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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=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;\\007"', 'PS1': ' \\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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=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;\\007"', 'PS1': ' \\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 , Laurent Gautier , Benjamin Milo Bolstad , and Crispin Miller with contributions from Magnus Astrand , Leslie M. Cope , Robert Gentleman, Jeff Gentry, Conrad Halling , Wolfgang Huber, James MacDonald , Benjamin I. P. Rubinstein, Christopher Workman , John Zhang Maintainer: Rafael A. Irizarry 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