This run was done this AM on my linux box, and older 32 bit Dell optiplex (core
2 duo).
The failure message is at the very end. (It's due to be replaced in a couple
of weeks.)
The sequence of steps was
svn up
tools/rsync-recommended
./configure
make
make check-all |& tee zzz
Terry T.
Result of ./config
R is now configured for i686-pc-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -g -O2
Fortran 77 compiler: f95 -g -O2
Default C++ compiler: g++
C++98 compiler: g++
C++11 compiler: g++ -std=gnu++11
C++14 compiler: g++ -std=gnu++14
C++17 compiler:
Fortran 90/95 compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries: readline, curl
Additional capabilities: PNG, JPEG, NLS, cairo, ICU
Options enabled: shared BLAS, R profiling
Capabilities skipped: TIFF
Options not enabled: memory profiling
Recommended packages: yes
----
sessionInfo() after invoking R --vanilla
R Under development (unstable) (2017-04-06 r72489)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/local/src/R-devel/lib/libRblas.so
LAPACK: /usr/local/src/R-devel/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0
----------------------
The results of "make" showed nothing remarkable.
Here is make test-all
make[1]: Entering directory '/usr/local/src/R-devel/tests'
make[2]: Entering directory '/usr/local/src/R-devel/tests'
make[3]: Entering directory '/usr/local/src/R-devel/tests/Examples'
Testing examples for package ?base?
comparing ?base-Ex.Rout? to ?base-Ex.Rout.prev? ... NOTE
1573,1607c1573,1608
< [35] "MANDATORY_PATH" "MFLAGS"
< [37] "PAGER" "PATH"
< [39] "PWD" "QT4_IM_MODULE"
< [41] "QT_ACCESSIBILITY" "QT_IM_MODULE"
< [43] "QT_LINUX_ACCESSIBILITY_ALWAYS_ON" "R_ARCH"
< [45] "R_BROWSER" "R_BZIPCMD"
< [47] "R_CMD" "R_DOC_DIR"
< [49] "R_ENVIRON" "R_ENVIRON_USER"
< [51] "R_GZIPCMD" "R_HOME"
< [53] "R_INCLUDE_DIR" "R_LIBS"
< [55] "R_LIBS_SITE" "R_LIBS_USER"
< [57] "R_OSTYPE" "R_PAPERSIZE"
< [59] "R_PAPERSIZE_USER" "R_PDFVIEWER"
< [61] "R_PLATFORM" "R_PRINTCMD"
< [63] "R_PROFILE" "R_PROFILE_USER"
< [65] "R_RD4PDF" "R_SESSION_TMPDIR"
< [67] "R_SHARE_DIR" "R_SYSTEM_ABI"
< [69] "R_TEXI2DVICMD" "R_UNZIPCMD"
< [71] "R_VERSION" "R_ZIPCMD"
< [73] "SED" "SESSION"
< [77] "SHELL" "SHLVL"
< [79] "SSH_AGENT_PID" "SSH_AUTH_SOCK"
< [81] "TAR" "TERM"
< [83] "TEXINPUTS" "UPSTART_EVENTS"
< [85] "UPSTART_INSTANCE" "UPSTART_JOB"
< [87] "UPSTART_SESSION" "USER"
< [89] "WINDOWID" "XAUTHORITY"
< [91] "XDG_CONFIG_DIRS" "XDG_CURRENT_DESKTOP"
< [93] "XDG_DATA_DIRS" "XDG_GREETER_DATA_DIR"
< [95] "XDG_MENU_PREFIX" "XDG_RUNTIME_DIR"
< [97] "XDG_SEAT" "XDG_SEAT_PATH"
< [99] "XDG_SESSION_DESKTOP" "XDG_SESSION_ID"
< [101] "XDG_SESSION_PATH" "XDG_SESSION_TYPE"
