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> On Mon, 2021-04-05 at 00:44 +0200, karl@××××××××.se wrote: |
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... |
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> > $ cp -a ... |
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> > $ cd ... |
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> > $ make -j1 |
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> > ... |
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> > $ echo $? |
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> > 0 |
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> > |
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> > It builds without failure in that case. |
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> > |
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> |
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> That's (potentially) good news. Can you now try it with the |
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> CFLAGS/CXXFLAGS and LDFLAGS from your `emerge --info`? If the build |
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> fails in that case, then we know it's one of those flags causing a |
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> problem. |
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|
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It seems -j1 succeeds where -j4 fails, and it might be memory related. |
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|
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/// |
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|
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# make clean |
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# make |
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|
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does fail |
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|
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# make clean |
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# ./configure |
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... |
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R is now configured for x86_64-pc-linux-gnu |
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|
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Source directory: . |
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Installation directory: /usr/local |
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|
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C compiler: gcc -g -O2 |
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Fortran fixed-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 |
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|
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Default C++ compiler: g++ -std=gnu++11 -g -O2 |
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C++14 compiler: g++ -std=gnu++14 -g -O2 |
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C++17 compiler: g++ -std=gnu++17 -g -O2 |
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C++20 compiler: |
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Fortran free-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 |
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Obj-C compiler: gcc -g -O2 -fobjc-exceptions |
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|
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Interfaces supported: X11, tcltk |
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External libraries: pcre2, readline, curl |
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Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU |
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Options enabled: shared BLAS, R profiling |
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|
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Capabilities skipped: |
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Options not enabled: memory profiling |
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|
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Recommended packages: yes |
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|
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# make |
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|
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ok (=succeeds) |
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|
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adding (as environment variables) |
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CBUILD="x86_64-pc-linux-gnu" |
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CFLAGS="-O2 -pipe" |
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make clean; make |
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ok |
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|
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CHOST="x86_64-pc-linux-gnu" |
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CXXFLAGS="-O2 -pipe" |
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ok |
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|
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FCFLAGS="-O2 -pipe" |
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FFLAGS="-O2 -pipe" |
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ok |
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|
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LDFLAGS="-Wl,-O1 -Wl,--as-needed" |
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ok |
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|
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From ..../portage/dev-lang/R-4.0.4/work/R-4.0.4/config.log |
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# make distclean |
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# ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --docdir=/usr/share/doc/R-4.0.4 --htmldir=/usr/share/doc/R-4.0.4/html --with-sysroot=/ --libdir=/usr/lib64 --enable-byte-compiled-packages --enable-R-shlib --disable-R-framework --with-blas=-lblas rdocdir=/usr/share/doc/R-4.0.4 --disable-java --enable-nls --enable-openmp --disable-R-profiling --disable-memory-profiling --enable-static --enable-R-static-lib --without-cairo --without-ICU --with-jpeglib --without-lapack --with-recommended-packages --with-libpng --with-readline --with-libtiff --without-tcltk --without-tk-config --without-tcl-config --with-x |
