git: 4e051b961c7e - main - biology/gffread: remove local poudriere files
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Date: Mon, 07 Mar 2022 22:45:16 UTC
The branch main has been updated by rene:
URL: https://cgit.FreeBSD.org/ports/commit/?id=4e051b961c7e0a940fd8e183113d85223b5b3f72
commit 4e051b961c7e0a940fd8e183113d85223b5b3f72
Author: Rene Ladan <rene@FreeBSD.org>
AuthorDate: 2022-03-07 22:44:38 +0000
Commit: Rene Ladan <rene@FreeBSD.org>
CommitDate: 2022-03-07 22:44:38 +0000
biology/gffread: remove local poudriere files
---
biology/gffread/gffread-0.12.7.log-12-2-amd64 | 262 -------------------------
biology/gffread/gffread-0.12.7.log-13-0-amd64 | 264 --------------------------
2 files changed, 526 deletions(-)
diff --git a/biology/gffread/gffread-0.12.7.log-12-2-amd64 b/biology/gffread/gffread-0.12.7.log-12-2-amd64
deleted file mode 100644
index 03ec053fefed..000000000000
--- a/biology/gffread/gffread-0.12.7.log-12-2-amd64
+++ /dev/null
@@ -1,262 +0,0 @@
-build started at Wed Nov 10 14:44:00 CST 2021
-port directory: /usr/ports/wip/gffread
-package name: gffread-0.12.7
-building for: FreeBSD 12-2-amd64-default 12.2-RELEASE-p10 FreeBSD 12.2-RELEASE-p10 amd64
-maintained by: jwb@FreeBSD.org
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-=======================<phase: pkg-depends >============================
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - not found
-===> Installing existing package /packages/All/pkg-1.17.3.pkg
-[12-2-amd64-default] Installing pkg-1.17.3...
-[12-2-amd64-default] Extracting pkg-1.17.3: .......... done
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Returning to build of gffread-0.12.7
-===========================================================================
-=======================<phase: fetch-depends >============================
-===========================================================================
-=======================<phase: fetch >============================
-===> License MIT accepted by the user
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Fetching all distfiles required by gffread-0.12.7 for building
-===========================================================================
-=======================<phase: checksum >============================
-===> License MIT accepted by the user
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Fetching all distfiles required by gffread-0.12.7 for building
-=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz.
-=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz.
-===========================================================================
-=======================<phase: extract-depends>============================
-===========================================================================
-=======================<phase: extract >============================
-===> License MIT accepted by the user
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Fetching all distfiles required by gffread-0.12.7 for building
-===> Extracting for gffread-0.12.7
-=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz.
-=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz.
-===========================================================================
-=======================<phase: patch-depends >============================
-===========================================================================
-=======================<phase: patch >============================
-===> Patching for gffread-0.12.7
-===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files
-===========================================================================
-=======================<phase: build-depends >============================
-===> gffread-0.12.7 depends on package: gmake>=4.3 - not found
-===> Installing existing package /packages/All/gmake-4.3_2.pkg
-[12-2-amd64-default] Installing gmake-4.3_2...
-[12-2-amd64-default] `-- Installing gettext-runtime-0.21...
-[12-2-amd64-default] | `-- Installing indexinfo-0.3.1...
-[12-2-amd64-default] | `-- Extracting indexinfo-0.3.1: .... done
-[12-2-amd64-default] `-- Extracting gettext-runtime-0.21: .......... done
-[12-2-amd64-default] Extracting gmake-4.3_2: .......... done
-===> gffread-0.12.7 depends on package: gmake>=4.3 - found
-===> Returning to build of gffread-0.12.7
-===========================================================================
-=======================<phase: lib-depends >============================
-===========================================================================
-=>> Recording filesystem state for prebuild... done
-=======================<phase: configure >============================
-===> gffread-0.12.7 depends on package: gmake>=4.3 - found
-===> Configuring for gffread-0.12.7
-===========================================================================
-=======================<phase: build >============================
-===> Building for gffread-0.12.7
-gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o
-gclib/gff.cpp:37:12: warning: unused variable 'CLASSCODE_J_RANK' [-Wunused-const-variable]
-const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps
- ^
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gffread.cpp -o gffread.o
-1 warning generated.