< [103] "XDG_VTNR" "XMODIFIERS"
---
> [35] "MAKE_TERMERR" "MAKE_TERMOUT"
> [37] "MANDATORY_PATH" "MFLAGS"
> [39] "PAGER" "PATH"
> [41] "PWD" "QT4_IM_MODULE"
> [43] "QT_ACCESSIBILITY" "QT_IM_MODULE"
> [45] "QT_LINUX_ACCESSIBILITY_ALWAYS_ON" "R_ARCH"
> [47] "R_BROWSER" "R_BZIPCMD"
> [49] "R_CMD" "R_DOC_DIR"
> [51] "R_ENVIRON" "R_ENVIRON_USER"
> [53] "R_GZIPCMD" "R_HOME"
> [55] "R_INCLUDE_DIR" "R_LIBS"
> [57] "R_LIBS_SITE" "R_LIBS_USER"
> [59] "R_OSTYPE" "R_PAPERSIZE"
> [61] "R_PAPERSIZE_USER" "R_PDFVIEWER"
> [63] "R_PLATFORM" "R_PRINTCMD"
> [65] "R_PROFILE" "R_PROFILE_USER"
> [67] "R_RD4PDF" "R_SESSION_TMPDIR"
> [69] "R_SHARE_DIR" "R_SYSTEM_ABI"
> [71] "R_TEXI2DVICMD" "R_UNZIPCMD"
> [73] "R_VERSION" "R_ZIPCMD"
> [75] "SED" "SESSION"
> [77] "SESSIONTYPE" "SESSION_MANAGER"
> [79] "SHELL" "SHLVL"
> [81] "SSH_AGENT_PID" "SSH_AUTH_SOCK"
> [83] "TAR" "TERM"
> [85] "TEXINPUTS" "UPSTART_EVENTS"
> [87] "UPSTART_INSTANCE" "UPSTART_JOB"
> [89] "UPSTART_SESSION" "USER"
> [91] "WINDOWID" "XAUTHORITY"
> [93] "XDG_CONFIG_DIRS" "XDG_CURRENT_DESKTOP"
> [95] "XDG_DATA_DIRS" "XDG_GREETER_DATA_DIR"
> [97] "XDG_MENU_PREFIX" "XDG_RUNTIME_DIR"
> [99] "XDG_SEAT" "XDG_SEAT_PATH"
> [101] "XDG_SESSION_DESKTOP" "XDG_SESSION_ID"
> [103] "XDG_SESSION_PATH" "XDG_SESSION_TYPE"
> [105] "XDG_VTNR" "XMODIFIERS"
7903a7905,7906
> MAKE_TERMERR: /dev/pts/10
> MAKE_TERMOUT: /dev/pts/10
7936c7939
< R_SESSION_TMPDIR: /tmp/RtmpSrm93R
---
> R_SESSION_TMPDIR: /tmp/RtmpFkpTbp
11007c11010
< [37] "tests" "tools"
"zzz"
---
> [37] "tests" "tools"
Testing examples for package ?tools?
comparing ?tools-Ex.Rout? to ?tools-Ex.Rout.save? ... OK
Testing examples for package ?utils?
comparing ?utils-Ex.Rout? to ?utils-Ex.Rout.prev? ... OK
Testing examples for package ?grDevices?
comparing ?grDevices-Ex.Rout? to ?grDevices-Ex.Rout.save? ... OK
Testing examples for package ?graphics?
comparing ?graphics-Ex.Rout? to ?graphics-Ex.Rout.save? ... OK
Testing examples for package ?stats?
comparing ?stats-Ex.Rout? to ?stats-Ex.Rout.save? ... OK
Testing examples for package ?datasets?
comparing ?datasets-Ex.Rout? to ?datasets-Ex.Rout.save? ... OK
Testing examples for package ?methods?
comparing ?methods-Ex.Rout? to ?methods-Ex.Rout.prev? ... OK
Testing examples for package ?grid?
comparing ?grid-Ex.Rout? to ?grid-Ex.Rout.save? ... OK
Testing examples for package ?splines?
comparing ?splines-Ex.Rout? to ?splines-Ex.Rout.save? ... OK
Testing examples for package ?stats4?
comparing ?stats4-Ex.Rout? to ?stats4-Ex.Rout.save? ... OK
Testing examples for package ?tcltk?
comparing ?tcltk-Ex.Rout? to ?tcltk-Ex.Rout.prev? ... OK
Testing examples for package ?compiler?
