Mock Version: 1.4.14
Mock Version: 1.4.14
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-affy.spec'], chrootPath='/var/lib/mock/f31-build-97182-32906/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x15580c0da0>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-affy.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1565568000
Wrote: /builddir/build/SRPMS/R-affy-1.58.0-5.fc31.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-affy.spec'], chrootPath='/var/lib/mock/f31-build-97182-32906/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x15580c0da0>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-affy.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1565568000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.agQxak
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf affy
+ /usr/bin/mkdir -p affy
+ cd affy
+ /usr/bin/gzip -dc /builddir/build/SOURCES/affy_1.58.0.tar.gz
+ /usr/bin/tar -xof -
+ 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 -e s/zlibbioc// affy/DESCRIPTION
+ cat affy/DESCRIPTION affy/NAMESPACE
Package: affy
Version: 1.58.0
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@u.washington.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, 
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
NeedsCompilation: yes
Packaged: 2018-04-30 22:44:25 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.ukgDzj
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
+ umask 022
+ cd /builddir/build/BUILD
+ cd affy
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.LuMuRk
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64
+ cd affy
+ rm -rf /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64
+ mkdir -p /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64/usr/lib64/R/library
+ R CMD INSTALL affy -l /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64/usr/lib64/R/library
BUILDSTDERR: * installing *source* package 'affy' ...
BUILDSTDERR: ** using staged installation
BUILDSTDERR: ** libs
BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64/usr/lib64/R/library/00LOCK-affy/00new/affy/libs
BUILDSTDERR: ** R
BUILDSTDERR: ** data
BUILDSTDERR: ** demo
BUILDSTDERR: ** inst
BUILDSTDERR: ** byte-compile and prepare package for lazy loading
BUILDSTDERR: ** help
BUILDSTDERR: *** installing help indices
BUILDSTDERR:     finding HTML links ... done
BUILDSTDERR:     finding level-2 HTML links ... done
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
gcc -I"/usr/include/R" -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/lib64/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c chipbackground.c -o chipbackground.o
gcc -I"/usr/include/R" -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/lib64/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c getall_locations.c -o getall_locations.o
gcc -I"/usr/include/R" -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/lib64/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c mas5calls.c -o mas5calls.o
gcc -I"/usr/include/R" -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/lib64/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c rma2.c -o rma2.o
gcc -I"/usr/include/R" -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/lib64/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection  -c rma_common.c -o rma_common.o
gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/usr/lib64/R/lib -lR
  converting help for package 'affy'
    AffyBatch-class                         html  
    AffyRNAdeg                              html  
    MAplot                                  html  
    ProbeSet-class                          html  
    ProgressBarText-class                   html  
    SpikeIn                                 html  
    affy-deprecated                         html  
    affy-options                            html  
    affy.scalevalue.exprSet                 html  
    barplot.ProbeSet                        html  
    bg.adjust                               html  
    bgc                                     html  
    cdfFromBioC                             html  
    cdfenv.example                          html  
    cleancdfname                            html  
    debug.affy123                           html  
    expresso                                html  
    expressoWidget                          html  
    fit.li.wong                             html  
    generateExprSet-methods                 html  
    generateExprVal-methods                 html  
    generateExprVal.method.avgdiff          html  
    generateExprVal.method.playerout        html  
    hlog                                    html  
    justrma                                 html  
BUILDSTDERR:     list.celfil** building package indices
BUILDSTDERR: ** installing vignettes
BUILDSTDERR: ** testing if installed package can be loaded from temporary location
BUILDSTDERR: ** checking absolute paths in shared objects and dynamic libraries
BUILDSTDERR: ** testing if installed package can be loaded from final location
BUILDSTDERR: ** testing if installed package keeps a record of temporary installation path
BUILDSTDERR: * DONE (affy)
+ test -d affy/src
+ cd affy/src
+ rm -f chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o affy.so
+ rm -rf /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64/usr/lib64/R/library/R.css
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.58.0-5.fc31 --unique-debug-suffix -1.58.0-5.fc31.riscv64 --unique-debug-src-base R-affy-1.58.0-5.fc31.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/affy
BUILDSTDERR: 82 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
es                           html  
    maffy.subset                            html  
    mas5                                    html  
    mas5calls                               html  
    merge.AffyBatch                         html  
    mva.pairs                               html  
    normalize-methods                       html  
    normalize.constant                      html  
    normalize.contrast                      html  
    normalize.invariantset                  html  
    normalize.loess                         html  
    normalize.qspline                       html  
    normalize.quantiles                     html  
    normalize.quantiles.robust              html  
    pairs.AffyBatch                         html  
    plot.ProbeSet                           html  
    plot.density                            html  
    plotLocation                            html  
    pmcorrect                               html  
    ppsetApply                              html  
    probeMatch-methods                      html  
    probeNames-methods                      html  
    read.affybatch                          html  
    read.probematrix                        html  
    rma                                     html  
    setAffyOptions                          html  
    summary                                 html  
    tukey.biweight                          html  
    whatcdf                                 html  
    xy2indices                              html  
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64/usr/lib64/R/library/affy/libs/affy.so
extracting debug info from /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64/usr/lib64/R/library/affy/libs/affy.so
original debug info size: 196kB, size after compression: 188kB
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.gKejmk
+ umask 022
+ cd /builddir/build/BUILD
+ cd affy
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Processing files: R-affy-1.58.0-5.fc31.riscv64
Provides: R(affy) = 1.58.0 R-affy = 1.58.0-5.fc31 R-affy(riscv-64) = 1.58.0-5.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(Biobase) >= 2.5.5 R(BiocGenerics) >= 0.1.12 R(affyio) >= 1.13.3 R(grDevices) R(graphics) R(methods) R(preprocessCore) R(stats) R(utils) R-core >= 2.8.0 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) rtld(GNU_HASH)
Suggests: R(affydata) R(tkWidgets) >= 1.19.0 R(widgetTools)
Processing files: R-affy-debugsource-1.58.0-5.fc31.riscv64
Provides: R-affy-debugsource = 1.58.0-5.fc31 R-affy-debugsource(riscv-64) = 1.58.0-5.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-affy-debuginfo-1.58.0-5.fc31.riscv64
Provides: R-affy-debuginfo = 1.58.0-5.fc31 R-affy-debuginfo(riscv-64) = 1.58.0-5.fc31 debuginfo(build-id) = fe43ba5c71dbed1b9a8f07243637515c5c84efd4
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-affy-debugsource(riscv-64) = 1.58.0-5.fc31
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64
Wrote: /builddir/build/RPMS/R-affy-debugsource-1.58.0-5.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/R-affy-debuginfo-1.58.0-5.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/R-affy-1.58.0-5.fc31.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Jukowk
+ umask 022
+ cd /builddir/build/BUILD
+ cd affy
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-affy-1.58.0-5.fc31.riscv64
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Child return code was: 0