From aa89b021255683449d1bb33d5f89d62fb44580c2 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:06:05 +0000 Subject: [PATCH 1/5] Update medaka to 1.12.0 --- recipes/medaka/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 2b96f89fbca10..5f88d62a844c5 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Medaka" %} -{% set version = "1.11.3" %} -{% set sha256 = "940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9" %} +{% set version = "1.12.0" %} +{% set sha256 = "039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6" %} # Bot PRs - Always review requirements.txt for new release package: @@ -14,7 +14,7 @@ source: - patch build: - number: 1 + number: 0 entry_points: - medaka = medaka.medaka:main - medaka_counts = medaka.medaka_counts:main From a995c2af0e3b31de7b07343c9f8173e9ab0ee0df Mon Sep 17 00:00:00 2001 From: mencian Date: Mon, 17 Jun 2024 14:44:19 -0500 Subject: [PATCH 2/5] clean up recipe --- recipes/medaka/LICENSE.md | 364 --------------------- recipes/medaka/build.sh | 8 +- recipes/medaka/build_failure.linux-64.yaml | 105 ------ recipes/medaka/build_failure.osx-64.yaml | 105 ------ recipes/medaka/meta.yaml | 26 +- 5 files changed, 19 insertions(+), 589 deletions(-) delete mode 100644 recipes/medaka/LICENSE.md delete mode 100644 recipes/medaka/build_failure.linux-64.yaml delete mode 100644 recipes/medaka/build_failure.osx-64.yaml diff --git a/recipes/medaka/LICENSE.md b/recipes/medaka/LICENSE.md deleted file mode 100644 index 56dddbbdb5f2d..0000000000000 --- a/recipes/medaka/LICENSE.md +++ /dev/null @@ -1,364 +0,0 @@ -This Source Code Form is subject to the terms of the Mozilla Public -License, v. 2.0. If a copy of the MPL was not distributed with this -file, You can obtain one at http://mozilla.org/MPL/2.0/. - -(c) 2016 Oxford Nanopore Technologies Ltd. - - -Mozilla Public License Version 2.0 -================================== - -### 1. Definitions - -**1.1. “Contributor”** - means each individual or legal entity that creates, contributes to - the creation of, or owns Covered Software. - -**1.2. “Contributor Version”** - means the combination of the Contributions of others (if any) used - by a Contributor and that particular Contributor's Contribution. - -**1.3. “Contribution”** - means Covered Software of a particular Contributor. - -**1.4. “Covered Software”** - means Source Code Form to which the initial Contributor has attached - the notice in Exhibit A, the Executable Form of such Source Code - Form, and Modifications of such Source Code Form, in each case - including portions thereof. - -**1.5. “Incompatible With Secondary Licenses”** - means - -* **(a)** that the initial Contributor has attached the notice described - in Exhibit B to the Covered Software; or -* **(b)** that the Covered Software was made available under the terms of - version 1.1 or earlier of the License, but not also under the - terms of a Secondary License. - -**1.6. “Executable Form”** - means any form of the work other than Source Code Form. - -**1.7. “Larger Work”** - means a work that combines Covered Software with other material, in - a separate file or files, that is not Covered Software. - -**1.8. “License”** - means this document. - -**1.9. “Licensable”** - means having the right to grant, to the maximum extent possible, - whether at the time of the initial grant or subsequently, any and - all of the rights conveyed by this License. - -**1.10. “Modifications”** - means any of the following: - -* **(a)** any file in Source Code Form that results from an addition to, - deletion from, or modification of the contents of Covered - Software; or -* **(b)** any new file in Source Code Form that contains any Covered - Software. - -**1.11. “Patent Claims” of a Contributor** - means any patent claim(s), including without limitation, method, - process, and apparatus claims, in any patent Licensable by such - Contributor that would be infringed, but for the grant of the - License, by the making, using, selling, offering for sale, having - made, import, or transfer of either its Contributions or its - Contributor Version. - -**1.12. “Secondary License”** - means either the GNU General Public License, Version 2.0, the GNU - Lesser General Public License, Version 2.1, the GNU Affero General - Public License, Version 3.0, or any later versions of those - licenses. - -**1.13. “Source Code Form”** - means the form of the work preferred for making modifications. - -**1.14. “You” (or “Your”)** - means an individual or a legal entity exercising rights under this - License. For legal entities, “You” includes any entity that - controls, is controlled by, or is under common control with You. For - purposes of this definition, “control” means **(a)** the power, direct - or indirect, to cause the direction or management of such entity, - whether by contract or otherwise, or **(b)** ownership of more than - fifty percent (50%) of the outstanding shares or beneficial - ownership of such entity. - - -### 2. License Grants and Conditions - -#### 2.1. Grants - -Each Contributor hereby grants You a world-wide, royalty-free, -non-exclusive license: - -* **(a)** under intellectual property rights (other than patent or trademark) - Licensable by such Contributor to use, reproduce, make available, - modify, display, perform, distribute, and otherwise exploit its - Contributions, either on an unmodified basis, with Modifications, or - as part of a Larger Work; and -* **(b)** under Patent Claims of such Contributor to make, use, sell, offer - for sale, have made, import, and otherwise transfer either its - Contributions or its Contributor Version. - -#### 2.2. Effective Date - -The licenses granted in Section 2.1 with respect to any Contribution -become effective for each Contribution on the date the Contributor first -distributes such Contribution. - -#### 2.3. Limitations on Grant Scope - -The licenses granted in this Section 2 are the only rights granted under -this License. No additional rights or licenses will be implied from the -distribution or licensing of Covered Software under this License. -Notwithstanding Section 2.1(b) above, no patent license is granted by a -Contributor: - -* **(a)** for any code that a Contributor has removed from Covered Software; - or -* **(b)** for infringements caused by: **(i)** Your and any other third party's - modifications of Covered Software, or **(ii)** the combination of its - Contributions with other software (except as part of its Contributor - Version); or -* **(c)** under Patent Claims infringed by Covered Software in the absence of - its Contributions. - -This License does not grant any rights in the trademarks, service marks, -or logos of any Contributor (except as may be necessary to comply with -the notice requirements in Section 3.4). - -#### 2.4. Subsequent Licenses - -No Contributor makes additional grants as a result of Your choice to -distribute the Covered Software under a subsequent version of this -License (see Section 10.2) or under the terms of a Secondary License (if -permitted under the terms of Section 3.3). - -#### 2.5. Representation - -Each Contributor represents that the Contributor believes its -Contributions are its original creation(s) or it has sufficient rights -to grant the rights to its Contributions conveyed by this License. - -#### 2.6. Fair Use - -This License is not intended to limit any rights You have under -applicable copyright doctrines of fair use, fair dealing, or other -equivalents. - -#### 2.7. Conditions - -Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted -in Section 2.1. - - -### 3. Responsibilities - -#### 3.1. Distribution of Source Form - -All distribution of Covered Software in Source Code Form, including any -Modifications that You create or to which You contribute, must be under -the terms of this License. You must inform recipients that the Source -Code Form of the Covered Software is governed by the terms of this -License, and how they can obtain a copy of this License. You may not -attempt to alter or restrict the recipients' rights in the Source Code -Form. - -#### 3.2. Distribution of Executable Form - -If You distribute Covered Software in Executable Form then: - -* **(a)** such Covered Software must also be made available in Source Code - Form, as described in Section 3.1, and You must inform recipients of - the Executable Form how they can obtain a copy of such Source Code - Form by reasonable means in a timely manner, at a charge no more - than the cost of distribution to the recipient; and - -* **(b)** You may distribute such Executable Form under the terms of this - License, or sublicense it under different terms, provided that the - license for the Executable Form does not attempt to limit or alter - the recipients' rights in the Source Code Form under this License. - -#### 3.3. Distribution of a Larger Work - -You may create and distribute a Larger Work under terms of Your choice, -provided that You also comply with the requirements of this License for -the Covered Software. If the Larger Work is a combination of Covered -Software with a work governed by one or more Secondary Licenses, and the -Covered Software is not Incompatible With Secondary Licenses, this -License permits You to additionally distribute such Covered Software -under the terms of such Secondary License(s), so that the recipient of -the Larger Work may, at their option, further distribute the Covered -Software under the terms of either this License or such Secondary -License(s). - -#### 3.4. Notices - -You may not remove or alter the substance of any license notices -(including copyright notices, patent notices, disclaimers of warranty, -or limitations of liability) contained within the Source Code Form of -the Covered Software, except that You may alter any license notices to -the extent required to remedy known factual inaccuracies. - -#### 3.5. Application of Additional Terms - -You may choose to offer, and to charge a fee for, warranty, support, -indemnity or liability obligations to one or more recipients