Hi all,
With the bug in tre identified I am trying to move forward - one step at
a time.
As I am getting some errors that prevent make completing with version
3.2.3, and R-devel introduces new issues (that I will face when I get to
them) I would appreciate some guidance with output of "make check" (of
3.1.3) and the final message I run into when trying to build 3.2.3.
Maybe they are related, maybe not.
In short - where should I be looking in more detail (e.g., with debugger
again), and are the errors possibly related to a library (e.g., lzma/xz
as it has been mentioned in other mails).
make check
root at x065:[/data/prj/cran/32/R-3.1.3.1]make check
make[1]: Entering directory '/data/prj/cran/32/R-3.1.3.1/tests'
make[2]: Entering directory '/data/prj/cran/32/R-3.1.3.1/tests'
make[3]: Entering directory '/data/prj/cran/32/R-3.1.3.1/tests/Examples'
Testing examples for package 'base'
Error: testing 'base' failed
Execution halted
Makefile:33: recipe for target 'test-Examples-Base' failed
make[3]: *** [test-Examples-Base] Error 1
make[3]: Leaving directory '/data/prj/cran/32/R-3.1.3.1/tests/Examples'
Makefile.common:166: recipe for target 'test-Examples' failed
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory '/data/prj/cran/32/R-3.1.3.1/tests'
Makefile.common:154: recipe for target 'test-all-basics' failed
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory '/data/prj/cran/32/R-3.1.3.1/tests'
Makefile:236: recipe for target 'check' failed
make: *** [check] Error 2
Failing (64-bit) build of R-3.2.3
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
xlc_r -qarch=pwr5 -I/home/cran/64/R/include -DNDEBUG
-I/usr/local/include -g -c MASS.c -o MASS.o
xlc_r -qarch=pwr5 -I/home/cran/64/R/include -DNDEBUG
-I/usr/local/include -g -c lqs.c -o lqs.o
xlc_r -qarch=pwr5 -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc
-L/home/cran/64/R/lib -L/opt/lib -liconv -o MASS.so MASS.o lqs.o -lm
-L/home/cran/64/R/lib -lR
ld: 0711-224 WARNING: Duplicate symbol: p_xargc
ld: 0711-224 WARNING: Duplicate symbol: p_xargv
ld: 0711-224 WARNING: Duplicate symbol: p_xrcfg
ld: 0711-224 WARNING: Duplicate symbol: p_xrc
ld: 0711-224 WARNING: Duplicate symbol: end
ld: 0711-224 WARNING: Duplicate symbol: .log
ld: 0711-224 WARNING: Duplicate symbol: log
ld: 0711-224 WARNING: Duplicate symbol: .sqrt
ld: 0711-224 WARNING: Duplicate symbol: sqrt
ld: 0711-224 WARNING: Duplicate symbol: guesses
ld: 0711-224 WARNING: Duplicate symbol: .strcmp
ld: 0711-224 WARNING: Duplicate symbol: strcmp
ld: 0711-224 WARNING: Duplicate symbol: .isnan
ld: 0711-224 WARNING: Duplicate symbol: isnan
ld: 0711-224 WARNING: Duplicate symbol: .pow
ld: 0711-224 WARNING: Duplicate symbol: pow
ld: 0711-224 WARNING: Duplicate symbol: .exp
ld: 0711-224 WARNING: Duplicate symbol: exp
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.