comparing ?compiler-Ex.Rout? to ?compiler-Ex.Rout.prev? ... OK
Testing examples for package ?parallel?
comparing ?parallel-Ex.Rout? to ?parallel-Ex.Rout.prev? ... OK
make[3]: Leaving directory '/usr/local/src/R-devel/tests/Examples'
make[2]: Leaving directory '/usr/local/src/R-devel/tests'
make[2]: Entering directory '/usr/local/src/R-devel/tests'
running strict specific tests
make[3]: Entering directory '/usr/local/src/R-devel/tests'
running code in 'eval-etc.R' ... OK
comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
comparing 'simple-true.Rout' to './simple-true.Rout.save' ...
OK
running code in 'arith-true.R' ... OK
comparing 'arith-true.Rout' to './arith-true.Rout.save' ...
OK
running code in 'arith.R' ... OK
comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
comparing 'method-dispatch.Rout' to
'./method-dispatch.Rout.save' ... OK
running code in 'any-all.R' ... OK
comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save'
... OK
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
running sloppy specific tests
make[3]: Entering directory '/usr/local/src/R-devel/tests'
running code in 'complex.R' ... OK
comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'print-tests.R' ... OK
comparing 'print-tests.Rout' to './print-tests.Rout.save' ...
OK
running code in 'lapack.R' ... OK
comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
make[2]: Leaving directory '/usr/local/src/R-devel/tests'
make[2]: Entering directory '/usr/local/src/R-devel/tests'
running regression tests ...
make[3]: Entering directory '/usr/local/src/R-devel/tests'
running code in 'array-subset.R' ... OK
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-1d.R' ... OK
running code in 'reg-tests-2.R' ... OK
comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ...
OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'r-strict-tst.R' ... OK
running code in 'reg-IO.R' ... OK
comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4-examples.R' ... OK
running code in 'reg-BLAS.R' ... OK
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
make[3]: Entering directory '/usr/local/src/R-devel/tests'
running code in 'reg-tests-3.R' ... OK
comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ...
OK
running code in 'reg-examples3.R' ...Makefile.common:98: recipe for
target 'reg-
examples3.Rout' failed
make[3]: *** [reg-examples3.Rout] Error 1
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
Makefile.common:273: recipe for target 'test-Reg' failed
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory '/usr/local/src/R-devel/tests'
Makefile.common:165: recipe for target 'test-all-basics' failed
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory '/usr/local/src/R-devel/tests'
Makefile:239: recipe for target 'check-all' failed
make: *** [check-all] Error 2
You may want to retry that after a make distclean, in case anything changed in the toolchain. -pd> On 6 Apr 2017, at 14:43 , Therneau, Terry M., Ph.D. <therneau at mayo.edu> wrote: > > This run was done this AM on my linux box, and older 32 bit Dell optiplex (core 2 duo). The failure message is at the very end. (It's due to be replaced in a couple of weeks.) The sequence of steps was > > svn up > tools/rsync-recommended > ./configure > make > make check-all |& tee zzz > > > Terry T. > > > Result of ./config > R is now configured for i686-pc-linux-gnu > > Source