From therneau at mayo.edu  Thu Apr  6 14:43:24 2017
From: therneau at mayo.edu (Therneau, Terry M., Ph.D.)
Date: Thu, 06 Apr 2017 07:43:24 -0500
Subject: [Rd] failure of make check-all
Message-ID: <47cabe$662clt@ironport10.mayo.edu>

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



[Rd] failure of make check-all
Therneau, Terry M., Ph.D.