Bug 1457396

Summary:	Review Request: R-BiocParallel - Bioconductor facilities for parallel evaluation
Product:	[Fedora] Fedora	Reporter:	Tom "spot" Callaway <tcallawa>
Component:	Package Review	Assignee:	Mattias Ellert <mattias.ellert>
Status:	CLOSED ERRATA	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	medium	Docs Contact:
Priority:	medium
Version:	rawhide	CC:	mattias.ellert, package-review
Target Milestone:	---	Flags:	mattias.ellert: fedora-review+
Target Release:	---
Hardware:	All
OS:	Linux
Whiteboard:
Fixed In Version:		Doc Type:	If docs needed, set a value
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2017-06-21 12:19:49 UTC	Type:	---
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:
Bug Depends On:	1457390, 1457395
Bug Blocks:

Description Tom "spot" Callaway 2017-05-31 15:58:55 UTC

Spec URL: https://spot.fedorapeople.org/R-BiocParallel.spec
SRPM URL: https://spot.fedorapeople.org/R-BiocParallel-1.10.1-1.fc26.src.rpm
Description: 
This package provides modified versions and novel implementation of functions 
for parallel evaluation, tailored to use with Bioconductor objects.
Fedora Account System Username: spot

Comment 1 Mattias Ellert 2017-06-03 07:35:34 UTC

Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated


Issues:
=======

There are a few issues:

[!]: Package uses nothing in %doc for runtime.
     The DESCRIPTION file in an R package should not be tagged %doc
[!]: Requires correct, justified where necessary.
     The spec file lists texlive-latex in Requires and not in BuildRequires.
     It should be the other way around.
[!]: Final provides and requires are sane (see attachments).
     The Requires on texlive-latex does not make sense.

But these are minor and can easily be fixed before importing the
package, so there is no need for one more iteration of reviewing.

There are some warnings during the build during the html generation:

Rd warning: /builddir/build/BUILD/BiocParallel/BiocParallel/man/MulticoreParam-class.Rd:233: missing file link 'makeCluster'
Rd warning: /builddir/build/BUILD/BiocParallel/BiocParallel/man/SnowParam-class.Rd:272: missing file link 'makeCluster'
Rd warning: /builddir/build/BUILD/BiocParallel/BiocParallel/man/bpaggregate.Rd:47: missing file link 'simplify2array'
Rd warning: /builddir/build/BUILD/BiocParallel/BiocParallel/man/bpmapply.Rd:46: missing file link 'simplify2array'

Not critical, but if it can be fixed...

Approved.

===== MUST items =====

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.
     The DESCRIPTION file states "License: GPL-2 | GPL-3".
     No other license statements found in sources.
[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.
     No license file in sources.
[x]: License field in the package spec file matches the actual license.
     Spec file states "License: GPLv2 or GPLv3".
[-]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[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
[!]: Package uses nothing in %doc for runtime.
     The DESCRIPTION file in an R package should not be tagged %doc
[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.
[!]: Requires correct, justified where necessary.
     The spec file lists texlive-latex in Requires and not in BuildRequires.
     It should be the other way around.
     Otherwise matches the Imports in DESCRIPTION with R-methods added.
     (which looks correct sonce there are 'library(methods)' in the sources)
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[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).
     rpmlint complains about the spelling of Bioconductor - this can
     be ignored.
[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.
[!]: Final provides and requires are sane (see attachments).
     The Requires on texlive-latex does not make sense.
[?]: 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.
     The tests are disabled due to missing test requirements.
[-]: 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 1.10.1, packaged version is 1.10.1

===== EXTRA items =====

Generic:
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: R-BiocParallel-1.10.1-1.fc27.noarch.rpm
          R-BiocParallel-1.10.1-1.fc27.src.rpm
R-BiocParallel.noarch: W: spelling-error Summary(en_US) Bioconductor -> Bio conductor, Bio-conductor, Nonconductor
R-BiocParallel.src: W: spelling-error Summary(en_US) Bioconductor -> Bio conductor, Bio-conductor, Nonconductor
2 packages and 0 specfiles checked; 0 errors, 2 warnings.




