Mock Version: 1.4.21
Mock Version: 1.4.21
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.spec'], chrootPath='/var/lib/mock/f33-build-292921-54989/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 0x3fa8f4f700>timeout=432000uid=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.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=1595808000
Wrote: /builddir/build/SRPMS/R-Rsolid-0.9.31-33.fc33.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.spec'], chrootPath='/var/lib/mock/f33-build-292921-54989/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 0x3fa8f4f700>timeout=432000uid=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.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=1595808000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.5yZ4Lk
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf Rsolid
+ /usr/bin/mkdir -p Rsolid
+ cd Rsolid
+ /usr/bin/gzip -dc /builddir/build/SOURCES/Rsolid_0.9-31.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (R-Rsolid-R3.patch):'
Patch #0 (R-Rsolid-R3.patch):
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .fixed --fuzz=0
patching file Rsolid/NAMESPACE
patching file Rsolid/src/util.c
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.cot33k
+ umask 022
+ cd /builddir/build/BUILD
+ cd Rsolid
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.YUuG9i
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64
++ dirname /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64
+ cd Rsolid
+ mkdir -p /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64/usr/lib64/R/library
+ R CMD INSTALL Rsolid --configure-args=--with-hdf5=/usr -l /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64/usr/lib64/R/library
* installing *source* package 'Rsolid' ...
** using staged installation
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/include/R" -DNDEBUG -I/usr/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 Rdriver.c -o Rdriver.o
Rdriver.c: In function 'rdriver':
Rdriver.c:271:8: warning: unused variable 'p_yxloc' [-Wunused-variable]
  271 |   SEXP p_yxloc;
      |        ^~~~~~~
Rdriver.c:270:8: warning: unused variable 'p_intensities' [-Wunused-variable]
  270 |   SEXP p_intensities;
      |        ^~~~~~~~~~~~~
Rdriver.c:269:8: warning: unused variable 'ligation_names' [-Wunused-variable]
  269 |   SEXP ligation_names;
      |        ^~~~~~~~~~~~~~
Rdriver.c:268:8: warning: unused variable 'primer_names' [-Wunused-variable]
  268 |   SEXP primer_names;
      |        ^~~~~~~~~~~~
Rdriver.c:266:15: warning: unused variable 'i' [-Wunused-variable]
  266 |   int status, i;
      |               ^
Rdriver.c:264:13: warning: unused variable 'panel_info' [-Wunused-variable]
  264 |   panelInfo panel_info;
      |             ^~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -I/usr/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 reader.c -o reader.o
reader.c: In function 'ligationIter_data':
reader.c:315:7: warning: unused variable 'offset' [-Wunused-variable]
  315 |   int offset;
      |       ^~~~~~
gcc -I"/usr/include/R" -DNDEBUG -I/usr/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 reader_util.c -o reader_util.o
gcc -I"/usr/include/R" -DNDEBUG -I/usr/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 util.c -o util.o
util.c: In function 'callBases':
util.c:163:41: warning: unused variable 'dscore' [-Wunused-variable]
  163 |   double *input=REAL(mat), dtmp, dtmp2, dscore;
      |                                         ^~~~~~
util.c:169:19: warning: 'tmpscore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  169 |   char *tmpchar, *tmpscore;
      |                   ^~~~~~~~
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 Rsolid.so Rdriver.o reader.o reader_util.o util.o -L/usr/lib -lhdf5 -L/usr/lib64/R/lib -lR
installing to /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64/usr/lib64/R/library/00LOCK-Rsolid/00new/Rsolid/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rsolid'
    finding HTML links ... done
    Rsolid                                  html  
    finding level-2 HTML links ... done
Rd warning: /builddir/build/BUILD/Rsolid/Rsolid/man/Rsolid.Rd:44: missing link 'snow'
Rd warning: /builddir/build/BUILD/Rsolid/Rsolid/man/Rsolid.Rd:45: missing link 'Rmpi'
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsolid)
+ test -d Rsolid/src
+ cd Rsolid/src
+ rm -f Rdriver.o reader.o reader_util.o util.o Rsolid.so
+ rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64/usr/lib64/R/library/R.css
+ rm -rf Rsolid/src/hdf5-1.8.3
+ rm -rf Rsolid/config.status
+ rm -rf Rsolid/configure
+ /usr/lib/rpm/find-debuginfo.sh -j8 --strict-build-id -m -i --build-id-seed 0.9.31-33.fc33 --unique-debug-suffix -0.9.31-33.fc33.riscv64 --unique-debug-src-base R-Rsolid-0.9.31-33.fc33.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Rsolid
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64/usr/lib64/R/library/Rsolid/libs/Rsolid.so
extracting debug info from /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64/usr/lib64/R/library/Rsolid/libs/Rsolid.so
original debug info size: 120kB, size after compression: 116kB
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
72 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Hx0DQk
+ umask 022
+ cd /builddir/build/BUILD
+ cd Rsolid
+ /usr/bin/R CMD check Rsolid
* using log directory '/builddir/build/BUILD/Rsolid/Rsolid.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: riscv64-redhat-linux-gnu (64-bit)
* using session charset: ASCII
* checking for file 'Rsolid/DESCRIPTION' ... OK
* this is package 'Rsolid' version '0.9-31'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... WARNING
The following files should most likely be executable (for the owner):
  cleanup
Please fix their permissions
* checking whether package 'Rsolid' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
quantile:
  function(x, ...)
