd55ca12cb9 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -1,86 +1,86 @@ PORTNAME= ncbi-entrez-direct DISTVERSION= 14.9.20210423 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz DIST_SUBDIR= edirect-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Access to the NCBI's suite of interconnected databases WWW= https://www.ncbi.nlm.nih.gov/books/NBK179288/ LICENSE= PD BUILD_DEPENDS= bash:shells/bash RUN_DEPENDS= p5-libwww>=0:www/p5-libwww \ p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \ p5-XML-Simple>=0:textproc/p5-XML-Simple \ curl:ftp/curl USES= go:modules perl5 shebangfix USE_GITHUB= nodefault CONFLICTS_INSTALL= ebook-tools p5-XML-Compile # bin/einfo bin/xml2json # Dependency versions: # make clean extract # cd ${WRKSRC}/cmd # rm -r vendor # ../../../files/build-cmd # files/modules.txt: cd ${WRKSRC}/cmd && go mod vendor GHSD= vendor/github.com GLSD= vendor/golang.org GH_TUPLE= fatih:color:v1.10.0:a/${GHSD}/fatih/color \ surgebase:porter2:56e4718818e8:b/${GHSD}/surgebase/porter2 \ gedex:inflector:16278e9db813:c/${GHSD}/gedex/inflector \ klauspost:cpuid:v1.3.1:d/${GHSD}/klauspost/cpuid \ pbnjay:memory:b12e5d931931:e/${GHSD}/pbnjay/memory \ mattn:go-colorable:v0.1.8:f/${GHSD}/mattn/go-colorable \ mattn:go-isatty:v0.0.12:g/${GHSD}/mattn/go-isatty \ fiam:gounidecode:8deddbd03fec:h/${GHSD}/fiam/gounidecode \ golang:text:v0.3.5:i/${GLSD}/x/text \ - golang:sys:d5e6a3e2c0ae:j/${GLSD}/x/sys + golang:sys:v0.5.0:j/${GLSD}/x/sys SHEBANG_FILES= nquire edirect.pl word-at-a-time accn-at-a-time \ amino-acid-composition between-two-genes exclude-uid-lists \ filter-stop-words intersect-uid-lists phrase-search \ skip-if-file-exists theme-aliases test-edirect hgvs2spdi PSCRIPTS= efetch efilter einfo elink epost esearch esummary nquire SCRIPTS= accn-at-a-time amino-acid-composition archive-pubmed \ between-two-genes download-ncbi-data download-pubmed \ download-sequence efetch efilter einfo elink epost \ esample esearch esummary exclude-uid-lists expand-current \ fetch-pubmed filter-stop-words gbf2xml index-extras \ index-pubmed intersect-uid-lists join-into-groups-of \ nquire phrase-search pm-collect pm-index pm-invert pm-merge \ pm-prepare pm-promote pm-refresh pm-stash rchive \ reorder-columns run-ncbi-converter skip-if-file-exists \ ecommon.sh sort-uniq-count sort-uniq-count-rank stream-pubmed \ theme-aliases transmute word-at-a-time xml2tbl xtract xy-plot \ hlp-xtract.txt transmute xml2json xtract test-edirect \ align-columns hgvs2spdi sort-table print-columns post-extract: @${MV} ${WRKDIR}/edirect/* ${WRKSRC} @${RMDIR} ${WRKDIR}/edirect @${MV} ${WRKSRC}/vendor ${WRKSRC}/cmd pre-configure: @cd ${WRKSRC} && ${REINPLACE_CMD} \ -e 's|$$PATH:$$pth|$$PATH:${PREFIX}/bin|g' \ -e 's|"$$pth"|${PREFIX}/bin|g' \ ${PSCRIPTS} do-build: @${CP} ${FILESDIR}/modules.txt ${WRKSRC}/cmd/vendor @${CP} -R ${WRKSRC}/eutils ${WRKSRC}/cmd/vendor @cd ${WRKSRC}/cmd && ${SETENV} ${MAKE_ENV} ${FILESDIR}/build-cmd do-install: cd ${WRKSRC} && ${INSTALL_SCRIPT} ${SCRIPTS} ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKSRC}/edirect.pl ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/cmd/*.FreeBSD ${STAGEDIR}${PREFIX}/bin .include diff --git a/biology/ncbi-entrez-direct/distinfo b/biology/ncbi-entrez-direct/distinfo index e959f316b0e8..563875c07842 