Rpmlint (installed packages)
----------------------------
sh: /usr/bin/python: No such file or directory
R-BiocParallel.noarch: W: spelling-error Summary(en_US) Bioconductor -> Bio conductor, Bio-conductor, Nonconductor
1 packages and 0 specfiles checked; 0 errors, 1 warnings.



Requires
--------
R-BiocParallel (rpmlib, GLIBC filtered):
    /bin/sh
    R-core
    R-futile.logger
    R-methods
    R-parallel
    R-snow
    R-stats
    R-utils
    texlive-latex



Provides
--------
R-BiocParallel:
    R-BiocParallel



Source checksums
----------------
http://www.bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.10.1.tar.gz :
  CHECKSUM(SHA256) this package     : e06a6913390376507711abb0521fbc40727153d09bc20ef6399fdb347d77ad22
  CHECKSUM(SHA256) upstream package : e06a6913390376507711abb0521fbc40727153d09bc20ef6399fdb347d77ad22


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 1457396 -L deps
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, R, Shell-api
Disabled plugins: Java, C/C++, Python, fonts, SugarActivity, Ocaml, Perl, Haskell, PHP
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6

Built with local dependencies:
    /home/ellert/R-BiocParallel/deps/R-futile.logger-1.4.3-2.fc27.noarch.rpm
    /home/ellert/R-BiocParallel/deps/R-lambda.r-1.1.9-1.fc27.noarch.rpm
    /home/ellert/R-BiocParallel/deps/R-snow-0.4.2-1.fc27.noarch.rpm
    /home/ellert/R-BiocParallel/deps/R-futile.options-1.0.0-1.fc27.noarch.rpm

Comment 2 Gwyn Ciesla 2017-06-07 14:26:54 UTC

Package request has been approved: https://admin.fedoraproject.org/pkgdb/package/rpms/R-BiocParallel

Comment 3 Fedora Update System 2017-06-08 20:41:24 UTC

R-3.4.0-2.fc25 R-RCurl-1.95.4.8-1.fc25 R-Rcompression-0.93.2-15.fc25 R-XML-3.98.1.7-1.fc25 R-bitops-1.0.6-5.fc25 rkward-0.6.5-6.fc25 rpy-2.8.5-4.fc25 has been submitted as an update to Fedora 25. https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

Comment 4 Fedora Update System 2017-06-08 20:42:27 UTC

R-3.4.0-2.fc25 R-RCurl-1.95.4.8-1.fc25 R-Rcompression-0.93.2-15.fc25 R-XML-3.98.1.7-1.fc25 R-bitops-1.0.6-5.fc25 rkward-0.6.5-6.fc25 rpy-2.8.5-4.fc25 has been submitted as an update to Fedora 25. https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

Comment 5 Fedora Update System 2017-06-09 13:38:47 UTC

R-3.4.0-2.fc25, R-RCurl-1.95.4.8-1.fc25, R-Rcompression-0.93.2-15.fc25, R-XML-3.98.1.7-1.fc25, R-bitops-1.0.6-5.fc25, rkward-0.6.5-6.fc25, rpy-2.8.5-4.fc25 has been pushed to the Fedora 25 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

