Attachment 903360 Details for Bug 1105920 – build.log

build.log

<fdopen> (text/plain), 8.63 KB, created by Dennis Gilmore on 2014-06-09 02:05:28 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Dennis Gilmore

Created: 2014-06-09 02:05:28 UTC

Size: 8.63 KB

patch

obsolete

>Mock Version: 1.1.39
>Mock Version: 1.1.39
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-affy.spec'], False, '/var/lib/mock/f21-build-2109141-392789/root/', None, 86400, True, False, 1000, 425, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}, logger=<mockbuild.trace_decorator.getLog object at 0x25c6b90>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-affy.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}
>warning: bogus date in %changelog: Sun Aug 31 2009 pingou <pingou@pingoured.fr> 1.22.1-3
>warning: Could not canonicalize hostname: buildvm-08.phx2.fedoraproject.org
>Building target platforms: x86_64
>Building for target x86_64
>Wrote: /builddir/build/SRPMS/R-affy-1.40.0-2.fc21.src.rpm
>Child return code was: 0
>LEAVE do --> 
>
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps  builddir/build/SPECS/R-affy.spec'], False, '/var/lib/mock/f21-build-2109141-392789/root/', None, 86400, True, False, 1000, 425, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}, logger=<mockbuild.trace_decorator.getLog object at 0x25c6b90>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps  builddir/build/SPECS/R-affy.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}
>warning: bogus date in %changelog: Sun Aug 31 2009 pingou <pingou@pingoured.fr> 1.22.1-3
>Building target platforms: x86_64
>Building for target x86_64
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.uoeZ2Y
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd /builddir/build/BUILD
>+ rm -rf affy
>+ /usr/bin/mkdir -p affy
>+ cd affy
>+ /usr/bin/tar -xf -
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/affy_1.40.0.tar.gz
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ sed -i '/importFrom(zlibbioc)/d' affy/NAMESPACE
>+ sed -i '/importFrom(BiocInstaller, biocinstallRepos)/d' affy/NAMESPACE
>+ sed -i '/import(zlibbioc)/d' affy/NAMESPACE
>+ sed -i -e s/BiocInstaller,// affy/DESCRIPTION
>+ sed -i '/        zlibbioc/d' affy/DESCRIPTION
>+ cat affy/DESCRIPTION affy/NAMESPACE
>Package: affy
>Version: 1.40.0
>Title: Methods for Affymetrix Oligonucleotide Arrays
>Author: Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier
>        <lgautier@gmail.com>, Benjamin Milo Bolstad
>        <bmb@bmbolstad.com>, and Crispin Miller
>        <cmiller@picr.man.ac.uk> with contributions from Magnus
>        Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope
>        <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad
>        Halling <challing@agilixcorp.com>, Wolfgang Huber, James
>        MacDonald <jmacdon@med.umich.edu>, Benjamin I. P. Rubinstein,
>        Christopher Workman <workman@cbs.dtu.dk>, John Zhang
>Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
>Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
>Imports: affyio (>= 1.13.3),  graphics, grDevices,
>        methods, preprocessCore, stats, utils, zlibbioc
>Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools
>LinkingTo: preprocessCore
>Description: The package contains functions for exploratory
>        oligonucleotide array analysis. The dependence on tkWidgets
>        only concerns few convenience functions. 'affy' is fully
>        functional without it.
>License: LGPL (>= 2.0)
>Collate: ProgressBarText.R ppset.ttest.R ppsetApply.R expressoWidget.R
>        getCDFenv.R AffyRNAdeg.R avdiff.R barplot.ProbeSet.R
>        bg.Affy.chipwide.R bg.R expresso.R fit.li.wong.R
>        generateExprVal.method.avgdiff.R
>        generateExprVal.method.liwong.R generateExprVal.method.mas.R
>        generateExprVal.method.medianpolish.R
>        generateExprVal.method.playerout.R hlog.R justrma.R
>        loess.normalize.R maffy.R mas5.R merge.AffyBatch.R
>        normalize.constant.R normalize.contrasts.R
>        normalize.invariantset.R normalize.loess.R normalize.qspline.R
>        normalize.quantiles.R pairs.AffyBatch.R plot.density.R