100644 --- a/biology/ncbi-entrez-direct/distinfo +++ b/biology/ncbi-entrez-direct/distinfo @@ -1,23 +1,23 @@ -TIMESTAMP = 1619443745 +TIMESTAMP = 1678294976 SHA256 (edirect-14.9.20210423/edirect.tar.gz) = 9d6534226164fc5dfae7abcf25bfdbd08db068b27f1c13b8a3c4681cda5b0cea SIZE (edirect-14.9.20210423/edirect.tar.gz) = 829737 SHA256 (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = a00342a7ffb8b119346dce56e152a111cbb9eab3970c429cc2ed4272aec2858e SIZE (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = 1267532 SHA256 (edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz) = d06994daa4d561c2ab477a7072bb7e40a8d39904c88ebf649a1b89105aabdf35 SIZE (edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz) = 156593 SHA256 (edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz) = d872f3fb5fcc8d8ff25e915670f7ce867a035cfd7a38a2e01ef1550f8770331b SIZE (edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz) = 6784 SHA256 (edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz) = 3bf2da7358c8ed33c05bac2ca733749ade03eadf184d81cc7b16fcbe2e230f1d SIZE (edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz) = 367144 SHA256 (edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz) = 8903a451771edca578c2aa09848f23027dc02df2c67f675f4dd1aae257a71ad6 SIZE (edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz) = 3076 SHA256 (edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz) = 1027954f9abbe06b6e117e3047af70204dd0eb4f8c27fcd459fb2574b279755f SIZE (edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz) = 9571 SHA256 (edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz) = addbdc341d7685ed4cc8d2d8a8fd2bd9b784bde00d0ea99fb251039fc10c611c SIZE (edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz) = 4548 SHA256 (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = b763f4eb0d0f130821b52484565b32bae1585c4cb0edc57adb94f13b67765176 SIZE (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = 190666 SHA256 (edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz) = f85d1185ba116cd40ef8cf702fe1d960ed41d039c08fd314dbeb5866f3166f27 SIZE (edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz) = 8348127 -SHA256 (edirect-14.9.20210423/golang-sys-d5e6a3e2c0ae_GH0.tar.gz) = 6cd44aa33cb0fc4caedadde44b3a943bece0aa67d803c00bfb09b03222845f19 -SIZE (edirect-14.9.20210423/golang-sys-d5e6a3e2c0ae_GH0.tar.gz) = 1539001 +SHA256 (edirect-14.9.20210423/golang-sys-v0.5.0_GH0.tar.gz) = 810c8f1b7704674971ab6b2b614aba20a5a1765018fd2c639f528dbbcbf88b1f +SIZE (edirect-14.9.20210423/golang-sys-v0.5.0_GH0.tar.gz) = 1429723 diff --git a/biology/ncbi-entrez-direct/files/modules.txt b/biology/ncbi-entrez-direct/files/modules.txt index bf713fd9c42b..77a6af417917 100644 --- a/biology/ncbi-entrez-direct/files/modules.txt +++ b/biology/ncbi-entrez-direct/files/modules.txt @@ -1,33 +1,40 @@ # eutils v0.0.0-00010101000000-000000000000 => ../eutils -## explicit +## explicit; go 1.15 eutils # github.com/fatih/color v1.10.0 -## explicit +## explicit; go 1.13 github.com/fatih/color # github.com/fiam/gounidecode v0.0.0-20150629112515-8deddbd03fec ## explicit github.com/fiam/gounidecode/unidecode # github.com/gedex/inflector v0.0.0-20170307190818-16278e9db813 +## explicit github.com/gedex/inflector # github.com/klauspost/cpuid v1.3.1 +## explicit; go 