Comment 6 Fedora Update System 2017-06-09 16:20:00 UTC

R-3.4.0-2.fc25 R-BH-1.62.0.1-2.fc25 R-Biobase-2.36.2-1.fc25 R-BiocGenerics-0.22.0-1.fc25 R-BiocParallel-1.10.1-1.fc25 R-Biostrings-2.44.0-1.fc25 R-BufferedMatrix-1.40.0-1.fc25 R-BufferedMatrixMethods-1.40.0-1.fc25 R-DBI-0.6.1-1.fc25 R-DelayedArray-0.2.7-1.fc25 R-GenomeInfoDb-1.12.1-1.fc25 R-GenomeInfoDbData-0.99.0-1.fc25 R-GenomicAlignments-1.12.1-1.fc25 R-GenomicRanges-1.28.3-1.fc25 R-IRanges-2.10.1-1.fc25 R-R6-2.2.1-1.fc25 R-RCurl-1.95.4.8-1.fc25 R-RInside-0.2.14-2.fc25 R-RODBC-1.3.15-1.fc25 R-RSQLite-1.1.2-2.fc25 R-Rcompression-0.93.2-15.fc25 R-Rsamtools-1.28.0-1.fc25 R-Rsolid-0.9.31-20.fc25 R-S4Vectors-0.14.3-1.fc25 R-SummarizedExperiment-1.6.3-1.fc25 R-XML-3.98.1.7-1.fc25 R-XVector-0.16.0-1.fc25 R-acepack-1.4.1-2.fc25 R-affy-1.54.0-1.fc25 R-affyio-1.46.0-1.fc25 R-biglm-0.9.1-8.fc25 R-bitops-1.0.6-5.fc25 R-caTools-1.17.1-4.fc25 R-digest-0.6.12-1.fc25 R-expm-0.999.2-1.fc25 R-futile.logger-1.4.3-1.fc25 R-futile.options-1.0.0-1.fc25 R-highlight-0.4.7.1-2.fc25 R-lambda.r-1.1.9-1.fc25 R-littler-0.3.2-2.fc25 R-lmtest-0.9.35-1.fc25 R-maanova-1.46.1-1.fc25 R-magrittr-1.5-1.fc25 R-matrixStats-0.52.2-1.fc25 R-msm-1.6.4-1.fc25 R-multtest-2.32.0-1.fc25 R-mvtnorm-1.0.6-1.fc25 R-plogr-0.1.1-1.fc25 R-preprocessCore-1.38.1-1.fc25 R-qtl-1.40.8-3.fc25 R-rlecuyer-0.3.4-1.fc25 R-rtracklayer-1.36.3-1.fc25 R-snow-0.4.2-1.fc25 R-testthat-1.0.2-1.fc25 R-waveslim-1.7.5-4.fc25 R-wavethresh-4.6.8-1.fc25 rkward-0.6.5-6.fc25 rpy-2.8.5-4.fc25 has been submitted as an update to Fedora 25. https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

Comment 7 Fedora Update System 2017-06-10 12:34:06 UTC

R-3.4.0-2.fc25, R-BH-1.62.0.1-2.fc25, R-Biobase-2.36.2-1.fc25, R-BiocGenerics-0.22.0-1.fc25, R-BiocParallel-1.10.1-1.fc25, R-Biostrings-2.44.0-1.fc25, R-BufferedMatrix-1.40.0-1.fc25, R-BufferedMatrixMethods-1.40.0-1.fc25, R-DBI-0.6.1-1.fc25, R-DelayedArray-0.2.7-1.fc25, R-GenomeInfoDb-1.12.1-1.fc25, R-GenomeInfoDbData-0.99.0-1.fc25, R-GenomicAlignments-1.12.1-1.fc25, R-GenomicRanges-1.28.3-1.fc25, R-IRanges-2.10.1-1.fc25, R-R6-2.2.1-1.fc25, R-RCurl-1.95.4.8-1.fc25, R-RInside-0.2.14-2.fc25, R-RODBC-1.3.15-1.fc25, R-RSQLite-1.1.2-2.fc25, R-Rcompression-0.93.2-15.fc25, R-Rsamtools-1.28.0-1.fc25, R-Rsolid-0.9.31-20.fc25, R-S4Vectors-0.14.3-1.fc25, R-SummarizedExperiment-1.6.3-1.fc25, R-XML-3.98.1.7-1.fc25, R-XVector-0.16.0-1.fc25, R-acepack-1.4.1-2.fc25, R-affy-1.54.0-1.fc25, R-affyio-1.46.0-1.fc25, R-biglm-0.9.1-8.fc25, R-bitops-1.0.6-5.fc25, R-caTools-1.17.1-4.fc25, R-digest-0.6.12-1.fc25, R-expm-0.999.2-1.fc25, R-futile.logger-1.4.3-1.fc25, R-futile.options-1.0.0-1.fc25, R-highlight-0.4.7.1-2.fc25, R-lambda.r-1.1.9-1.fc25, R-littler-0.3.2-2.fc25, R-lmtest-0.9.35-1.fc25, R-maanova-1.46.1-1.fc25, R-magrittr-1.5-1.fc25, R-matrixStats-0.52.2-1.fc25, R-msm-1.6.4-1.fc25, R-multtest-2.32.0-1.fc25, R-mvtnorm-1.0.6-1.fc25, R-plogr-0.1.1-1.fc25, R-preprocessCore-1.38.1-1.fc25, R-qtl-1.40.8-3.fc25, R-rlecuyer-0.3.4-1.fc25, R-rtracklayer-1.36.3-1.fc25, R-snow-0.4.2-1.fc25, R-testthat-1.0.2-1.fc25, R-waveslim-1.7.5-4.fc25, R-wavethresh-4.6.8-1.fc25, rkward-0.6.5-6.fc25, rpy-2.8.5-4.fc25 has been pushed to the Fedora 25 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