>        plotLocation.R plot.ProbeSet.R pmcorrect.mas.R AffyBatch.R
>        mva.pairs.R ProbeSet.R read.affybatch.R rma.R summary.R
>        tukey.biweight.R whatcdf.R xy2indices.R zzz.R
>biocViews: Microarray, OneChannel, Preprocessing
>LazyLoad: yes
>Packaged: 2013-10-15 03:16:40 UTC; biocbuild
>useDynLib("affy")
>importFrom(BiocGenerics, updateObject, colnames, boxplot, image)
>import(affyio)
>importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
>                  Versioned, VersionedBiobase, Versions)
>importClassesFrom(methods, ANY, character, environment, integer,
>                  matrix, missing, numeric)
>importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
>                  assayData, classVersion, "classVersion<-",
>                  description, "description<-", experimentData, exprs,
>                  "exprs<-", featureNames, "featureNames<-",
>                  isCurrent, isVersioned,
>		  notes,
>                  "notes<-", pData, "pData<-", phenoData,
>                  "phenoData<-", preproc, "preproc<-", protocolData,
>                  "protocolData<-", rowMedians, sampleNames, "sampleNames<-",
>                  se.exprs, "se.exprs<-")
>importMethodsFrom(methods, initialize, show)
>importFrom(Biobase, addVigs2WinMenu, assayDataElementReplace,
>           assayDataNew, multiassign, read.AnnotatedDataFrame,
>           read.MIAME, testBioCConnection)
>importMethodsFrom(BiocGenerics, normalize)
>importFrom(graphics, abline, axis, barplot, frame, hist,
>           lines, matplot, mtext, pairs, par, plot, points,
>           smoothScatter, text)
>importFrom(grDevices, dev.interactive, gray)
>importFrom(methods, as, callNextMethod, getMethod, is, new,
>           slot)
>importFrom(preprocessCore, normalize.quantiles,
>           normalize.quantiles.robust, rma.background.correct)
>importFrom(stats, approx, density, IQR, lm, loess, loess.control,
>           median, medpolish, model.response, model.weights, optim,
>           pnorm, predict, quantile, runif, sd, smooth.spline,
>           splinefun, t.test, terms, var, wilcox.test)
>importFrom(utils, available.packages, contrib.url, data, flush.console,
>           install.packages, object.size)
>##export everything that does not start with a .
>exportPattern("^[^\\.]")
>export(.setAffyOptions)
>exportMethods(show, boxplot, image, exprs, featureNames, geneNames, sampleNames,
>              se.exprs, updateObject)
>exportClasses("AffyBatch")
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.npVp9l
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.3q2ggJ
>+ exit 0
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd affy
>+ exit 0
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64
>++ dirname /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64
>+ cd affy
>+ rm -rf /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64
>+ mkdir -p /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64/usr/lib64/R/library
>+ R CMD INSTALL affy -l /builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64/usr/lib64/R/library
>ERROR: dependency 'zlibbioc' is not available for package 'affy'
>* removing '/builddir/build/BUILDROOT/R-affy-1.40.0-2.fc21.x86_64/usr/lib64/R/library/affy'
>error: Bad exit status from /var/tmp/rpm-tmp.3q2ggJ (%install)
>RPM build errors:
>    bogus date in %changelog: Sun Aug 31 2009 pingou <pingou@pingoured.fr> 1.22.1-3
>    Bad exit status from /var/tmp/rpm-tmp.3q2ggJ (%install)
>Child return code was: 1
>EXCEPTION: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps  builddir/build/SPECS/R-affy.spec']
>Traceback (most recent call last):
>  File "/usr/lib/python2.7/site-packages/mockbuild/trace_decorator.py", line 70, in trace
>    result = func(*args, **kw)
>  File "/usr/lib/python2.7/site-packages/mockbuild/util.py", line 376, in do
>    raise mockbuild.exception.Error, ("Command failed. See logs for output.\n # %s" % (command,), child.returncode)
>Error: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps  builddir/build/SPECS/R-affy.spec']
>LEAVE do --> EXCEPTION RAISED
>

Actions: View

Attachments on bug 1105920: 903360 | 903361 | 903362