of Covered -Software. However, You may do so only on Your own behalf, and not on -behalf of any Contributor. You must make it absolutely clear that any -such warranty, support, indemnity, or liability obligation is offered by -You alone, and You hereby agree to indemnify every Contributor for any -liability incurred by such Contributor as a result of warranty, support, -indemnity or liability terms You offer. You may include additional -disclaimers of warranty and limitations of liability specific to any -jurisdiction. - - -### 4. Inability to Comply Due to Statute or Regulation - -If it is impossible for You to comply with any of the terms of this -License with respect to some or all of the Covered Software due to -statute, judicial order, or regulation then You must: **(a)** comply with -the terms of this License to the maximum extent possible; and **(b)** -describe the limitations and the code they affect. Such description must -be placed in a text file included with all distributions of the Covered -Software under this License. Except to the extent prohibited by statute -or regulation, such description must be sufficiently detailed for a -recipient of ordinary skill to be able to understand it. - - -### 5. Termination - -**5.1.** The rights granted under this License will terminate automatically -if You fail to comply with any of its terms. However, if You become -compliant, then the rights granted under this License from a particular -Contributor are reinstated **(a)** provisionally, unless and until such -Contributor explicitly and finally terminates Your grants, and **(b)** on an -ongoing basis, if such Contributor fails to notify You of the -non-compliance by some reasonable means prior to 60 days after You have -come back into compliance. Moreover, Your grants from a particular -Contributor are reinstated on an ongoing basis if such Contributor -notifies You of the non-compliance by some reasonable means, this is the -first time You have received notice of non-compliance with this License -from such Contributor, and You become compliant prior to 30 days after -Your receipt of the notice. - -**5.2.** If You initiate litigation against any entity by asserting a patent -infringement claim (excluding declaratory judgment actions, -counter-claims, and cross-claims) alleging that a Contributor Version -directly or indirectly infringes any patent, then the rights granted to -You by any and all Contributors for the Covered Software under Section -2.1 of this License shall terminate. - -**5.3.** In the event of termination under Sections 5.1 or 5.2 above, all -end user license agreements (excluding distributors and resellers) which -have been validly granted by You or Your distributors under this License -prior to termination shall survive termination. - - -### 6. Disclaimer of Warranty - -> Covered Software is provided under this License on an “as is” -> basis, without warranty of any kind, either expressed, implied, or -> statutory, including, without limitation, warranties that the -> Covered Software is free of defects, merchantable, fit for a -> particular purpose or non-infringing. The entire risk as to the -> quality and performance of the Covered Software is with You. -> Should any Covered Software prove defective in any respect, You -> (not any Contributor) assume the cost of any necessary servicing, -> repair, or correction. This disclaimer of warranty constitutes an -> essential part of this License. No use of any Covered Software is -> authorized under this License except under this disclaimer. - -### 7. Limitation of Liability - -> Under no circumstances and under no legal theory, whether tort -> (including negligence), contract, or otherwise, shall any -> Contributor, or anyone who distributes Covered Software as -> permitted above, be liable to You for any direct, indirect, -> special, incidental, or consequential damages of any character -> including, without limitation, damages for lost profits, loss of -> goodwill, work stoppage, computer failure or malfunction, or any -> and all other commercial damages or losses, even if such party -> shall have been informed of the possibility of such damages. This -> limitation of liability shall not apply to liability for death or -> personal injury resulting from such party's negligence to the -> extent applicable law prohibits such limitation. Some -> jurisdictions do not allow the exclusion or limitation of -> incidental or consequential damages, so this exclusion and -> limitation may not apply to You. - - -### 8. Litigation - -Any litigation relating to this License may be brought only in the -courts of a jurisdiction where the defendant maintains its principal -place of business and such litigation shall be governed by laws of that -jurisdiction, without reference to its conflict-of-law provisions. -Nothing in this Section shall prevent a party's ability to bring -cross-claims or counter-claims. - - -### 9. Miscellaneous - -This License represents the complete agreement