Comment 8 Fedora Update System 2017-06-21 12:19:49 UTC

R-3.4.0-2.fc25, R-BH-1.62.0.1-2.fc25, R-Biobase-2.36.2-1.fc25, R-BiocGenerics-0.22.0-1.fc25, R-BiocParallel-1.10.1-1.fc25, R-Biostrings-2.44.0-1.fc25, R-BufferedMatrix-1.40.0-1.fc25, R-BufferedMatrixMethods-1.40.0-1.fc25, R-DBI-0.6.1-1.fc25, R-DelayedArray-0.2.7-1.fc25, R-GenomeInfoDb-1.12.1-1.fc25, R-GenomeInfoDbData-0.99.0-1.fc25, R-GenomicAlignments-1.12.1-1.fc25, R-GenomicRanges-1.28.3-1.fc25, R-IRanges-2.10.1-1.fc25, R-R6-2.2.1-1.fc25, R-RCurl-1.95.4.8-1.fc25, R-RInside-0.2.14-2.fc25, R-RODBC-1.3.15-1.fc25, R-RSQLite-1.1.2-2.fc25, R-Rcompression-0.93.2-15.fc25, R-Rsamtools-1.28.0-1.fc25, R-Rsolid-0.9.31-20.fc25, R-S4Vectors-0.14.3-1.fc25, R-SummarizedExperiment-1.6.3-1.fc25, R-XML-3.98.1.7-1.fc25, R-XVector-0.16.0-1.fc25, R-acepack-1.4.1-2.fc25, R-affy-1.54.0-1.fc25, R-affyio-1.46.0-1.fc25, R-biglm-0.9.1-8.fc25, R-bitops-1.0.6-5.fc25, R-caTools-1.17.1-4.fc25, R-digest-0.6.12-1.fc25, R-expm-0.999.2-1.fc25, R-futile.logger-1.4.3-1.fc25, R-futile.options-1.0.0-1.fc25, R-highlight-0.4.7.1-2.fc25, R-lambda.r-1.1.9-1.fc25, R-littler-0.3.2-2.fc25, R-lmtest-0.9.35-1.fc25, R-maanova-1.46.1-1.fc25, R-magrittr-1.5-1.fc25, R-matrixStats-0.52.2-1.fc25, R-msm-1.6.4-1.fc25, R-multtest-2.32.0-1.fc25, R-mvtnorm-1.0.6-1.fc25, R-plogr-0.1.1-1.fc25, R-preprocessCore-1.38.1-1.fc25, R-qtl-1.40.8-3.fc25, R-rlecuyer-0.3.4-1.fc25, R-rtracklayer-1.36.3-1.fc25, R-snow-0.4.2-1.fc25, R-testthat-1.0.2-1.fc25, R-waveslim-1.7.5-4.fc25, R-wavethresh-4.6.8-1.fc25, rkward-0.6.5-6.fc25, rpy-2.8.5-4.fc25 has been pushed to the Fedora 25 stable repository. If problems still persist, please make note of it in this bug report.