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... |
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R is now configured for x86_64-pc-linux-gnu |
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|
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Source directory: . |
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Installation directory: /usr |
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|
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C compiler: x86_64-pc-linux-gnu-gcc -g -O2 |
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Fortran fixed-form compiler: x86_64-pc-linux-gnu-gfortran -fno-optimize-sibling-calls -g -O2 |
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|
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Default C++ compiler: x86_64-pc-linux-gnu-g++ -std=gnu++11 -g -O2 |
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C++14 compiler: x86_64-pc-linux-gnu-g++ -std=gnu++14 -g -O2 |
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C++17 compiler: x86_64-pc-linux-gnu-g++ -std=gnu++17 -g -O2 |
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C++20 compiler: |
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Fortran free-form compiler: x86_64-pc-linux-gnu-gfortran -fno-optimize-sibling-calls -g -O2 |
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Obj-C compiler: x86_64-pc-linux-gnu-gcc -g -O2 -fobjc-exceptions |
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|
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Interfaces supported: X11 |
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External libraries: pcre2, readline, BLAS(generic), curl |
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Additional capabilities: PNG, JPEG, TIFF, NLS |
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Options enabled: shared R library |
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|
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Capabilities skipped: cairo, ICU |
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Options not enabled: shared BLAS, R profiling, memory profiling |
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|
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Recommended packages: yes |
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|
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# make |
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ok |
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|
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add CFLAGS="-O2 -pipe" CXXFLAGS="-O2 -pipe" FCFLAGS="-O2 -pipe" FFLAGS="-O2 -pipe" LDFLAGS="-Wl,-O1 -Wl,--as-needed" |
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# make distclean |
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# ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --docdir=/usr/share/doc/R-4.0.4 --htmldir=/usr/share/doc/R-4.0.4/html --with-sysroot=/ --libdir=/usr/lib64 --enable-byte-compiled-packages --enable-R-shlib --disable-R-framework --with-blas=-lblas rdocdir=/usr/share/doc/R-4.0.4 --disable-java --enable-nls --enable-openmp --disable-R-profiling --disable-memory-profiling --enable-static --enable-R-static-lib --without-cairo --without-ICU --with-jpeglib --without-lapack --with-recommended-packages --with-libpng --with-readline --with-libtiff --without-tcltk --without-tk-config --without-tcl-config --with-x CFLAGS="-O2 -pipe" CXXFLAGS="-O2 -pipe" FCFLAGS="-O2 -pipe" FFLAGS="-O2 -pipe" LDFLAGS="-Wl,-O1 -Wl,--as-needed" |
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... |
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R is now configured for x86_64-pc-linux-gnu |
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|
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Source directory: . |
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Installation directory: /usr |
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|
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C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe |
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Fortran fixed-form compiler: x86_64-pc-linux-gnu-gfortran -fno-optimize-sibling-calls -O2 -pipe |
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|
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Default C++ compiler: x86_64-pc-linux-gnu-g++ -std=gnu++11 -O2 -pipe |
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C++14 compiler: x86_64-pc-linux-gnu-g++ -std=gnu++14 -O2 -pipe |
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C++17 compiler: x86_64-pc-linux-gnu-g++ -std=gnu++17 -O2 -pipe |
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C++20 compiler: |
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Fortran free-form compiler: x86_64-pc-linux-gnu-gfortran -fno-optimize-sibling-calls -O2 -pipe |
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Obj-C compiler: x86_64-pc-linux-gnu-gcc -g -O2 -fobjc-exceptions |
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|
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Interfaces supported: X11 |
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External libraries: pcre2, readline, BLAS(generic), curl |
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Additional capabilities: PNG, JPEG, TIFF, NLS |
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Options enabled: shared R library |
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|
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Capabilities skipped: cairo, ICU |
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Options not enabled: shared BLAS, R profiling, memory profiling |
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|
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Recommended packages: yes |
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|
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# make -j1 |
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ok |
