valgrind (#4666)

.dev/.bash_aliases

@@ -11,6 +11,7 @@ alias gdm='git difftool master &> /dev/null'
 alias Rdevel='~/build/R-devel/bin/R --vanilla'
 alias Rdevel-strict-gcc='~/build/R-devel-strict-gcc/bin/R --vanilla'
 alias Rdevel-strict-clang='~/build/R-devel-strict-clang/bin/R --vanilla'
+alias Rdevel-valgrind='~/build/R-devel-valgrind/bin/R --vanilla'
 alias Rdevel32='~/build/32bit/R-devel/bin/R --vanilla'
 alias R310='~/build/R-3.1.0/bin/R --vanilla'
 alias revdepsh='cd ~/build/revdeplib/ && export TZ=UTC && export R_LIBS_SITE=none && export R_LIBS=~/build/revdeplib/ && export _R_CHECK_FORCE_SUGGESTS_=false'

.dev/CRAN_Release.cmd

@@ -368,29 +368,29 @@ print(Sys.time()); started.at<-proc.time(); try(test.data.table()); print(Sys.ti
 ###############################################
 
 cd ~/build
-rm -rf R-devel    # easiest way to remove ASAN from compiled packages in R-devel/library
-                  # to avoid "ASan runtime does not come first in initial library list" error; no need for LD_PRELOAD
-tar xvf R-devel.tar.gz
-cd R-devel
-./configure --without-recommended-packages --disable-byte-compiled-packages --disable-openmp --with-valgrind-instrumentation=1 CC="gcc" CFLAGS="-O0 -g -Wall -pedantic" LIBS="-lpthread"
+mkdir R-devel-valgrind  # separate build to avoid differences in installed packages, and
+                        # to avoid "ASan runtime does not come first in initial library list" error; no need for LD_PRELOAD
+tar xvf R-devel.tar.gz -C R-devel-valgrind --strip-components 1
+cd R-devel-valgrind
+./configure --without-recommended-packages --with-valgrind-instrumentation=2 --with-system-valgrind-headers CC="gcc" CFLAGS="-O2 -g -Wall -pedantic"
 make
 cd ~/GitHub/data.table
-vi ~/.R/Makevars  # make the -O0 -g line active, for info on source lines with any problems
-Rdevel CMD INSTALL data.table_1.13.1.tar.gz
-Rdevel -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes --show-leak-kinds=definite"
+vi ~/.R/Makevars  # make the -O2 -g line active, for info on source lines with any problems
+Rdevel-valgrind CMD INSTALL data.table_1.13.1.tar.gz
+R_DONT_USE_TK=true Rdevel-valgrind -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes --show-leak-kinds=definite,possible --gen-suppressions=all --suppressions=./.dev/valgrind.supp -s"
+# the default for --show-leak-kinds is 'definite,possible' which we're setting explicitly here as a reminder. CRAN uses the default too.
+#   including 'reachable' (as 'all' does) generates too much output from R itself about by-design permanent blocks
 # gctorture(TRUE)      # very slow, many days
 # gctorture2(step=100)
-print(Sys.time()); require(data.table); print(Sys.time()); started.at<-proc.time(); try(test.data.table()); print(Sys.time()); print(timetaken(started.at))
-# 3m require; 62m test
+print(Sys.time()); require(data.table); print(Sys.time()); started.at<-proc.time(); try(test.data.table(script="*.Rraw")); print(Sys.time()); print(timetaken(started.at))
+# 3m require; 62m test  # level 1 -O0
+# 1m require; 33m test  # level 2 -O2
+q() # valgrind output printed after q()
 
