failure of make check-all

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failure of make check-all

Therneau, Terry M., Ph.D.
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

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Re: failure of make check-all

Peter Dalgaard-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. <[hidden email]> 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
>
> ______________________________________________
> [hidden email] 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: [hidden email]  Priv: [hidden email]

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Re: failure of make check-all

Therneau, Terry M., Ph.D.
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) &ii;

-------------

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
>

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Re: failure of make check-all

Peter Dalgaard-2
In reply to this post by Peter Dalgaard-2

> On 6 Apr 2017, at 15:51 , Therneau, Terry M., Ph.D. <[hidden email]> 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) &ii;
>
> -------------
>
> 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: [hidden email]  Priv: [hidden email]

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Re: failure of make check-all

Tomas Kalibera
In reply to this post by Therneau, Terry M., Ph.D.

The warning that dummy_ii returns address of local variable is benign,
this function is intended to do so.
I've silenced it in R-devel.

Tomas


On 04/06/2017 03:51 PM, Therneau, Terry M., Ph.D. 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.
>
> 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) &ii;
>
> -------------
>
> 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
>>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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