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|
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# make clean |
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# make -j4 |
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... |
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make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/tests' |
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you should 'make docs' now ... |
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make[1]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/doc' |
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make[1]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4' |
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make[1]: 'stamp-java' is up to date. |
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make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4' |
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WARNING: ignoring environment value of R_HOME |
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WARNING: ignoring environment value of R_HOME |
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WARNING: ignoring environment value of R_HOME |
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Segmentation fault |
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make[1]: *** [Makefile:77: NEWS.3.rds] Error 139 |
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make[1]: *** Waiting for unfinished jobs.... |
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make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/doc' |
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make: [Makefile:72: docs] Error 2 (ignored) |
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make[1]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library' |
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make[2]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library' |
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installing parsed Rd |
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make[3]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library' |
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WARNING: ignoring environment value of R_HOME |
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WARNING: ignoring environment value of R_HOME |
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WARNING: ignoring environment value of R_HOME |
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WARNING: ignoring environment value of R_HOME |
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Segmentation fault |
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make[3]: *** [Makefile:73: stats.Rdts] Error 1 |
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make[3]: *** Waiting for unfinished jobs.... |
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Error in readRDS(mapfile) : error reading from connection |
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Execution halted |
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Warning message: |
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system call failed: Cannot allocate memory |
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Segmentation fault |
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make[3]: *** [Makefile:73: methods.Rdts] Error 1 |
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make[3]: *** [Makefile:73: base.Rdts] Error 1 |
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utils |
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make[3]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library' |
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make[2]: *** [Makefile:81: Rdobjects] Error 2 |
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make[2]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library' |
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make[1]: *** [Makefile:62: docs] Error 2 |
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make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library' |
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make: [Makefile:73: docs] Error 2 (ignored) |
| 182 |
make[1]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library/Recommended' |
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make[2]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library/Recommended' |
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begin installing recommended package MASS |
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begin installing recommended package lattice |
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begin installing recommended package codetools |
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begin installing recommended package foreign |
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WARNING: ignoring environment value of R_HOME |
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Fatal error: couldn't allocate memory for pointer stack |
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Segmentation fault |
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make[2]: *** [Makefile:53: lattice.ts] Error 1 |
| 192 |
make[2]: *** Waiting for unfinished jobs.... |
| 193 |
WARNING: ignoring environment value of R_HOME |
| 194 |
Segmentation fault |
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make[2]: *** [Makefile:53: codetools.ts] Error 1 |
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WARNING: ignoring environment value of R_HOME |
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* installing *source* package ?foreign? ... |
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** package ?foreign? successfully unpacked and MD5 sums checked |
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** using non-staged installation |
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** libs |
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make[3]: Entering directory '/tmp/Rtmpyf37hQ/R.INSTALL6e75db12a27/foreign/src' |
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x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c R_systat.c -o R_systat.o |