directory: . > Installation directory: /usr/local > > C compiler: gcc -g -O2 > Fortran 77 compiler: f95 -g -O2 > > Default C++ compiler: g++ > C++98 compiler: g++ > C++11 compiler: g++ -std=gnu++11 > C++14 compiler: g++ -std=gnu++14 > C++17 compiler: > Fortran 90/95 compiler: gfortran -g -O2 > Obj-C compiler: > > Interfaces supported: X11, tcltk > External libraries: readline, curl > Additional capabilities: PNG, JPEG, NLS, cairo, ICU > Options enabled: shared BLAS, R profiling > > Capabilities skipped: TIFF > Options not enabled: memory profiling > > Recommended packages: yes > > ---- > sessionInfo() after invoking R --vanilla > > R Under development (unstable) (2017-04-06 r72489) > Platform: i686-pc-linux-gnu (32-bit) > Running under: Ubuntu 16.04.2 LTS > > Matrix products: default > BLAS: /usr/local/src/R-devel/lib/libRblas.so > LAPACK: /usr/local/src/R-devel/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] compiler_3.5.0 > > ---------------------- > The results of "make" showed nothing remarkable. > > Here is make test-all > > make[1]: Entering directory '/usr/local/src/R-devel/tests' > make[2]: Entering directory '/usr/local/src/R-devel/tests' > make[3]: Entering directory '/usr/local/src/R-devel/tests/Examples' > Testing examples for package ?base? > comparing ?base-Ex.Rout? to ?base-Ex.Rout.prev? ... NOTE > 1573,1607c1573,1608 > < [35] "MANDATORY_PATH" "MFLAGS" > < [37] "PAGER" "PATH" > < [39] "PWD" "QT4_IM_MODULE" > < [41] "QT_ACCESSIBILITY" "QT_IM_MODULE" > < [43] "QT_LINUX_ACCESSIBILITY_ALWAYS_ON" "R_ARCH" > < [45] "R_BROWSER" "R_BZIPCMD" > < [47] "R_CMD" "R_DOC_DIR" > < [49] "R_ENVIRON" "R_ENVIRON_USER" > < [51] "R_GZIPCMD" "R_HOME" > < [53] "R_INCLUDE_DIR" "R_LIBS" > < [55] "R_LIBS_SITE" "R_LIBS_USER" > < [57] "R_OSTYPE" "R_PAPERSIZE" > < [59] "R_PAPERSIZE_USER" "R_PDFVIEWER" > < [61] "R_PLATFORM" "R_PRINTCMD" > < [63] "R_PROFILE" "R_PROFILE_USER" > < [65] "R_RD4PDF" "R_SESSION_TMPDIR" > < [67] "R_SHARE_DIR" "R_SYSTEM_ABI" > < [69] "R_TEXI2DVICMD" "R_UNZIPCMD" > < [71] "R_VERSION" "R_ZIPCMD" > < [73] "SED" "SESSION" > < [77] "SHELL" "SHLVL" > < [79] "SSH_AGENT_PID" "SSH_AUTH_SOCK" > < [81] "TAR" "TERM" > < [83] "TEXINPUTS" "UPSTART_EVENTS" > < [85] "UPSTART_INSTANCE" "UPSTART_JOB" > < [87] "UPSTART_SESSION" "USER" > < [89] "WINDOWID" "XAUTHORITY" > < [91] "XDG_CONFIG_DIRS" "XDG_CURRENT_DESKTOP" > < [93] "XDG_DATA_DIRS" "XDG_GREETER_DATA_DIR" > < [95] "XDG_MENU_PREFIX" "XDG_RUNTIME_DIR" > < [97] "XDG_SEAT" "XDG_SEAT_PATH" > < [99] "XDG_SESSION_DESKTOP" "XDG_SESSION_ID" > < [101] "XDG_SESSION_PATH" "XDG_SESSION_TYPE" > < [103] "XDG_VTNR" "XMODIFIERS" > --- > > [35] "MAKE_TERMERR" "MAKE_TERMOUT" > > [37] "MANDATORY_PATH" "MFLAGS" > > [39] "PAGER" "PATH" > > [41] "PWD" "QT4_IM_MODULE" > > [43] "QT_ACCESSIBILITY" "QT_IM_MODULE" > > [45] "QT_LINUX_ACCESSIBILITY_ALWAYS_ON" "R_ARCH" > > [47] "R_BROWSER" "R_BZIPCMD" > > [49] "R_CMD" "R_DOC_DIR" > > [51] "R_ENVIRON" "R_ENVIRON_USER" > > [53] "R_GZIPCMD" "R_HOME" > > [55] "R_INCLUDE_DIR" "R_LIBS" > > [57] "R_LIBS_SITE" "R_LIBS_USER" > > [59] "R_OSTYPE" "R_PAPERSIZE" > > [61] "R_PAPERSIZE_USER" "R_PDFVIEWER" > > [63] "R_PLATFORM" "R_PRINTCMD" > > [65] "R_PROFILE" "R_PROFILE_USER" > > [67] "R_RD4PDF" "R_SESSION_TMPDIR" > > [69] "R_SHARE_DIR" "R_SYSTEM_ABI" > > [71] "R_TEXI2DVICMD" "R_UNZIPCMD" > > [73] "R_VERSION" "R_ZIPCMD" > > [75] "SED" "SESSION" > > [77] "SESSIONTYPE" "SESSION_MANAGER" > > [79] "SHELL" "SHLVL" > > [81] "SSH_AGENT_PID" "SSH_AUTH_SOCK" > > [83] "TAR" "TERM" > > [85] "TEXINPUTS" "UPSTART_EVENTS" > > [87] "UPSTART_INSTANCE" "UPSTART_JOB" > > [89] "UPSTART_SESSION" "USER" > > [91] "WINDOWID" "XAUTHORITY" > > [93] "XDG_CONFIG_DIRS" "XDG_CURRENT_DESKTOP" > > [95] "XDG_DATA_DIRS" "XDG_GREETER_DATA_DIR" > > [97] "XDG_MENU_PREFIX" "XDG_RUNTIME_DIR" > > [99] "XDG_SEAT" "XDG_SEAT_PATH" > > [101] "XDG_SESSION_DESKTOP" "XDG_SESSION_ID" > > [103] "XDG_SESSION_PATH" "XDG_SESSION_TYPE" > > [105] "XDG_VTNR" "XMODIFIERS" > 7903a7905,7906 > > MAKE_TERMERR: /dev/pts/10 > > MAKE_TERMOUT: /dev/pts/10 > 7936c7939 > < R_SESSION_TMPDIR: /tmp/RtmpSrm93R > --- > > R_SESSION_TMPDIR: /tmp/RtmpFkpTbp > 11007c11010 > < [37] "tests" "tools" "zzz" > --- > > [37] "tests" "tools" > Testing examples for package ?tools? > comparing ?tools-Ex.Rout? to ?tools-Ex.Rout.save? ... OK > Testing examples for package ?utils? > comparing ?utils-Ex.Rout? to ?utils-Ex.Rout.prev? ... OK > Testing examples for package ?grDevices? > comparing ?grDevices-Ex.Rout? to ?grDevices-Ex.Rout.save? ... OK > Testing examples for package ?graphics? > comparing ?graphics-Ex.Rout? to ?graphics-Ex.Rout.save? ... OK > Testing examples for package ?stats? > comparing ?stats-Ex.Rout? to ?stats-Ex.Rout.save? ... OK > Testing examples for package ?datasets? > comparing ?datasets-Ex.Rout? to ?datasets-Ex.Rout.save? ... OK > Testing examples for package ?methods? > comparing ?methods-Ex.Rout? to ?methods-Ex.Rout.prev? ... OK > Testing examples for package ?grid? > comparing ?grid-Ex.Rout? to ?grid-Ex.Rout.save? ... OK > Testing examples for package ?splines? > comparing ?splines-Ex.Rout? to ?splines-Ex.Rout.save? ... OK > Testing examples for package ?stats4? > comparing ?stats4-Ex.Rout? to ?stats4-Ex.Rout.save? ... OK > Testing examples for package ?tcltk? > comparing ?tcltk-Ex.Rout? to ?tcltk-Ex.Rout.prev? ... OK > Testing examples for package ?compiler? > comparing ?compiler-Ex.Rout? to ?compiler-Ex.Rout.prev? ... OK > Testing examples for package ?parallel? > comparing ?parallel-Ex.Rout? to ?parallel-Ex.Rout.prev? ... OK > make[3]: Leaving directory '/usr/local/src/R-devel/tests/Examples' > make[2]: Leaving directory '/usr/local/src/R-devel/tests' > make[2]: Entering directory '/usr/local/src/R-devel/tests' > running strict specific tests > make[3]: Entering directory '/usr/local/src/R-devel/tests' > running code in 'eval-etc.R' ... OK > comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK > running code in 'simple-true.R' ... OK > comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK > running code in 'arith-true.R' ... OK > comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK > running code in 'arith.R' ... OK > comparing 'arith.Rout' to './arith.Rout.save' ... OK > running code in 'lm-tests.R' ... OK > comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK > running code in 'ok-errors.R' ... OK > comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK > running code in 'method-dispatch.R' ... OK > comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK > running code in 'any-all.R' ... OK > comparing 'any-all.Rout' to './any-all.Rout.save' ... OK > running code in 'd-p-q-r-tests.R' ... OK > comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK > make[3]: Leaving directory '/usr/local/src/R-devel/tests' > running