quantile.norm:
  function(y, target, cycles)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  quantile.norm
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls without 'PACKAGE' argument:
  .Call("callBases", ...)
  .Call("callBases", ...)
  .Call("rowMaxPos", ...)
  .Call("rdriver", ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
readspch: warning in matrix(0, nr = nbeads, nc =
  total.nligation.cycles): partial argument match of 'nr' to 'nrow'
readspch: warning in matrix(0, nr = nbeads, nc =
  total.nligation.cycles): partial argument match of 'nc' to 'ncol'
readspch: warning in matrix(NA, nr = max.ligation.cycles, nc =
  max.primer.cycles): partial argument match of 'nr' to 'nrow'
readspch: warning in matrix(NA, nr = max.ligation.cycles, nc =
  max.primer.cycles): partial argument match of 'nc' to 'ncol'
Rsolid: no visible global function definition for 'write.table'
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: Rsolid.Rd:61-63: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Rsolid.Rd':
  'snow' 'Rmpi'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'makeTarget' 'quantile.norm' 'readspch'
Undocumented data sets:
  'prop.Hs'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'Rsolid/libs/Rsolid.so':
  Found '__printf_chk', possibly from 'printf' (C)
    Objects: 'reader.o', 'reader_util.o'
  Found 'putchar', possibly from 'putchar' (C)
    Object: 'reader_util.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Objects: 'reader.o', 'reader_util.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 4 NOTEs
See
  '/builddir/build/BUILD/Rsolid/Rsolid.Rcheck/00check.log'
for details.
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: R-Rsolid-0.9.31-33.fc33.riscv64
Provides: R(Rsolid) = 0.9-31 R-Rsolid = 0.9.31-33.fc33 R-Rsolid(riscv-64) = 0.9.31-33.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(ABI) = 3.6 R-core 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) libhdf5.so.103()(64bit) rtld(GNU_HASH)
Processing files: R-Rsolid-devel-0.9.31-33.fc33.riscv64
Provides: R-Rsolid-devel = 0.9.31-33.fc33 R-Rsolid-devel(riscv-64) = 0.9.31-33.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Rsolid-debugsource-0.9.31-33.fc33.riscv64
Provides: R-Rsolid-debugsource = 0.9.31-33.fc33 R-Rsolid-debugsource(riscv-64) = 0.9.31-33.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Rsolid-debuginfo-0.9.31-33.fc33.riscv64
Provides: R-Rsolid-debuginfo = 0.9.31-33.fc33 R-Rsolid-debuginfo(riscv-64) = 0.9.31-33.fc33 debuginfo(build-id) = a4023e1948b4dbf12b1841fed9df6ca9339ebe1e
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-Rsolid-debugsource(riscv-64) = 0.9.31-33.fc33
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64
Wrote: /builddir/build/RPMS/R-Rsolid-debugsource-0.9.31-33.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/R-Rsolid-0.9.31-33.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/R-Rsolid-debuginfo-0.9.31-33.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/R-Rsolid-devel-0.9.31-33.fc33.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.l5xAOk
+ umask 022
+ cd /builddir/build/BUILD
+ cd Rsolid
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-33.fc33.riscv64
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0