-c++ -fstack-protector-strong -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o
-gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-===========================================================================
-=>> Checking for filesystem violations... done
-=======================<phase: run-depends >============================
-===========================================================================
-=>> Recording filesystem state for prestage... done
-=======================<phase: stage >============================
-===> Staging for gffread-0.12.7
-===> Generating temporary packing list
-gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-install -c gffread /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin
-strip /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin/gffread
-gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-====> Compressing man pages (compress-man)
-===========================================================================
-====> Running Q/A tests (stage-qa)
-====> Checking for pkg-plist issues (check-plist)
-===> Parsing plist
-===> Checking for items in STAGEDIR missing from pkg-plist
-===> Checking for items in pkg-plist which are not in STAGEDIR
-===> No pkg-plist issues found (check-plist)
-=>> Checking for staging violations... done
-=======================<phase: package >============================
-===> Building package for gffread-0.12.7
-install -l rs /tmp/pkgs/gffread-0.12.7.pkg /tmp/pkgs/gffread-0.12.7.txz
-===========================================================================
-=>> Recording filesystem state for preinst... done
-=======================<phase: install >============================
-===> Installing for gffread-0.12.7
-===> Checking if gffread is already installed
-===> Registering installation for gffread-0.12.7
-[12-2-amd64-default] Installing gffread-0.12.7...
-===========================================================================
-=>> Checking shared library dependencies
- 0x0000000000000001 NEEDED Shared library: [libc++.so.1]
- 0x0000000000000001 NEEDED Shared library: [libc.so.7]
- 0x0000000000000001 NEEDED Shared library: [libcxxrt.so.1]
- 0x0000000000000001 NEEDED Shared library: [libm.so.5]
-=======================<phase: deinstall >============================
-===> Deinstalling for gffread
-===> Deinstalling gffread-0.12.7
-Updating database digests format: ..... done
-Checking integrity... done (0 conflicting)
-Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
-
-Installed packages to be REMOVED:
- gffread: 0.12.7
-
-Number of packages to be removed: 1
-[12-2-amd64-default] [1/1] Deinstalling gffread-0.12.7...
-[12-2-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done
-===========================================================================
-=>> Checking for extra files and directories
-[00:00:24] Installing from package
-[12-2-amd64-default] Installing gffread-0.12.7...
-[12-2-amd64-default] Extracting gffread-0.12.7: .... done
-[00:00:24] Cleaning up
-===> Cleaning for gffread-0.12.7
-[00:00:24] Deinstalling package
-Updating database digests format: . done
-Checking integrity... done (0 conflicting)
-Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
-
-Installed packages to be REMOVED:
- gffread: 0.12.7
-
-Number of packages to be removed: 1
-[12-2-amd64-default] [1/1] Deinstalling gffread-0.12.7...
-[12-2-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done
-build of wip/gffread | gffread-0.12.7 ended at Wed Nov 10 14:44:09 CST 2021
-build time: 00:00:09
diff --git a/biology/gffread/gffread-0.12.7.log-13-0-amd64 b/biology/gffread/gffread-0.12.7.log-13-0-amd64
deleted file mode 100644
index d28b274e37cf..000000000000
--- a/biology/gffread/gffread-0.12.7.log-13-0-amd64
+++ /dev/null
@@ -1,264 +0,0 @@
-build started at Wed Nov 10 14:44:25 CST 2021
-port directory: /usr/ports/wip/gffread
-package name: gffread-0.12.7
-building for: FreeBSD 13-0-amd64-default 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 amd64
-maintained by: jwb@FreeBSD.org
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---End PLIST_SUB--
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-===> License MIT accepted by the user
-===========================================================================
-=======================<phase: pkg-depends >============================
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - not found
-===> Installing existing package /packages/All/pkg-1.17.3.pkg
-[13-0-amd64-default] Installing pkg-1.17.3...
-[13-0-amd64-default] Extracting pkg-1.17.3: .......... done
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Returning to build of gffread-0.12.7
-===========================================================================
-=======================<phase: fetch-depends >============================
-===========================================================================
-=======================<phase: fetch >============================
-===> License MIT accepted by the user
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Fetching all distfiles required by gffread-0.12.7 for building
-===========================================================================
-=======================<phase: checksum >============================
-===> License MIT accepted by the user
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Fetching all distfiles required by gffread-0.12.7 for building
-=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz.
-=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz.
-===========================================================================
-=======================<phase: extract-depends>============================
-===========================================================================
-=======================<phase: extract >============================
-===> License MIT accepted by the user
-===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found
-===> Fetching all distfiles required by gffread-0.12.7 for building
-===> Extracting for gffread-0.12.7
-=> SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz.
-=> SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz.
-===========================================================================
-=======================<phase: patch-depends >============================
-===========================================================================
-=======================<phase: patch >============================
-===> Patching for gffread-0.12.7
-===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/wip/gffread/files
-===========================================================================
-=======================<phase: build-depends >============================
-===> gffread-0.12.7 depends on package: gmake>=4.3 - not found
-===> Installing existing package /packages/All/gmake-4.3_2.pkg
-[13-0-amd64-default] Installing gmake-4.3_2...