concerning the subject -matter hereof. If any provision of this License is held to be -unenforceable, such provision shall be reformed only to the extent -necessary to make it enforceable. Any law or regulation which provides -that the language of a contract shall be construed against the drafter -shall not be used to construe this License against a Contributor. - - -### 10. Versions of the License - -#### 10.1. New Versions - -Mozilla Foundation is the license steward. Except as provided in Section -10.3, no one other than the license steward has the right to modify or -publish new versions of this License. Each version will be given a -distinguishing version number. - -#### 10.2. Effect of New Versions - -You may distribute the Covered Software under the terms of the version -of the License under which You originally received the Covered Software, -or under the terms of any subsequent version published by the license -steward. - -#### 10.3. Modified Versions - -If you create software not governed by this License, and you want to -create a new license for such software, you may create and use a -modified version of this License if you rename the license and remove -any references to the name of the license steward (except to note that -such modified license differs from this License). - -#### 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses - -If You choose to distribute Source Code Form that is Incompatible With -Secondary Licenses under the terms of this version of the License, the -notice described in Exhibit B of this License must be attached. - -## Exhibit A - Source Code Form License Notice - - This Source Code Form is subject to the terms of the Mozilla Public - License, v. 2.0. If a copy of the MPL was not distributed with this - file, You can obtain one at http://mozilla.org/MPL/2.0/. - -If it is not possible or desirable to put the notice in a particular -file, then You may include the notice in a location (such as a LICENSE -file in a relevant directory) where a recipient would be likely to look -for such a notice. - -You may add additional accurate notices of copyright ownership. - -## Exhibit B - “Incompatible With Secondary Licenses” Notice - - This Source Code Form is "Incompatible With Secondary Licenses", as - defined by the Mozilla Public License, v. 2.0. - - diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh index a17d134c7c243..909346d2b1f85 100644 --- a/recipes/medaka/build.sh +++ b/recipes/medaka/build.sh @@ -1,10 +1,10 @@ -#!/bin/bash +#!/bin/bash -euo export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CFLAGS="-I${PREFIX}/include ${LDFLAGS}" +export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}" # disable Makefile driven build of htslib.a sed -i.bak "s/'build_ext': HTSBuild//" setup.py @@ -13,4 +13,6 @@ sed -i.bak "s/'build_ext': HTSBuild//" setup.py sed -i.bak 's/extra_objects.*//' build.py sed -i.bak 's/^libraries=\[/libraries=\["hts",/' build.py -$PYTHON -m pip install . --no-deps --ignore-installed -vvv +rm -rf *.bak + +${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/medaka/build_failure.linux-64.yaml b/recipes/medaka/build_failure.linux-64.yaml deleted file mode 100644 index 362238bbedeef..0000000000000 --- a/recipes/medaka/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: fe8244e36e00fce9b146f015c871e6714fe382a6b7375f652967216782b9cb0f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |2- - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("tensorflow==2.10.0=cuda112py310he87a039_0"), MatchSpec("__cuda"), MatchSpec("pysam==0.16.0.1=py27ha863e18_1"), MatchSpec("python_abi=2.7[build=*_cp27mu]")} - Encountered problems while solving: - - package pysam-0.16.0.1-py27ha863e18_1 requires python_abi 2.7.* *_cp27mu, but none of the providers can be installed - - nothing provides __cuda needed by tensorflow-2.10.0-cuda112py310he87a039_0 - - Could not solve for environment specs - The following packages are incompatible - [32mopenssl >=1.1.1w,<1.1.2a [0m is requested and can be installed; - [32mpysam >=0.16.0.1 [0m is installable with the potential options - [32mpysam [0.16.0.1|0.17.0|...|0.20.0][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.21.0][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpysam 0.21.0[0m would require - [31mopenssl >=3.1.0,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam 0.22.0[0m would require - [31mopenssl >=3.1.3,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam [0.22.0|0.22.1][0m would require - [31mopenssl >=3.2.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam 0.22.1[0m would require - [31mopenssl >=3.3.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because there are no viable options - [31mpython 3.11.0[0m would require - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.0[0m would require - [31mopenssl >=3.0.5,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.0[0m would require - [31mopenssl >=3.0.7,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython [3.11.1|3.11.2|3.11.3][0m would require - [31mopenssl >=3.1.0,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.4[0m would require - [31mopenssl >=3.1.