Your message dated Thu, 24 Apr 2025 13:07:51 +0000 with message-id <e1u7wix-0002uf...@fasolo.debian.org> and subject line Bug#1103199: fixed in r-bioc-oligo 1.70.0+ds-3 has caused the Debian Bug report #1103199, regarding r-bioc-oligo: FTBFS: ParserGzXYS.c:62:11: error: implicit declaration of function 'Calloc'; did you mean 'calloc'? [-Wimplicit-function-declaration] 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.) -- 1103199: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103199 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:r-bioc-oligo Version: 1.70.0+ds-2 Severity: serious Tags: ftbfs trixie sid Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R debian/rules override_dh_auto_install make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_install I: R Package: oligo Version: 1.70.0 I: Building using R version 4.5.0-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Mon, 13 Jan 2025 15:18:40 +0100 mkdir -p /<<BUILDDIR>>/r-bioc-oligo-1.70.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-oligo-1.70.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 15:18:40 +0100'" * installing *source* package âoligoâ ... ** this is package âoligoâ version â1.70.0â files âinst/doc/oug.pdfâ, âinst/scripts/oug.pdfâ, âinst/scripts/primer.pdfâ are missing file âtests/doRUnit.Râ has the wrong MD5 checksum ** using staged installation ** libs using C compiler: âgcc (Debian 14.2.0-19) 14.2.0â make[2]: Entering directory '/<<PKGBUILDDIR>>/src' gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/preprocessCore/include' -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c DABG.c -o DABG.o gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/preprocessCore/include' -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c ParserGzXYS.c -o ParserGzXYS.o ParserGzXYS.c: In function âgzxys_header_fieldâ: ParserGzXYS.c:62:11: error: implicit declaration of function âCallocâ; did you mean âcallocâ? [-Wimplicit-function-declaration] 62 | final = Calloc(strlen(result)+1, char); | ^~~~~~ | calloc ParserGzXYS.c:62:36: error: expected expression before âcharâ 62 | final = Calloc(strlen(result)+1, char); | ^~~~ ParserGzXYS.c: In function âR_read_gzxys_filesâ: ParserGzXYS.c:147:9: error: implicit declaration of function âFreeâ; did you mean âfreeâ? [-Wimplicit-function-declaration] 147 | Free(d0); | ^~~~ | free make[2]: *** [/usr/lib/R/etc/Makeconf:202: ParserGzXYS.o] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' make[2]: Entering directory '/<<PKGBUILDDIR>>/src' make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' ERROR: compilation failed for package âoligoâ * removing â/<<PKGBUILDDIR>>/debian/r-bioc-oligo/usr/lib/R/site-library/oligoâ dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-oligo-1.70.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 15:18:40 +0100'" returned exit code 1 make[1]: *** [debian/rules:7: override_dh_auto_install] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:4: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- The above is just how the build ends and not necessarily the most relevant part. If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202504/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you could not reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:r-bioc-oligo, so that this is still visible in the BTS web page for this package. Thanks.
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--- Begin Message ---Source: r-bioc-oligo Source-Version: 1.70.0+ds-3 Done: Rebecca N. Palmer <rebecca_pal...@zoho.com> We believe that the bug you reported is fixed in the latest version of r-bioc-oligo, 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 1103...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Rebecca N. Palmer <rebecca_pal...@zoho.com> (supplier of updated r-bioc-oligo 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: SHA512 Format: 1.8 Date: Wed, 23 Apr 2025 17:40:35 +0100 Source: r-bioc-oligo Architecture: source Version: 1.70.0+ds-3 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net> Changed-By: Rebecca N. Palmer <rebecca_pal...@zoho.com> Closes: 1103199 Changes: r-bioc-oligo (1.70.0+ds-3) unstable; urgency=medium . * Team upload. * Use R_Calloc/Realloc/Free, for R 4.5 compatibility. (Closes: #1103199) Checksums-Sha1: 914e5431917884d997f721baf9452d7049fb99af 2275 r-bioc-oligo_1.70.0+ds-3.dsc d2ec0fc50e67caa48149572621f7c07ec12a0b93 7180 r-bioc-oligo_1.70.0+ds-3.debian.tar.xz d0aec348863b9bf58cacec30f425d60bbe24b32a 13350 r-bioc-oligo_1.70.0+ds-3_amd64.buildinfo Checksums-Sha256: 5d1dc2b275b4a879207090e68803cb0732276bd6d8ad9fe75fec0696f09eba99 2275 r-bioc-oligo_1.70.0+ds-3.dsc 8c8852c1db1b798337ecf71fb515328bbf53e60a6f26bb46a1363786ee73e19f 7180 r-bioc-oligo_1.70.0+ds-3.debian.tar.xz a5a7fd6d23c226362bcf5ab79abd52695c7da986b950f76aca1954628be20d34 13350 r-bioc-oligo_1.70.0+ds-3_amd64.buildinfo Files: 489da22e57d7f0a90ba7dae2db75768a 2275 gnu-r optional r-bioc-oligo_1.70.0+ds-3.dsc 965c35ed51774d5bcfb71c2034085979 7180 gnu-r optional r-bioc-oligo_1.70.0+ds-3.debian.tar.xz 7337af79945156b611c736e78d127405 13350 gnu-r optional r-bioc-oligo_1.70.0+ds-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmgKMawRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGQHA/+MifSJaoRIJQM828qKRVs5b8B5dU2PK2N d+TpujBZxr7xz7vwsclXJxm1DROeFQw/wdcLcGqCnqS30LXcwy0XYcB0I2Fj5wq+ esPfup+NxihTOHvQndSlXTux3REXS/za37lNfeJX5PydNPoInoc52zueFAqLVana LkyxeL87aYG3VF7pqSSK86ZBLAQmbe+Pn6FS1/quss8p+yeQiy8A4+vpi2LWLvrX HhMLz0OJndjF8/dp6+9ZzIpIdCt2S2NIsM51lm8Bc9qM22WPg1kWaIas8zCcUBh6 5yb26Jgh3WM0W9ktWTb6mSBdnfgJUfpH4T/W/v8mN/IrYqhzgV139Axo78xGS6RM VhUvICzn1VOaMCylIOBxn8xAVdUQ6g1ArMCr/rJnpxzpXWY4VIvj9/t6eNkKzJHH CBqOxjpyN1SBgRiKx92nFgbh6WBbMtLmc07YvxBGr52HCxCD3gjzHt3Xxvc4QBMZ J0YzuDL45n2b9Xswj36wdHW+opIgrluvE2W302Awkmn5YhiWlPbtVyQICF7eR8YQ 5WFvEHVcVnAhQULM8HJoMNnGeZXLunUk6zTFtfjlq7Tv2m92h4fGVJeb+eygrrZV 6FrloPMkh/dWBE0MxmqtrlsXjjP+mMw5aHYFdsf8Rd2jociaxA4+8GdJlCcjOS1l xJNsaBTJX9M= =6SER -----END PGP SIGNATURE-----
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