-[13-0-amd64-default] `-- Installing gettext-runtime-0.21...
-[13-0-amd64-default] | `-- Installing indexinfo-0.3.1...
-[13-0-amd64-default] | `-- Extracting indexinfo-0.3.1: .... done
-[13-0-amd64-default] `-- Extracting gettext-runtime-0.21: .......... done
-[13-0-amd64-default] Extracting gmake-4.3_2: .......... done
-===> gffread-0.12.7 depends on package: gmake>=4.3 - found
-===> Returning to build of gffread-0.12.7
-===========================================================================
-=======================<phase: lib-depends >============================
-===========================================================================
-=>> Recording filesystem state for prebuild... done
-=======================<phase: configure >============================
-===> gffread-0.12.7 depends on package: gmake>=4.3 - found
-===> Configuring for gffread-0.12.7
-===========================================================================
-=======================<phase: build >============================
-===> Building for gffread-0.12.7
-gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o
-gclib/gff.cpp:37:12: warning: unused variable 'CLASSCODE_J_RANK' [-Wunused-const-variable]
-const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps
- ^
-c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gffread.cpp -o gffread.o
-1 warning generated.
-c++ -fstack-protector-strong -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o
-gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-===========================================================================
-=>> Checking for filesystem violations... done
-=======================<phase: run-depends >============================
-===========================================================================
-=>> Recording filesystem state for prestage... done
-=======================<phase: stage >============================
-===> Staging for gffread-0.12.7
-===> Generating temporary packing list
-gmake[1]: Entering directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-install -c gffread /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin
-strip /wrkdirs/usr/ports/wip/gffread/work/stage/usr/local/bin/gffread
-gmake[1]: Leaving directory '/wrkdirs/usr/ports/wip/gffread/work/gffread-0.12.7'
-====> Compressing man pages (compress-man)
-===========================================================================
-====> Running Q/A tests (stage-qa)
-====> Checking for pkg-plist issues (check-plist)
-===> Parsing plist
-===> Checking for items in STAGEDIR missing from pkg-plist
-===> Checking for items in pkg-plist which are not in STAGEDIR
-===> No pkg-plist issues found (check-plist)
-=>> Checking for staging violations... done
-=======================<phase: package >============================
-===> Building package for gffread-0.12.7
-install -l rs /tmp/pkgs/gffread-0.12.7.pkg /tmp/pkgs/gffread-0.12.7.txz
-===========================================================================
-=>> Recording filesystem state for preinst... done
-=======================<phase: install >============================
-===> Installing for gffread-0.12.7
-===> Checking if gffread is already installed
-===> Registering installation for gffread-0.12.7
-[13-0-amd64-default] Installing gffread-0.12.7...
-===========================================================================
-=>> Checking shared library dependencies
- 0x0000000000000001 NEEDED Shared library: [libc++.so.1]
- 0x0000000000000001 NEEDED Shared library: [libc.so.7]
- 0x0000000000000001 NEEDED Shared library: [libcxxrt.so.1]
- 0x0000000000000001 NEEDED Shared library: [libm.so.5]
-=======================<phase: deinstall >============================
-===> Deinstalling for gffread
-===> Deinstalling gffread-0.12.7
-Updating database digests format: ..... done
-Checking integrity... done (0 conflicting)
-Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
-
-Installed packages to be REMOVED:
- gffread: 0.12.7
-
-Number of packages to be removed: 1
-[13-0-amd64-default] [1/1] Deinstalling gffread-0.12.7...
-[13-0-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done
-===========================================================================
-=>> Checking for extra files and directories
-[00:00:25] Installing from package
-[13-0-amd64-default] Installing gffread-0.12.7...
-[13-0-amd64-default] Extracting gffread-0.12.7: .... done
-[00:00:25] Cleaning up
-===> Cleaning for gffread-0.12.7
-[00:00:25] Deinstalling package
-Updating database digests format: . done
-Checking integrity... done (0 conflicting)
-Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
-
-Installed packages to be REMOVED:
- gffread: 0.12.7
-
-Number of packages to be removed: 1
-[13-0-amd64-default] [1/1] Deinstalling gffread-0.12.7...
-[13-0-amd64-default] [1/1] Deleting files for gffread-0.12.7: .... done
-build of wip/gffread | gffread-0.12.7 ended at Wed Nov 10 14:44:34 CST 2021
-build time: 00:00:09