sloppy specific tests > make[3]: Entering directory '/usr/local/src/R-devel/tests' > running code in 'complex.R' ... OK > comparing 'complex.Rout' to './complex.Rout.save' ... OK > running code in 'print-tests.R' ... OK > comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK > running code in 'lapack.R' ... OK > comparing 'lapack.Rout' to './lapack.Rout.save' ... OK > running code in 'datasets.R' ... OK > comparing 'datasets.Rout' to './datasets.Rout.save' ... OK > running code in 'datetime.R' ... OK > comparing 'datetime.Rout' to './datetime.Rout.save' ... OK > running code in 'iec60559.R' ... OK > comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK > make[3]: Leaving directory '/usr/local/src/R-devel/tests' > make[2]: Leaving directory '/usr/local/src/R-devel/tests' > make[2]: Entering directory '/usr/local/src/R-devel/tests' > running regression tests ... > make[3]: Entering directory '/usr/local/src/R-devel/tests' > running code in 'array-subset.R' ... OK > running code in 'reg-tests-1a.R' ... OK > running code in 'reg-tests-1b.R' ... OK > running code in 'reg-tests-1c.R' ... OK > running code in 'reg-tests-1d.R' ... OK > running code in 'reg-tests-2.R' ... OK > comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK > running code in 'reg-examples1.R' ... OK > running code in 'reg-examples2.R' ... OK > running code in 'reg-packages.R' ... OK > running code in 'p-qbeta-strict-tst.R' ... OK > running code in 'r-strict-tst.R' ... OK > running code in 'reg-IO.R' ... OK > comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK > running code in 'reg-IO2.R' ... OK > comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK > running code in 'reg-plot.R' ... OK > comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK > running code in 'reg-S4-examples.R' ... OK > running code in 'reg-BLAS.R' ... OK > make[3]: Leaving directory '/usr/local/src/R-devel/tests' > make[3]: Entering directory '/usr/local/src/R-devel/tests' > running code in 'reg-tests-3.R' ... OK > comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK > running code in 'reg-examples3.R' ...Makefile.common:98: recipe for target 'reg- > examples3.Rout' failed > make[3]: *** [reg-examples3.Rout] Error 1 > make[3]: Leaving directory '/usr/local/src/R-devel/tests' > Makefile.common:273: recipe for target 'test-Reg' failed > make[2]: *** [test-Reg] Error 2 > make[2]: Leaving directory '/usr/local/src/R-devel/tests' > Makefile.common:165: recipe for target 'test-all-basics' failed > make[1]: *** [test-all-basics] Error 1 > make[1]: Leaving directory '/usr/local/src/R-devel/tests' > Makefile:239: recipe for target 'check-all' failed > make: *** [check-all] Error 2 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
Peter,
Retry how much of it? That is, where does it go in the sequence from svn up
to make
check? I'll update my notes so as to do it correctly.
In any case, I put it first and reran the whole command chain. I had recently
upgraded
linux from 14.xx LTS to 16.04 LTS so it makes sense to start over. This removed
the large
diff in base-Ex.Rout from the first part of the log, but the terminal error
still remains:
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
make[3]: Entering directory '/usr/local/src/R-devel/tests'
running code in 'reg-tests-3.R' ... OK
comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ...