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x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c Rdbfread.c -o Rdbfread.o |
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x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c Rdbfwrite.c -o Rdbfwrite.o |
| 205 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c SASxport.c -o SASxport.o |
| 206 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c avl.c -o avl.o |
| 207 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c dbfopen.c -o dbfopen.o |
| 208 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c file-handle.c -o file-handle.o |
| 209 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c format.c -o format.o |
| 210 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c init.c -o init.o |
| 211 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c minitab.c -o minitab.o |
| 212 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c pfm-read.c -o pfm-read.o |
| 213 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c sfm-read.c -o sfm-read.o |
| 214 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c spss.c -o spss.o |
| 215 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c stataread.c -o stataread.o |
| 216 |
x86_64-pc-linux-gnu-gcc -shared -L/home/sys/R-4.0.4/work/R-4.0.4/lib -Wl,-O1 -Wl,--as-needed -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/home/sys/R-4.0.4/work/R-4.0.4/lib -lR |
| 217 |
make[3]: Leaving directory '/tmp/Rtmpyf37hQ/R.INSTALL6e75db12a27/foreign/src' |
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installing to /home/sys/R-4.0.4/work/R-4.0.4/library/foreign/libs |
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** R |
| 220 |
** inst |
| 221 |
** byte-compile and prepare package for lazy loading |
| 222 |
** help |
| 223 |
*** installing help indices |
| 224 |
** building package indices |
| 225 |
** testing if installed package can be loaded |
| 226 |
* DONE (foreign) |
| 227 |
WARNING: ignoring environment value of R_HOME |
| 228 |
* installing *source* package ?MASS? ... |
| 229 |
** package ?MASS? successfully unpacked and MD5 sums checked |
| 230 |
** using non-staged installation |
| 231 |
** libs |
| 232 |
make[3]: Entering directory '/tmp/RtmpY6iU2f/R.INSTALL6e078f85fff/MASS/src' |
| 233 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c MASS.c -o MASS.o |
| 234 |
x86_64-pc-linux-gnu-gcc -I"/home/sys/R-4.0.4/work/R-4.0.4/include" -DNDEBUG -fpic -O2 -pipe -c lqs.c -o lqs.o |
| 235 |
x86_64-pc-linux-gnu-gcc -shared -L/home/sys/R-4.0.4/work/R-4.0.4/lib -Wl,-O1 -Wl,--as-needed -o MASS.so MASS.o lqs.o -L/home/sys/R-4.0.4/work/R-4.0.4/lib -lR |
| 236 |
make[3]: Leaving directory '/tmp/RtmpY6iU2f/R.INSTALL6e078f85fff/MASS/src' |
| 237 |
installing to /home/sys/R-4.0.4/work/R-4.0.4/library/MASS/libs |
| 238 |
** R |
| 239 |
** data |
| 240 |
*** moving datasets to lazyload DB |
| 241 |
** inst |
| 242 |
** byte-compile and prepare package for lazy loading |
| 243 |
** help |
| 244 |
*** installing help indices |
| 245 |
** building package indices |
| 246 |
** testing if installed package can be loaded |
| 247 |
* DONE (MASS) |
| 248 |
make[2]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library/Recommended' |
| 249 |
make[1]: *** [Makefile:39: recommended-packages] Error 2 |
| 250 |
make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/src/library/Recommended' |
| 251 |
make: *** [Makefile:77: stamp-recommended] Error 2 |
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|
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remove -pipe |
| 254 |
# ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --docdir=/usr/share/doc/R-4.0.4 --htmldir=/usr/share/doc/R-4.0.4/html --with-sysroot=/ --libdir=/usr/lib64 --enable-byte-compiled-packages --enable-R-shlib --disable-R-framework --with-blas=-lblas rdocdir=/usr/share/doc/R-4.0.4 --disable-java --enable-nls --enable-openmp --disable-R-profiling --disable-memory-profiling --enable-static --enable-R-static-lib --without-cairo --without-ICU --with-jpeglib --without-lapack --with-recommended-packages --with-libpng --with-readline --with-libtiff --without-tcltk --without-tk-config --without-tcl-config --with-x CFLAGS="-O2" CXXFLAGS="-O2" FCFLAGS="-O2" FFLAGS="-O2" LDFLAGS="-Wl,-O1 -Wl,--as-needed" |
| 255 |
... |
| 256 |
R is now configured for x86_64-pc-linux-gnu |
| 257 |
|
| 258 |
Source directory: . |
| 259 |
Installation directory: /usr |
| 260 |
|
| 261 |
C compiler: x86_64-pc-linux-gnu-gcc -O2 |
| 262 |
Fortran fixed-form compiler: x86_64-pc-linux-gnu-gfortran -fno-optimize-sibling-calls -O2 |
| 263 |
|
| 264 |
Default C++ compiler: x86_64-pc-linux-gnu-g++ -std=gnu++11 -O2 |
| 265 |
C++14 compiler: x86_64-pc-linux-gnu-g++ -std=gnu++14 -O2 |
| 266 |
C++17 compiler: x86_64-pc-linux-gnu-g++ -std=gnu++17 -O2 |
| 267 |
C++20 compiler: |
| 268 |
Fortran free-form compiler: x86_64-pc-linux-gnu-gfortran -fno-optimize-sibling-calls -O2 |
| 269 |
Obj-C compiler: x86_64-pc-linux-gnu-gcc -g -O2 -fobjc-exceptions |
| 270 |
|
| 271 |
Interfaces supported: X11 |
| 272 |
External libraries: pcre2, readline, BLAS(generic), curl |
| 273 |
Additional capabilities: PNG, JPEG, TIFF, NLS |
| 274 |
Options enabled: shared R library |
| 275 |
|
| 276 |
Capabilities skipped: cairo, ICU |
| 277 |
Options not enabled: shared BLAS, R profiling, memory profiling |
| 278 |
|
| 279 |
Recommended packages: yes |
| 280 |
|
| 281 |
# make -j4 |
| 282 |
... |
| 283 |
make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/tests' |
| 284 |
you should 'make docs' now ... |
| 285 |
make[1]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4/doc' |
| 286 |
make[1]: Entering directory '/home/sys/R-4.0.4/work/R-4.0.4' |
| 287 |
WARNING: ignoring environment value of R_HOME |
| 288 |
make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4' |
| 289 |
WARNING: ignoring environment value of R_HOME |
| 290 |
WARNING: ignoring environment value of R_HOME |
| 291 |
Segmentation fault |
| 292 |
make[1]: *** [Makefile:77: NEWS.3.rds] Error 139 |
| 293 |
make[1]: *** Waiting for unfinished jobs.... |
| 294 |
make[1]: Leaving directory '/home/sys/R-4.0.4/work/R-4.0.4/doc' |
| 295 |
... |
| 296 |
|
| 297 |
Regards, |
| 298 |
/Karl Hammar |
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