Target "all" is up to date.
installing to /home/cran/64/R/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii,
compress, :
internal error 5 in R_compress3
ERROR: lazydata failed for package 'MASS'
* removing '/home/cran/64/R/library/MASS'
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
cran at x068:[/home/cran/64/R]
On 2016-01-08 00:17, Michael Felt wrote:> Hi all, > > With the bug in tre identified I am trying to move forward - one step > at a time.Guess it is time to close testing via R-3.2.3. Next posts will be: a) when I have time b) based on R-devel Have a good day all! Michael> > As I am getting some errors that prevent make completing with version > 3.2.3, and R-devel introduces new issues (that I will face when I get > to them) I would appreciate some guidance with output of "make check" > (of 3.1.3) and the final message I run into when trying to build > 3.2.3. Maybe they are related, maybe not. > > In short - where should I be looking in more detail (e.g., with > debugger again), and are the errors possibly related to a library > (e.g., lzma/xz as it has been mentioned in other mails). > > make check > > root at x065:[/data/prj/cran/32/R-3.1.3.1]make check > make[1]: Entering directory '/data/prj/cran/32/R-3.1.3.1/tests' > make[2]: Entering directory '/data/prj/cran/32/R-3.1.3.1/tests' > make[3]: Entering directory '/data/prj/cran/32/R-3.1.3.1/tests/Examples' > Testing examples for package 'base' > Error: testing 'base' failed > Execution halted > Makefile:33: recipe for target 'test-Examples-Base' failed > make[3]: *** [test-Examples-Base] Error 1 > make[3]: Leaving directory '/data/prj/cran/32/R-3.1.3.1/tests/Examples' > Makefile.common:166: recipe for target 'test-Examples' failed > make[2]: *** [test-Examples] Error 2 > make[2]: Leaving directory '/data/prj/cran/32/R-3.1.3.1/tests' > Makefile.common:154: recipe for target 'test-all-basics' failed > make[1]: *** [test-all-basics] Error 1 > make[1]: Leaving directory '/data/prj/cran/32/R-3.1.3.1/tests' > Makefile:236: recipe for target 'check' failed > make: *** [check] Error 2 > > Failing (64-bit) build of R-3.2.3 > begin installing recommended package MASS > * installing *source* package 'MASS' ... > ** package 'MASS' successfully unpacked and MD5 sums checked > ** libs > xlc_r -qarch=pwr5 -I/home/cran/64/R/include -DNDEBUG > -I/usr/local/include -g -c MASS.c -o MASS.o > xlc_r -qarch=pwr5 -I/home/cran/64/R/include -DNDEBUG > -I/usr/local/include -g -c lqs.c -o lqs.o > xlc_r -qarch=pwr5 -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc > -L/home/cran/64/R/lib -L/opt/lib -liconv -o MASS.so MASS.o lqs.o -lm > -L/home/cran/64/R/lib -lR > ld: 0711-224 WARNING: Duplicate symbol: p_xargc > ld: 0711-224 WARNING: Duplicate symbol: p_xargv > ld: 0711-224 WARNING: Duplicate symbol: p_xrcfg > ld: 0711-224 WARNING: Duplicate symbol: p_xrc > ld: 0711-224 WARNING: Duplicate symbol: end > ld: 0711-224 WARNING: Duplicate symbol: .log > ld: 0711-224 WARNING: Duplicate symbol: log > ld: 0711-224 WARNING: Duplicate symbol: .sqrt > ld: 0711-224 WARNING: Duplicate symbol: sqrt > ld: 0711-224 WARNING: Duplicate symbol: guesses > ld: 0711-224 WARNING: Duplicate symbol: .strcmp > ld: 0711-224 WARNING: Duplicate symbol: strcmp > ld: 0711-224 WARNING: Duplicate symbol: .isnan > ld: 0711-224 WARNING: Duplicate symbol: isnan > ld: 0711-224 WARNING: Duplicate symbol: .pow > ld: 0711-224 WARNING: Duplicate symbol: pow > ld: 0711-224 WARNING: Duplicate symbol: .exp > ld: 0711-224 WARNING: Duplicate symbol: exp > ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more > information. > Target "all" is up to date. > installing to /home/cran/64/R/library/MASS/libs > ** R > ** data > *** moving datasets to lazyload DB > Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, > compress, : > internal error 5 in R_compress3 > ERROR: lazydata failed for package 'MASS' > * removing '/home/cran/64/R/library/MASS' > make: 1254-004 The error code from the last command is 1. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > cran at x068:[/home/cran/64/R] >
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