OK
running code in 'reg-examples3.R' ...Makefile.common:98: recipe for
target
'reg-examples3.Rout' failed
make[3]: *** [reg-examples3.Rout] Error 1
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
Makefile.common:273: recipe for target 'test-Reg' failed
Here are lines 97-100 of tests/Makefile.common:
.R.Rout:
@rm -f $@ $@.fail $@.log
@$(ECHO) $(ECHO_N) "running code in '$<' ...$(ECHO_C)"
> $@.log
@$(R) < $< > $@.fail 2>&1 || (cat $@.log && rm
$@.log && exit 1)
There is one complier warning message, it prints in pink so as not to miss it!
main.c: In function ?dummy_ii?:
main.c:1669:12: warning: function returns address of local variable
[-Wreturn-local-addr]
return (uintptr_t) ⅈ
-------------
So as to be more complete I did "cd tests; R" and
source("reg-examples3.R"), and lo and
behold the error is
> source('reg-examples3.R')
Loading required package: MASS
Loading required package: survival
Error in fitter(X, Y, strats, offset, init, control, weights = weights, :
object 'Ccoxmart2' not found
Looking at src/coxmart2.c and src/init.c I don't see anything different than
the other
dozen .C routines in my survival package. The file tests/book7.R in the package
exercises
this routine, and CMD check passes.
Hints?
Terry T.
On 04/06/2017 07:52 AM, peter dalgaard wrote:> You may want to retry that after a make distclean, in case anything changed
in the toolchain.
>
> -pd
>
> On 6 Apr 2017, at 15:51 , Therneau, Terry M., Ph.D. <therneau at mayo.edu> wrote: > > Peter, > Retry how much of it? That is, where does it go in the sequence from svn up to make check? I'll update my notes so as to do it correctly.From the configure step, I'd expect. Actually, now that I look at your output again, you seem to be compiling in the source directory, which is generally a bad idea, because you end up with derived files intermixed with source code all over the place. If you compile in a parallel directory, then you can in the worst case just wipe it and start over. Also, compiling in the source dir has confused "make" on previous occasions (ideally, it should work, but most of us don't check and so are poorly motivated to track down issues). So svn up # mkdir ../BUILD if not there already cd ../BUILD ../R/configure make ... Also, for checking the tests, I think the canonical way is path/to/R --vanilla < reg-examples3.R which may be subtly different from using source(). I'd surmise that your issue is something with the C-level routine registration, but I haven't followed the technicalities of that in full detail. Did your build rebuild the survival package? -pd> > In any case, I put it first and reran the whole command chain. I had recently upgraded linux from 14.xx LTS to 16.04 LTS so it makes sense to start over. This removed the large diff in base-Ex.Rout from the first part of the log, but the terminal error still remains: > > make[3]: Leaving directory '/usr/local/src/R-devel/tests' > make[3]: Entering directory '/usr/local/src/R-devel/tests' > running code in 'reg-tests-3.R' ... OK > comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK > running code in 'reg-examples3.R' ...Makefile.common:98: recipe for target 'reg-examples3.Rout' failed > make[3]: *** [reg-examples3.Rout] Error 1 > make[3]: Leaving directory '/usr/local/src/R-devel/tests' > Makefile.common:273: recipe for target 'test-Reg' failed > > Here are lines 97-100 of tests/Makefile.common: > > .R.Rout: > @rm -f $@ $@.fail $@.log > @$(ECHO) $(ECHO_N) "running code in '$<' ...$(ECHO_C)" > $@.log > @$(R) < $< > $@.fail 2>&1 || (cat $@.log && rm $@.log && exit 1) > > > There is one complier warning message, it prints in pink so as not to miss it! > > main.c: In function ?dummy_ii?: > main.c:1669:12: warning: function returns address of local variable [-Wreturn-local-addr] > return (uintptr_t) ⅈ > > ------------- > > So as to be more complete I did "cd tests; R" and source("reg-examples3.R"), and lo and behold the error is > >> source('reg-examples3.R') > Loading required package: MASS > Loading required package: survival > Error in fitter(X, Y, strats, offset, init, control, weights = weights, : > object 'Ccoxmart2' not found > > Looking at src/coxmart2.c and src/init.c I don't see anything different than the other dozen .C routines in my survival package. The file tests/book7.R in the package exercises this routine, and CMD check passes. > > Hints? > > Terry T. > > > > > > > On 04/06/2017 07:52 AM, peter dalgaard wrote: >> You may want to retry that after a make distclean, in case anything changed in the toolchain. >> >> -pd >> >-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com