Your message dated Mon, 22 Jun 2020 03:03:28 +0000 with message-id <e1jnck4-0003rf...@fasolo.debian.org> and subject line Bug#963439: fixed in ncbi-entrez-direct 13.1.20200102+dfsg-1 has caused the Debian Bug report #963439, regarding ncbi-entrez-direct: FTBFS: obj-x86_64-linux-gnu/src/golang.org/x/sys/unix/syscall_unix.go:16:2: cannot find package "golang.org/x/sys/internal/unsafeheader" in any of: to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 963439: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963439 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: ncbi-entrez-direct Version: 12.0.20190816+ds-2 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200620 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' edirect.pl > bin/edirect > chmod +x bin/edirect > echo '#!/bin/sh' > bin/eaddress > echo 'exec /usr/bin/edirect -address "$@"' >> bin/eaddress > chmod +x bin/eaddress > echo '#!/bin/sh' > bin/eblast > echo 'exec /usr/bin/edirect -blast "$@"' >> bin/eblast > chmod +x bin/eblast > echo '#!/bin/sh' > bin/ecitmatch > echo 'exec /usr/bin/edirect -citmatch "$@"' >> bin/ecitmatch > chmod +x bin/ecitmatch > echo '#!/bin/sh' > bin/econtact > echo 'exec /usr/bin/edirect -contact "$@"' >> bin/econtact > chmod +x bin/econtact > echo '#!/bin/sh' > bin/efilter > echo 'exec /usr/bin/edirect -filter "$@"' >> bin/efilter > chmod +x bin/efilter > echo '#!/bin/sh' > bin/elink > echo 'exec /usr/bin/edirect -link "$@"' >> bin/elink > chmod +x bin/elink > echo '#!/bin/sh' > bin/enotify > echo 'exec /usr/bin/edirect -notify "$@"' >> bin/enotify > chmod +x bin/enotify > echo '#!/bin/sh' > bin/epost > echo 'exec /usr/bin/edirect -post "$@"' >> bin/epost > chmod +x bin/epost > echo '#!/bin/sh' > bin/eproxy > echo 'exec /usr/bin/edirect -proxy "$@"' >> bin/eproxy > chmod +x bin/eproxy > echo '#!/bin/sh' > bin/esearch > echo 'exec /usr/bin/edirect -search "$@"' >> bin/esearch > chmod +x bin/esearch > echo '#!/bin/sh' > bin/espell > echo 'exec /usr/bin/edirect -spell "$@"' >> bin/espell > chmod +x bin/espell > echo '#!/bin/sh' > bin/esummary > echo 'exec /usr/bin/edirect -fetch -format docsum "$@"' >> bin/esummary > chmod +x bin/esummary > mkdir -p bin > sed -e 's/`has-asp`/false # &/' download-ncbi-data > bin/download-ncbi-data > chmod +x bin/download-ncbi-data > mkdir -p bin > sed -e 's/`has-asp`/false # &/' download-pubmed > bin/download-pubmed > chmod +x bin/download-pubmed > mkdir -p bin > sed -e 's/`has-asp`/false # &/' download-sequence > bin/download-sequence > chmod +x bin/download-sequence > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' edirutil > bin/edirutil > chmod +x bin/edirutil > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' ftp-cp > bin/ftp-cp > chmod +x bin/ftp-cp > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' ftp-ls > bin/ftp-ls > chmod +x bin/ftp-ls > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' gbf2xml > bin/gbf2xml > chmod +x bin/gbf2xml > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' nquire > bin/nquire > chmod +x bin/nquire > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' run-ncbi-converter > > bin/run-ncbi-converter > chmod +x bin/run-ncbi-converter > mkdir -p bin > sed -e '1s,^#!/usr/bin/env perl$,#!/usr/bin/perl,' transmute > bin/transmute > chmod +x bin/transmute > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fatih/ > ln -s /usr/share/gocode/src/github.com/fatih/color > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fatih/color > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/gedex/ > ln -s /usr/share/gocode/src/github.com/gedex/inflector > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/gedex/inflector > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/ > ln -s /usr/share/gocode/src/github.com/klauspost/cpuid > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/klauspost/cpuid > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/ > ln -s /usr/share/gocode/src/github.com/mattn/go-colorable > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/go-colorable > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/ > ln -s /usr/share/gocode/src/github.com/mattn/go-isatty > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/mattn/go-isatty > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/pbnjay/ > ln -s /<<PKGBUILDDIR>>/debian/vendor/github.com/pbnjay/memory > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/pbnjay/memory > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/rainycape/ > ln -s /usr/share/gocode/src/github.com/rainycape/unidecode > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/rainycape/unidecode > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/shirou/ > ln -s /usr/share/gocode/src/github.com/shirou/gopsutil > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/shirou/gopsutil > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/surgebase/ > ln -s /usr/share/gocode/src/github.com/surgebase/porter2 > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/surgebase/porter2 > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys/ > ln -s /usr/share/gocode/src/golang.org/x/sys/unix > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys/unix > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/ > ln -s /usr/share/gocode/src/golang.org/x/text > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/text > mkdir -p /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fiam > ln -s ../rainycape > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/github.com/fiam/gounidecode > go build -v -gccgoflags '-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro > -Wl,-z,now -Wl,--as-needed' -o bin/j2x j2x.go > go build: when using gc toolchain, please pass compile flags using -gcflags, > and linker flags using -ldflags > github.com/gedex/inflector > command-line-arguments > go build -v -gccgoflags '-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro > -Wl,-z,now -Wl,--as-needed' -o bin/rchive rchive.go common.go > obj-x86_64-linux-gnu/src/golang.org/x/sys/unix/syscall_unix.go:16:2: cannot > find package "golang.org/x/sys/internal/unsafeheader" in any of: > /usr/lib/go-1.14/src/golang.org/x/sys/internal/unsafeheader (from > $GOROOT) > > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/golang.org/x/sys/internal/unsafeheader > (from $GOPATH) > make[1]: *** [debian/rules:93: bin/rchive] Error 1 The full build log is available from: http://qa-logs.debian.net/2020/06/20/ncbi-entrez-direct_12.0.20190816+ds-2_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
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--- Begin Message ---Source: ncbi-entrez-direct Source-Version: 13.1.20200102+dfsg-1 Done: u...@debian.org (Aaron M. Ucko) We believe that the bug you reported is fixed in the latest version of ncbi-entrez-direct, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 963...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-entrez-direct package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 21 Jun 2020 22:32:39 -0400 Source: ncbi-entrez-direct Architecture: source Version: 13.1.20200102+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <u...@debian.org> Closes: 963439 Changes: ncbi-entrez-direct (13.1.20200102+dfsg-1) unstable; urgency=medium . * New upstream release. * .gitignore: Ignore new "saved" directory. * debian/control: Suggest curl (for index-extras). * debian/copyright: Add *.pdf (sourceless) to Files-Excluded. * debian/examples: Remove Scripps BioThings support, now considered official enough (mentioned in README, albeit as experimental). * debian/install: Install bt-*.txt and hlp-*.txt (bt-context.txt and hlp-xtract.txt at present) to a new /usr/lib/ncbi-entrez-direct directory. * debian/man/{archive-pubmed,download-ncbi-data,edirect,efetch,elink,esample, esearch,ftp-cp,fetch-pubmed,ftp-ls,index-pubmed,j2x,join-into-groups-of, nquire,phrase-search,rchive,sort-uniq-count,transmute,xtract}.1: Update for new release. * debian/man/{bt-link,bt-load,bt-save,bt-srch,expand-current,fetch-extras, t2x,xplore}.1: Document new commands. * debian/man/efetch.1: Correct old paste-o in -chr_stop's description. * debian/man/fetch-pubmed.1: Belatedly wordsmith description of -path. * debian/man/index-extras.1: Rename from index-bioc.1 and update. * debian/man/nquire.1: Belatedly drop accidental self-referential SEE ALSO. * debian/man/xtract.1: Explicitly mark suboptions as such; belatedly resync -indices' description. * debian/rules: - Account for new as-is scripts expand-current and fetch-extras; for newly official Scripps BioThings scripts bt-link, bt-load, bt-save, bt-srch, and xplore (some of which need tweaking to look for bt-context.txt in the right place); for new Go executable t2x; and for rename of as-is script index-bioc to index-extras (which moreover needs its interpreter specification corrected to #!/bin/bash via a new generic mechanism). - Move the xtract binary from /usr/bin to /usr/lib/ncbi-entrez-direct (so it can find hlp-xtract.txt) and substitute a wrapper script. - Broaden .../x/sys/unix to .../x/sys in GOLIBSRC(_). (Closes: #963439.) - Temporarily move new go.mod, go.sum, and s2p.go files to a "saved" directory to keep them from interfering with the build process. (They don't necessarily deserve outright exclusion, even with repacking already in use.) * debian/watch: Change repack suffix to +dfsg due to the additional need to exclude sourceless PDF documents. 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