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.5[0m would require - [31mopenssl >=3.1.2,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.6[0m would require - [31mopenssl >=3.1.3,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.7[0m would require - [31mopenssl >=3.2.0,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython [3.11.8|3.11.9][0m would require - [31mopenssl >=3.2.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpython_abi 3.11.* *_cp311[0m is not installable because it conflicts with any installable versions previously reported; - [32mtensorflow >=2.10,<2.11 [0m is installable with the potential options - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mtensorflow 2.10.0[0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [31mtensorflow 2.10.0[0m would require - [31m__cuda[0m, which is missing on the system. -# Last 100 lines of the build log. diff --git a/recipes/medaka/build_failure.osx-64.yaml b/recipes/medaka/build_failure.osx-64.yaml deleted file mode 100644 index 382a5d84d4aa9..0000000000000 --- a/recipes/medaka/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: fe8244e36e00fce9b146f015c871e6714fe382a6b7375f652967216782b9cb0f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |2- - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("openssl[version='>=3.0.0,<4.0a0']"), MatchSpec("libcurl==7.79.1=h97da3c1_1")} - Encountered problems while solving: - - package libcurl-7.79.1-h97da3c1_1 requires openssl >=3.0.0,<4.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - htslib >=1.14 is installable with the potential options - htslib [1.14|1.15|1.15.1] would require - libcurl [>=7.79.1,<8.0a0 |>=7.81.0,<8.0a0 |>=7.82.0,<8.0a0 ] with the potential options - libcurl [7.79.1|7.80.0|7.81.0|7.82.0] would require - openssl >=3.0.0,<4.0a0 , which can be installed; - libcurl [7.79.1|7.80.0|7.81.0|7.82.0] would require - openssl >=1.1.1l,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl 7.83.0 would require - openssl >=3.0.2,<4.0a0 , which can be installed; - libcurl 7.83.0 would require - openssl >=1.1.1n,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl 7.83.1 would require - openssl >=3.0.3,<4.0a0 , which can be installed; - libcurl 7.83.1 would require - openssl >=1.1.1o,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl [7.85.0|7.86.0] would require - openssl >=1.1.1q,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl [7.85.0|7.86.0] would require - openssl >=3.0.5,<4.0a0 , which can be installed; - libcurl 7.86.0 would require - openssl >=3.0.7,<4.0a0 , which can be installed; - libcurl [7.86.0|7.87.0] would require - krb5 >=1.20.1,<1.21.0a0 with the potential options - krb5 1.20.1 would require - openssl >=1.1.1s,<1.1.2a , which conflicts with any installable versions previously reported; - krb5 1.20.1 would require - openssl >=3.0.7,<4.0a0 , which can be installed; - openssl >=3.0.7,<4.0a0 , which can be installed; - libcurl [7.86.0|7.87.0] would require - openssl >=1.1.1s,<1.1.2a , which conflicts with any installable versions previously reported; - libcurl [7.88.0|7.88.1] would require - openssl >=3.0.8,<4.0a0 , which can be installed; - libcurl 7.88.1 would require - openssl >=3.1.0,<4.0a0 , which can be installed; - htslib [1.15.1|1.16] would require - libcurl >=7.83.1,<8.0a0 with the potential options - libcurl 7.83.1, which can be installed (as previously explained); - libcurl 7.83.1, which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which can be installed (as previously explained); - libcurl 7.86.0, which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which cannot be installed (as previously explained); - libcurl [7.88.0|7.88.1], which can be installed (as previously explained); - libcurl 7.88.1, which can be installed (as previously explained); - htslib 1.17 would require - libcurl >=8.0.1,<9.0a0 , which conflicts with any installable versions previously reported; - htslib 1.17 would require - libcurl >=7.88.1,<8.0a0 , which can be installed (as previously explained); - htslib 1.18 would require - libcurl >=8.2.0,<9.0a0 , which conflicts with any installable versions previously reported; - htslib [1.19|1.19.1] would require - libcurl >=8.5.0,<9.0a0 , which conflicts with any installable versions previously reported; - htslib 1.20 would require - libcurl >=8.7.1,<9.0a0 , which conflicts with any installable versions previously reported; - htslib 1.20 would require - libcurl >=8.8.0,<9.0a0 , which conflicts with any installable versions previously reported; - libcurl 7.