1.12 github.com/klauspost/cpuid # github.com/mattn/go-colorable v0.1.8 +## explicit; go 1.13 github.com/mattn/go-colorable # github.com/mattn/go-isatty v0.0.12 +## explicit; go 1.12 github.com/mattn/go-isatty # github.com/pbnjay/memory v0.0.0-20201129165224-b12e5d931931 +## explicit github.com/pbnjay/memory # github.com/stretchr/testify v1.7.0 -## explicit +## explicit; go 1.13 # github.com/surge/glog v0.0.0-20141108051140-2578deb2b95c ## explicit # github.com/surgebase/porter2 v0.0.0-20150829210152-56e4718818e8 ## explicit github.com/surgebase/porter2 -# golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae +# golang.org/x/sys v0.5.0 +## explicit; go 1.17 golang.org/x/sys/unix # golang.org/x/text v0.3.5 +## explicit; go 1.11 golang.org/x/text/runes golang.org/x/text/transform golang.org/x/text/unicode/norm # eutils => ../eutils diff --git a/biology/ncbi-entrez-direct/files/patch-cmd_go.mod b/biology/ncbi-entrez-direct/files/patch-cmd_go.mod new file mode 100644 index 000000000000..84d5b957c08e --- /dev/null +++ b/biology/ncbi-entrez-direct/files/patch-cmd_go.mod @@ -0,0 +1,29 @@ +--- cmd/go.mod.orig 2023-03-08 17:07:24 UTC ++++ cmd/go.mod +@@ -1,6 +1,6 @@ + module edirect + +-go 1.15 ++go 1.17 + + replace eutils => ../eutils + +@@ -8,7 +8,17 @@ require ( + eutils v0.0.0-00010101000000-000000000000 + github.com/fatih/color v1.10.0 + github.com/fiam/gounidecode v0.0.0-20150629112515-8deddbd03fec ++ github.com/surgebase/porter2 v0.0.0-20150829210152-56e4718818e8 ++) ++ ++require ( ++ github.com/gedex/inflector v0.0.0-20170307190818-16278e9db813 // indirect ++ github.com/klauspost/cpuid v1.3.1 // indirect ++ github.com/mattn/go-colorable v0.1.8 // indirect ++ github.com/mattn/go-isatty v0.0.12 // indirect ++ github.com/pbnjay/memory v0.0.0-20201129165224-b12e5d931931 // indirect + github.com/stretchr/testify v1.7.0 // indirect + github.com/surge/glog v0.0.0-20141108051140-2578deb2b95c // indirect +- github.com/surgebase/porter2 v0.0.0-20150829210152-56e4718818e8 ++ golang.org/x/sys v0.5.0 // indirect ++ golang.org/x/text v0.3.5 // indirect + ) diff --git a/biology/ncbi-entrez-direct/files/patch-cmd_go.sum b/biology/ncbi-entrez-direct/files/patch-cmd_go.sum new file mode 100644 index 000000000000..6b3d64b34b93 --- /dev/null +++ b/biology/ncbi-entrez-direct/files/patch-cmd_go.sum @@ -0,0 +1,15 @@ +--- cmd/go.sum.orig 2023-03-08 17:10:13 UTC ++++ cmd/go.sum +@@ -26,10 +26,11 @@ github.com/surgebase/porter2 v0.0.0-20150829210152-56e + golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= + golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae h1:/WDfKMnPU+m5M4xB+6x4kaepxRw6jWvR5iDRdvjHgy8= + golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.5.0 h1:MUK/U/4lj1t1oPg0HfuXDN/Z1wv31ZJ/YcPiGccS4DU= ++golang.org/x/sys v0.5.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg= + golang.org/x/text v0.3.5 h1:i6eZZ+zk0SOf0xgBpEpPD18qWcJda6q1sxt3S0kzyUQ= + golang.org/x/text v0.3.5/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= + golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= +-gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM= + gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= + gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo= + gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=