Date: Sat, 11 Mar 2023 08:39:17 GMT From: Robert Clausecker <fuz@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8ede8da5f192 - main - biology/ncbi-entrez-direct: fix build on riscv64 Message-ID: <202303110839.32B8dHwB081308@gitrepo.freebsd.org>
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The branch main has been updated by fuz: URL: https://cgit.FreeBSD.org/ports/commit/?id=8ede8da5f192ec5f79b5b26094d11e6a66ff0c5b commit 8ede8da5f192ec5f79b5b26094d11e6a66ff0c5b Author: Robert Clausecker <fuz@FreeBSD.org> AuthorDate: 2023-03-08 17:21:58 +0000 Commit: Robert Clausecker <fuz@FreeBSD.org> CommitDate: 2023-03-11 08:34:45 +0000 biology/ncbi-entrez-direct: fix build on riscv64 Bump golang.org/x/sys dependency to a version new enough to build on riscv64-freebsd. Sponsored by: Berliner Linux User Group e.V. Approved by: portmgr (build fix blanket) Differential Revision: https://reviews.freebsd.org/D38996 --- biology/ncbi-entrez-direct/Makefile | 4 ++-- biology/ncbi-entrez-direct/distinfo | 6 ++--- biology/ncbi-entrez-direct/files/modules.txt | 15 ++++++++---- biology/ncbi-entrez-direct/files/patch-cmd_go.mod | 29 +++++++++++++++++++++++ biology/ncbi-entrez-direct/files/patch-cmd_go.sum | 15 ++++++++++++ 5 files changed, 60 insertions(+), 9 deletions(-) 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 @@ -1,6 +1,6 @@ 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/${PORTVERSION}/ DISTFILES= edirect.tar.gz @@ -40,7 +40,7 @@ GH_TUPLE= fatih:color:v1.10.0:a/${GHSD}/fatih/color \ 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 \ 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 @@ -1,4 +1,4 @@ -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 @@ -19,5 +19,5 @@ SHA256 (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = b763f4 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 @@ -1,32 +1,39 @@ # 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 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=
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