Spec URL: https://ankursinha.fedorapeople.org/catch22/catch22.spec SRPM URL: https://ankursinha.fedorapeople.org/catch22/catch22-0.2.1-1.fc34.src.rpm Description: catch22 is a collection of 22 time-series features coded in C that can be run from Python, R, Matlab, and Julia. The catch22 features are a high-performing subset of the over 7000 features in hctsa. Features were selected based on their classification performance across a collection of 93 real-world time-series classification problems, as described in our open-access paper: - Lubba et al. (2019). catch22: CAnonical Time-series CHaracteristics (https://doi.org/10.1007/s10618-019-00647-x) The computational pipeline used to generate the catch22 feature set is in the op_importance(https://github.com/chlubba/op_importance) repository. For catch22-related information and resources, including a list of publications using catch22, see the catch22 wiki (https://github.com/chlubba/catch22/wiki). Fedora Account System Username:
I will take this review.
Running fedora-review against the F34 repo, because the Rawhide repo appears to be a bit broken at the moment. Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated ===== Issues ==== - I'm struggling a bit with the license. - LICENSE contains the text of GPLv3 - wrap_Python/setup{,_P3}.py both identify the license as GPLv3 - wrap_R/catch22/DESCRIPTION identifies the license as GPLv2+ - All *.m files under Matlab identify the license as GPLv3+ Does this imply that the license for the main package and the python wrapper are GPLv3, but the R wrapper is GPLv2+, and the octave interface (not currently built) is GPLv3+? - The python3 and R subpackages do not require the main package, so need to contain a copy of the license file. - The gcc invocation near the top of %build both compiles and links, so $LDFLAGS should be passed to gcc as well as $CFLAGS. - Regarding the SHOULD item "Packages should try to preserve timestamps of original installed files", add -p to the cp invocations in %prep. - rpmlint says: R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/AnIndex R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/catch22.rdb Did something fail to be generated correctly? ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Development (unversioned) .so files in -devel subpackage, if present. [x]: If your application is a C or C++ application you must list a BuildRequires against gcc, gcc-c++ or clang. [x]: Header files in -devel subpackage, if present. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [!]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Unknown or generated", "GNU General Public License v3.0 or later", "*No copyright* GNU General Public License, Version 3". 165 files have unknown license. Not sure about this. See the first entry in "Issues" above. [!]: License file installed when any subpackage combination is installed. [!]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [-]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [x]: Useful -debuginfo package or justification otherwise. [x]: Package is not known to require an ExcludeArch tag. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 10240 bytes in 1 files. [x]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package must not depend on deprecated() packages. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local Python: [x]: Python eggs must not download any dependencies during the build process. [x]: A package which is used by another package via an egg interface should provide egg info. [x]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Packages MUST NOT have dependencies (either build-time or runtime) on packages named with the unversioned python- prefix unless no properly versioned package exists. Dependencies on Python packages instead MUST use names beginning with python2- or python3- as appropriate. [x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files [x]: Binary eggs must be removed in %prep ===== SHOULD items ===== Generic: [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [x]: Fully versioned dependency in subpackages if applicable. [?]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: Sources are verified with gpgverify first in %prep if upstream publishes signatures. Note: gpgverify is not used. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [!]: Packages should try to preserve timestamps of original installed files. [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [x]: Rpmlint is run on debuginfo package(s). Note: No rpmlint messages. [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: catch22-0.2.1-1.fc34.x86_64.rpm python3-catch22-0.2.1-1.fc34.x86_64.rpm R-catch22-0.2.1-1.fc34.x86_64.rpm catch22-debuginfo-0.2.1-1.fc34.x86_64.rpm catch22-debugsource-0.2.1-1.fc34.x86_64.rpm catch22-0.2.1-1.fc34.src.rpm catch22.x86_64: W: spelling-error Summary(en_US) CAnonical -> Canonical catch22.x86_64: W: spelling-error %description -l en_US hctsa -> sachet catch22.x86_64: W: spelling-error %description -l en_US et -> ET, wt, rt catch22.x86_64: W: spelling-error %description -l en_US al -> AL, la, Al catch22.x86_64: W: spelling-error %description -l en_US CAnonical -> Canonical catch22.x86_64: W: spelling-error %description -l en_US https -> HTTP catch22.x86_64: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub catch22.x86_64: W: spelling-error %description -l en_US chlubba -> clubbable catch22.x86_64: W: no-manual-page-for-binary run_features python3-catch22.x86_64: W: summary-not-capitalized C catch22 for Python python3-catch22.x86_64: W: spelling-error %description -l en_US hctsa -> sachet python3-catch22.x86_64: W: spelling-error %description -l en_US et -> ET, wt, rt python3-catch22.x86_64: W: spelling-error %description -l en_US al -> AL, la, Al python3-catch22.x86_64: W: spelling-error %description -l en_US CAnonical -> Canonical python3-catch22.x86_64: W: spelling-error %description -l en_US https -> HTTP python3-catch22.x86_64: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub python3-catch22.x86_64: W: spelling-error %description -l en_US chlubba -> clubbable python3-catch22.x86_64: W: no-documentation R-catch22.x86_64: W: summary-not-capitalized C catch22 for R R-catch22.x86_64: W: spelling-error %description -l en_US hctsa -> sachet R-catch22.x86_64: W: spelling-error %description -l en_US et -> ET, wt, rt R-catch22.x86_64: W: spelling-error %description -l en_US al -> AL, la, Al R-catch22.x86_64: W: spelling-error %description -l en_US CAnonical -> Canonical R-catch22.x86_64: W: spelling-error %description -l en_US https -> HTTP R-catch22.x86_64: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub R-catch22.x86_64: W: spelling-error %description -l en_US chlubba -> clubbable R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/AnIndex R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/catch22.rdb catch22.src: W: spelling-error Summary(en_US) CAnonical -> Canonical catch22.src: W: spelling-error %description -l en_US hctsa -> sachet catch22.src: W: spelling-error %description -l en_US et -> ET, wt, rt catch22.src: W: spelling-error %description -l en_US al -> AL, la, Al catch22.src: W: spelling-error %description -l en_US CAnonical -> Canonical catch22.src: W: spelling-error %description -l en_US https -> HTTP catch22.src: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub catch22.src: W: spelling-error %description -l en_US chlubba -> clubbable 6 packages and 0 specfiles checked; 2 errors, 34 warnings. Rpmlint (debuginfo) ------------------- Checking: catch22-debuginfo-0.2.1-1.fc34.x86_64.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings. Rpmlint (installed packages) ---------------------------- catch22.x86_64: W: spelling-error Summary(en_US) CAnonical -> Canonical catch22.x86_64: W: spelling-error %description -l en_US hctsa -> sachet catch22.x86_64: W: spelling-error %description -l en_US et -> ET, wt, rt catch22.x86_64: W: spelling-error %description -l en_US al -> AL, la, Al catch22.x86_64: W: spelling-error %description -l en_US CAnonical -> Canonical catch22.x86_64: W: spelling-error %description -l en_US https -> HTTP catch22.x86_64: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub catch22.x86_64: W: spelling-error %description -l en_US chlubba -> clubbable catch22.x86_64: W: no-manual-page-for-binary run_features python3-catch22.x86_64: W: summary-not-capitalized C catch22 for Python python3-catch22.x86_64: W: spelling-error %description -l en_US hctsa -> sachet python3-catch22.x86_64: W: spelling-error %description -l en_US et -> ET, wt, rt python3-catch22.x86_64: W: spelling-error %description -l en_US al -> AL, la, Al python3-catch22.x86_64: W: spelling-error %description -l en_US CAnonical -> Canonical python3-catch22.x86_64: W: spelling-error %description -l en_US https -> HTTP python3-catch22.x86_64: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub python3-catch22.x86_64: W: spelling-error %description -l en_US chlubba -> clubbable python3-catch22.x86_64: W: no-documentation R-catch22.x86_64: W: summary-not-capitalized C catch22 for R R-catch22.x86_64: W: spelling-error %description -l en_US hctsa -> sachet R-catch22.x86_64: W: spelling-error %description -l en_US et -> ET, wt, rt R-catch22.x86_64: W: spelling-error %description -l en_US al -> AL, la, Al R-catch22.x86_64: W: spelling-error %description -l en_US CAnonical -> Canonical R-catch22.x86_64: W: spelling-error %description -l en_US https -> HTTP R-catch22.x86_64: W: spelling-error %description -l en_US github -> git hub, git-hub, GitHub R-catch22.x86_64: W: spelling-error %description -l en_US chlubba -> clubbable R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/AnIndex R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/catch22.rdb 5 packages and 0 specfiles checked; 2 errors, 26 warnings. Unversioned so-files -------------------- python3-catch22: /usr/lib64/python3.9/site-packages/catch22_C.cpython-39-x86_64-linux-gnu.so R-catch22: /usr/lib64/R/library/catch22/libs/catch22.so Source checksums ---------------- https://github.com/chlubba/catch22/archive/v0.2.1/catch22-0.2.1.tar.gz : CHECKSUM(SHA256) this package : 06c1f89a647021552389123897e6ee66c12570736cc53ed64a7a0ff7af597516 CHECKSUM(SHA256) upstream package : 06c1f89a647021552389123897e6ee66c12570736cc53ed64a7a0ff7af597516 Requires -------- catch22 (rpmlib, GLIBC filtered): libc.so.6()(64bit) libm.so.6()(64bit) rtld(GNU_HASH) python3-catch22 (rpmlib, GLIBC filtered): libc.so.6()(64bit) python(abi) rtld(GNU_HASH) R-catch22 (rpmlib, GLIBC filtered): R(ABI) R(Rcpp) R-core libR.so()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libm.so.6()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) rtld(GNU_HASH) catch22-debuginfo (rpmlib, GLIBC filtered): catch22-debugsource (rpmlib, GLIBC filtered): Provides -------- catch22: catch22 catch22(x86-64) python3-catch22: python-catch22 python3-catch22 python3-catch22(x86-64) python3.9-catch22 python3.9dist(catch22) python3dist(catch22) R-catch22: R(catch22) R-catch22 R-catch22(x86-64) catch22-debuginfo: catch22-debuginfo catch22-debuginfo(x86-64) debuginfo(build-id) catch22-debugsource: catch22-debugsource catch22-debugsource(x86-64) Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10 Command line :/usr/bin/fedora-review -b 1980562 -m fedora-34-x86_64 Buildroot used: fedora-34-x86_64 Active plugins: Shell-api, Generic, Python, C/C++ Disabled plugins: SugarActivity, R, Ocaml, fonts, Ruby, Haskell, Java, Perl, PHP Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH
(In reply to Jerry James from comment #2) > Running fedora-review against the F34 repo, because the Rawhide repo appears > to be a bit broken at the moment. Thanks for your review, Jerry. Upstream says the native R package should be preferred to the wrapper here, so I've dropped the R sub-package and I'll package that separately: https://cran.r-project.org/web/packages/Rcatch22/index.html > Package Review > ============== > > Legend: > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated > > ===== Issues ==== > > - I'm struggling a bit with the license. > - LICENSE contains the text of GPLv3 > - wrap_Python/setup{,_P3}.py both identify the license as GPLv3 > - wrap_R/catch22/DESCRIPTION identifies the license as GPLv2+ > - All *.m files under Matlab identify the license as GPLv3+ > > Does this imply that the license for the main package and the python > wrapper > are GPLv3, but the R wrapper is GPLv2+, and the octave interface (not > currently built) is GPLv3+? It would appear so. I've added licenses to each sub-package now to make it clearer. > > - The python3 and R subpackages do not require the main package, so need to > contain a copy of the license file. Fixed > > - The gcc invocation near the top of %build both compiles and links, so > $LDFLAGS should be passed to gcc as well as $CFLAGS. Fixed > > - Regarding the SHOULD item "Packages should try to preserve timestamps of > original installed files", add -p to the cp invocations in %prep. Fixed. > > - rpmlint says: > R-catch22.x86_64: E: zero-length /usr/lib64/R/library/catch22/help/AnIndex > R-catch22.x86_64: E: zero-length > /usr/lib64/R/library/catch22/help/catch22.rdb > > Did something fail to be generated correctly? > R package dropped. Updated spec/srpm: Spec URL: https://ankursinha.fedorapeople.org/catch22/catch22.spec SRPM URL: https://ankursinha.fedorapeople.org/catch22/catch22-0.2.1-1.fc34.src.rpm * Mon Aug 09 2021 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.1-1 - Add sub-package specific licenses - Add LDFLAGS - Preserve time stamps - Remove R sub-package: package Rcatch22 separately - Run python test - Add basic C test
That looks good. This package is APPROVED. One little nitpick: when you import, please put $LDFLAGS *before* -lm. That way -Wl,--as-needed applies to -lm. With the ongoing absorption of libm into libc, this will drop the libm dependency if at some future time all of the needed symbols have been moved to libc.
(fedscm-admin): The Pagure repository was created at https://src.fedoraproject.org/rpms/catch22
FEDORA-2021-22dea00fcf has been submitted as an update to Fedora 34. https://bodhi.fedoraproject.org/updates/FEDORA-2021-22dea00fcf
FEDORA-2021-22dea00fcf has been pushed to the Fedora 34 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2021-22dea00fcf \*` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2021-22dea00fcf See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2021-22dea00fcf has been pushed to the Fedora 34 stable repository. If problem still persists, please make note of it in this bug report.