* is installable with the potential options - libcurl [7.79.1|7.80.0|7.81.0|7.82.0], which can be installed (as previously explained); - libcurl [7.79.1|7.80.0|7.81.0|7.82.0], which cannot be installed (as previously explained); - libcurl 7.83.0, which can be installed (as previously explained); - libcurl 7.83.0, which cannot be installed (as previously explained); - libcurl 7.83.1, which can be installed (as previously explained); - libcurl 7.83.1, which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which cannot be installed (as previously explained); - libcurl [7.85.0|7.86.0], which can be installed (as previously explained); - libcurl 7.86.0, which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which can be installed (as previously explained); - libcurl [7.86.0|7.87.0], which cannot be installed (as previously explained); - libcurl [7.88.0|7.88.1], which can be installed (as previously explained); - libcurl 7.88.1, which can be installed (as previously explained); - libcurl [7.61.1|7.62.0|...|7.78.0], which can be installed; - openssl 1.1.1.* is not installable because it conflicts with any installable versions previously reported; - python 3.12.* *_cpython is installable with the potential options - python 3.12.0 would require - openssl >=3.1.3,<4.0a0 , which can be installed; - python 3.12.0rc3 would require - _python_rc, which does not exist (perhaps a missing channel); - python 3.12.1 would require - openssl >=3.2.0,<4.0a0 , which can be installed; - python [3.12.2|3.12.3] would require - openssl >=3.2.1,<4.0a0 , which can be installed. -# Last 100 lines of the build log. diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 5f88d62a844c5..e352e8b30e72f 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,14 +1,14 @@ -{% set name = "Medaka" %} +{% set name = "medaka" %} {% set version = "1.12.0" %} {% set sha256 = "039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6" %} # Bot PRs - Always review requirements.txt for new release package: - name: {{ name|lower }} + name: {{ name }} version: {{ version }} source: - url: https://github.com/nanoporetech/medaka/releases/download/v{{ version }}/medaka-{{ version }}.tar.gz + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/medaka-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patch @@ -25,8 +25,9 @@ build: requirements: build: - - {{ compiler('c') }} - - coreutils + - {{ compiler('cxx') }} + - cmake + - make host: - python - pip @@ -60,8 +61,6 @@ requirements: - bcftools >=1.14 - minimap2 >=2.17 - htslib >=1.14 - - libcurl - - openssl - wurlitzer test: @@ -74,14 +73,17 @@ test: - medaka_version_report about: - home: https://github.com/nanoporetech/medaka - summary: Neural network sequence error correction. - license: MPL-2.0 + home: "https://github.com/nanoporetech/medaka" + summary: "A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks." + license: "MPL-2.0" license_family: OTHER - license_file: LICENSE.md - dev_url: https://github.com/nanoporetech/medaka + license_file: "LICENSE.md" + dev_url: "https://github.com/nanoporetech/medaka" + doc_url: "https://github.com/nanoporetech/medaka/blob/master/README.md" extra: + additional-platforms: + - linux-aarch64 identifiers: - usegalaxy-eu:medaka_consensus - biotools:medaka From 476a685fac03f40d5b6ddba3085397839b3597ec Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Tue, 2 Jul 2024 11:14:55 +0300 Subject: [PATCH 3/5] medaka: Update libcurl to 8.x and openssl to 3.x Drop linux-aarch64 Signed-off-by: Martin Tzvetanov Grigorov --- recipes/medaka/conda_build_config.yaml | 4 ++-- recipes/medaka/meta.yaml | 2 -- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml index f45b292d8ac64..c11925f3b0d84 100644 --- a/recipes/medaka/conda_build_config.yaml +++ b/recipes/medaka/conda_build_config.yaml @@ -4,6 +4,6 @@ # lead solver conflicts in the future. Please review this on future # releases, especially if support for TensorFlow 2.11+ is added. libcurl: - - 7 + - 8 openssl: - - 1.1.1 + - 3 diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index e352e8b30e72f..0272e36f99cbf 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -82,8 +82,6 @@ about: doc_url: "https://github.com/nanoporetech/medaka/blob/master/README.md" extra: - additional-platforms: - - linux-aarch64 identifiers: - usegalaxy-eu:medaka_consensus - biotools:medaka From b98727cafe09e18b0e08e81b6244513f7b64addb Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 2 Jul 2024 12:11:31 +0300 Subject: [PATCH 4/5] Revert back to openssl 1.1.1 --- recipes/medaka/conda_build_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml index c11925f3b0d84..ebdb42545873b 100644 --- a/recipes/medaka/conda_build_config.yaml +++ b/recipes/medaka/conda_build_config.yaml @@ -6,4 +6,4 @@ libcurl: - 8 openssl: - - 3 + - 1.1.1 From c617fe62f839f7006d05fe037256fa0feba511a2 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jul 2024 14:06:02 +0000 Subject: [PATCH 5/5] Update medaka to 1.12.1 --- recipes/medaka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 0272e36f99cbf..197a10db806f1 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "medaka" %} -{% set version = "1.12.0" %} -{% set sha256 = "039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6" %} +{% set version = "1.12.1" %} +{% set sha256 = "df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf" %} # Bot PRs - Always review requirements.txt for new release package: