https://bugzilla.redhat.com/show_bug.cgi?id=1457453
Mattias Ellert <mattias.ell...@physics.uu.se> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |ASSIGNED
CC| |mattias.ell...@physics.uu.s
| |e
Assignee|nob...@fedoraproject.org |mattias.ell...@physics.uu.s
| |e
Flags| |fedora-review+
--- Comment #1 from Mattias Ellert <mattias.ell...@physics.uu.se> ---
Package Review
==============
Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
Issues:
=======
The build log shows several warninings about variables that may be
used without having been initialized:
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:880:6: warning: 'Roffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:878:6: warning: 'Loffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:1064:6: warning: 'Roffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:1062:6: warning: 'Loffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
Uninitialized variables can lead to random behaviour of the program,
so addressing these or reporting it upstream might be a good idea.
The log also shows several warnings about missing file links from the
documentaion generation. This is quite a long list, so I will not copy
it here. It is not critical, but if it can be fixed ...
APPROVED.
===== MUST items =====
C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[-]: Development (unversioned) .so files in -devel subpackage, if present.
Note: Unversioned so-files in private %_libdir subdirectory (see
attachment). Verify they are not in ld path.
This is not a developmen symlink.
This file is not in the default library path.
[-]: 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.
DESCRIPTION file states "License: Artistic-2.0".
No other license statements found in sources.
[-]: 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.
No license file in the sources.
[x]: License field in the package spec file matches the actual license.
Spec file states "License: Artistic 2.0".
[-]: License file installed when any subpackage combination is installed.
[x]: %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.
The Requires matches the Depends/Imports in the DESCRIPTION files
[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]: 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).
Complaints are false positives. (spelling, hidden files)
[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]: All build dependencies are listed in BuildRequires, except for any
that are listed in the exceptions section of Packaging Guidelines.
[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 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]: Large documentation must go in a -doc subpackage. Large could be size
(~1MB) or number of files.
Note: Documentation size is 0 bytes in 0 files.
[x]: Packages must not store files under /srv, /opt or /usr/local
R:
[x]: Package contains the mandatory BuildRequires.
[x]: The package has the standard %install section.
[x]: Package requires R-core.
===== 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).
[-]: 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.
[-]: Description and summary sections in the package spec file contains
translations for supported Non-English languages, if available.
[?]: Package should compile and build into binary rpms on all supported
architectures.
[?]: %check is present and all tests pass.
Checks are disbled due to missing test dependencies.
[-]: 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.
R:
[x]: The %check macro is present
[x]: Latest version is packaged.
Note: Latest upstream version is 1.12.1, packaged version is 1.12.1
===== 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).
Complaints are false positives. (spelling, hidden files)
[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: R-GenomicAlignments-1.12.1-1.fc27.x86_64.rpm
R-GenomicAlignments-debuginfo-1.12.1-1.fc27.x86_64.rpm
R-GenomicAlignments-1.12.1-1.fc27.src.rpm
R-GenomicAlignments.x86_64: W: spelling-error Summary(en_US) genomic -> gnomic,
ergonomic
R-GenomicAlignments.x86_64: W: spelling-error %description -l en_US genomic ->
gnomic, ergonomic
R-GenomicAlignments.x86_64: W: spelling-error %description -l en_US nucleotide
-> nucleation
R-GenomicAlignments.x86_64: W: hidden-file-or-dir /usr/lib/.build-id
R-GenomicAlignments.x86_64: W: hidden-file-or-dir /usr/lib/.build-id
R-GenomicAlignments.src: W: spelling-error Summary(en_US) genomic -> gnomic,
ergonomic
R-GenomicAlignments.src: W: spelling-error %description -l en_US genomic ->
gnomic, ergonomic
R-GenomicAlignments.src: W: spelling-error %description -l en_US nucleotide ->
nucleation
3 packages and 0 specfiles checked; 0 errors, 8 warnings.
Rpmlint (debuginfo)
-------------------
Checking: R-GenomicAlignments-debuginfo-1.12.1-1.fc27.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.
Rpmlint (installed packages)
----------------------------
sh: /usr/bin/python: No such file or directory
R-GenomicAlignments.x86_64: W: spelling-error Summary(en_US) genomic -> gnomic,
ergonomic
R-GenomicAlignments.x86_64: W: spelling-error %description -l en_US genomic ->
gnomic, ergonomic
R-GenomicAlignments.x86_64: W: spelling-error %description -l en_US nucleotide
-> nucleation
R-GenomicAlignments.x86_64: W: hidden-file-or-dir /usr/lib/.build-id
R-GenomicAlignments.x86_64: W: hidden-file-or-dir /usr/lib/.build-id
2 packages and 0 specfiles checked; 0 errors, 5 warnings.
Requires
--------
R-GenomicAlignments-debuginfo (rpmlib, GLIBC filtered):
R-GenomicAlignments (rpmlib, GLIBC filtered):
R-BiocGenerics
R-BiocParallel
R-Biostrings
R-GenomeInfoDb
R-GenomicRanges
R-IRanges
R-Rsamtools
R-S4Vectors
R-SummarizedExperiment
R-core
R-methods
R-stats
R-utils
libR.so()(64bit)
libc.so.6()(64bit)
rtld(GNU_HASH)
Provides
--------
R-GenomicAlignments-debuginfo:
R-GenomicAlignments-debuginfo
R-GenomicAlignments-debuginfo(x86-64)
R-GenomicAlignments:
R-GenomicAlignments
R-GenomicAlignments(x86-64)
Unversioned so-files
--------------------
R-GenomicAlignments:
/usr/lib64/R/library/GenomicAlignments/libs/GenomicAlignments.so
Source checksums
----------------
http://www.bioconductor.org/packages/release/bioc/src/contrib/GenomicAlignments_1.12.1.tar.gz
:
CHECKSUM(SHA256) this package :
90807b7de2a684d08a7e1b152138c52960f43a79d2f64de8c02512ed3548e688
CHECKSUM(SHA256) upstream package :
90807b7de2a684d08a7e1b152138c52960f43a79d2f64de8c02512ed3548e688
Generated by fedora-review 0.6.1 (f03e4e7) last change: 2016-05-02
Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1457453 -L
deps
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, R, Shell-api, C/C++
Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Perl, Haskell, PHP
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6
Built with local dependencies:
/home/ellert/R-GenomicAlignments/deps/R-S4Vectors-devel-0.14.3-1.fc27.x86_64.rpm
/home/ellert/R-GenomicAlignments/deps/R-GenomicRanges-1.28.3-1.fc27.x86_64.rpm
/home/ellert/R-GenomicAlignments/deps/R-Rsamtools-1.28.0-1.fc27.x86_64.rpm
/home/ellert/R-GenomicAlignments/deps/R-BiocParallel-1.10.1-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-GenomeInfoDbData-0.99.0-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-DelayedArray-0.2.7-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-SummarizedExperiment-1.6.3-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-lambda.r-1.1.9-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-Rsamtools-devel-1.28.0-1.fc27.x86_64.rpm
/home/ellert/R-GenomicAlignments/deps/R-GenomeInfoDb-1.12.1-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-futile.logger-1.4.3-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-snow-0.4.2-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-matrixStats-0.52.2-1.fc27.x86_64.rpm
/home/ellert/R-GenomicAlignments/deps/R-futile.options-1.0.0-1.fc27.noarch.rpm
/home/ellert/R-GenomicAlignments/deps/R-S4Vectors-0.14.3-1.fc27.x86_64.rpm
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