-# Investigated and ignore :
-# Tests 648 and 1262 (see their comments) have single precision issues under valgrind that don't occur on CRAN, even Solaris.
-# Old comment from gsumm.c ...  // long double usage here used to result in test 648 failing when run under valgrind
-                                // http://valgrind.org/docs/manual/manual-core.html#manual-core.limits"
+# Precision issues under valgrind are now avoided using test_longdouble in tests.Rraw, and exact_NaN in froll.Rraw
 # Ignore all "set address range perms" warnings :
 #   http://stackoverflow.com/questions/13558067/what-does-this-valgrind-warning-mean-warning-set-address-range-perms
 # Ignore heap summaries around test 1705 and 1707/1708 due to the fork() test opening/closing, I guess.
-# Tests 1729.4, 1729.8, 1729.11, 1729.13 again have precision issues under valgrind only.
 # Leaks for tests 1738.5, 1739.3 but no data.table .c lines are flagged, rather libcairo.so
 #   and libfontconfig.so via GEMetricInfo and GEStrWidth in libR.so
 

.dev/valgrind.supp

@@ -0,0 +1,24 @@
+{
+  <fontconfig>
+  Memcheck:Leak
+  ...
+  obj:*/libfontconfig.so.*
+  ...
+}
+
+{
+  <pango>
+  Memcheck:Leak
+  ...
+  obj:*libpango*.so.*
+  ...
+}
+
+{
+  <gobject>
+  Memcheck:Leak
+  ...
+  obj:*libgobject*.so.*
+  ...
+}
+

.travis.yml

@@ -8,7 +8,7 @@ r:
 
 os:
   - linux
-  - osx  # Takes 13m (+9m linux = 22m total); #3357; #3326; #3331. When off it's to speed up dev cycle; CRAN_Release.cmd has a reminder to turn back on.
+  # - osx  # Takes 13m (+9m linux = 22m total); #3357; #3326; #3331. When off it's to speed up dev cycle; CRAN_Release.cmd has a reminder to turn back on.
 
 brew_packages:
   - llvm

R/test.data.table.R

@@ -23,8 +23,11 @@ test.data.table = function(script="tests.Rraw", verbose=FALSE, pkg=".", silent=F
     scripts = dir(fulldir, "*.Rraw.*")
     scripts = scripts[!grepl("bench|other", scripts)]
     scripts = gsub("[.]bz2$","",scripts)
-    for (fn in scripts) {test.data.table(script=fn, verbose=verbose, pkg=pkg, silent=silent, showProgress=showProgress); cat("\n");}
-    return(invisible())
+    return(sapply(scripts, function(fn) {
+      err = try(test.data.table(script=fn, verbose=verbose, pkg=pkg, silent=silent, showProgress=showProgress))
+      cat("\n");
+      identical(err, TRUE)
+    }))
     # nocov end
   }
 
@@ -137,6 +140,7 @@ test.data.table = function(script="tests.Rraw", verbose=FALSE, pkg=".", silent=F
   cat("\n", date(),   # so we can tell exactly when these tests ran on CRAN to double-check the result is up to date
     "  endian==", .Platform$endian,
     ", sizeof(long double)==", .Machine$sizeof.longdouble,
+    ", longdouble.digits==", .Machine$longdouble.digits, # 64 normally, 53 for example under valgrind where some high accuracy tests need turning off, #4639
     ", sizeof(pointer)==", .Machine$sizeof.pointer,
     ", TZ==", if (is.na(tz)) "unset" else paste0("'",tz,"'"),
     ", Sys.timezone()=='", suppressWarnings(Sys.timezone()), "'",

inst/tests/froll.Rraw

@@ -9,6 +9,13 @@ if (exists("test.data.table", .GlobalEnv, inherits=FALSE)) {
   froll = data.table:::froll
 }
 
+exact_NaN = isTRUE(capabilities()["long.double"]) && identical(as.integer(.Machine$longdouble.digits), 64L)
+if (!exact_NaN) {
+  cat("\n**** Skipping 7 NaN/NA algo='exact' tests because .Machine$longdouble.digits==", .Machine$longdouble.digits, " (!=64); e.g. under valgrind\n\n", sep="")
+  # for Matt when he runs valgrind it is 53, but 64 when running regular R
+  # froll.c uses long double and appears to require full long double accuracy in the algo='exact'
+}
+
 ## rolling features
 
 #### atomic vectors input and single window returns atomic vectors
@@ -192,7 +199,7 @@ expected = list(
   c(rep(NA_real_,4), seq(1.5,2,0.25), rep(NA_real_, 1))
 )
 test(6000.040, ans1, expected)
-test(6000.041, ans2, expected)
+if (exact_NaN) test(6000.041, ans2, expected)
 ans1 = frollmean(d, 3, align="right", na.rm=TRUE)
 ans2 = frollmean(d, 3, align="right", algo="exact", na.rm=TRUE)
 expected = list(
@@ -208,7 +215,7 @@ expected = list(
   c(rep(NA_real_,3), seq(1.5,2,0.25), rep(NA_real_, 2))
 )
 test(6000.044, ans1, expected)
-test(6000.045, ans2, expected)
+if (exact_NaN) test(6000.045, ans2, expected)
 ans1 = frollmean(d, 3, align="center", na.rm=TRUE) # x even, n odd
 ans2 = frollmean(d, 3, align="center", algo="exact", na.rm=TRUE)
 expected = list(
@@ -224,7 +231,7 @@ expected = list(
   c(rep(NA_real_,3), 1.625, 1.875, rep(NA_real_, 3))
 )
 test(6000.048, ans1, expected)
-test(6000.049, ans2, expected)
+if (exact_NaN) test(6000.049, ans2, expected)
 ans1 = frollmean(d, 4, align="center", na.rm=TRUE) # x even, n even
 ans2 = frollmean(d, 4, align="center", algo="exact", na.rm=TRUE)
 expected = list(
@@ -241,7 +248,7 @@ expected = list(
   c(rep(NA_real_,3), 1.5, 1.75, 2, rep(NA_real_, 3))
 )
 test(6000.052, ans1, expected)
-test(6000.053, ans2, expected)
+if (exact_NaN) test(6000.053, ans2, expected)
 ans1 = frollmean(de, 3, align="center", na.rm=TRUE) # x odd, n odd
 ans2 = frollmean(de, 3, align="center", algo="exact", na.rm=TRUE)
 expected = list(
@@ -257,7 +264,7 @@ expected = list(
   c(rep(NA_real_, 3), 1.625, 1.875, rep(NA_real_,4))
 )
 test(6000.056, ans1, expected)
-test(6000.057, ans2, expected)
+if (exact_NaN) test(6000.057, ans2, expected)
 ans1 = frollmean(de, 4, align="center", na.rm=TRUE) # x odd, n even
 ans2 = frollmean(de, 4, align="center", algo="exact", na.rm=TRUE)
 expected = list(
@@ -273,7 +280,7 @@ expected = list(
   c(rep(NA_real_, 2), 1.5, 1.75, 2, rep(NA_real_,3))
 )
 test(6000.060, ans1, expected)
-test(6000.061, ans2, expected)
+if (exact_NaN) test(6000.061, ans2, expected)
 ans1 = frollmean(d, 3, align="left", na.rm=TRUE)
 ans2 = frollmean(d, 3, align="left", algo="exact", na.rm=TRUE)
 expected = list(
@@ -289,7 +296,7 @@ ans1 = frollmean(d, 2:3)
 ans2 = frollmean(d, 2:3, algo="exact")
 expected = list(c(NA, NA, NA, 1.75, NA, NA), rep(NA_real_, 6), c(NA, 0.875, 1.125, NA, NA, NA), c(NA, NA, 1, NA, NA, NA))
 test(6000.064, ans1, expected)
-test(6000.065, ans2, expected)
+if (exact_NaN) test(6000.065, ans2, expected)
 ans1 = frollmean(d, 2:3, na.rm=TRUE)
 ans2 = frollmean(d, 2:3, algo="exact", na.rm=TRUE)
 expected = list(c(NA, 0.5, 1.5, 1.75, 2, 3), c(NA, NA, 1, 1.75, 1.75, 2.5), c(NA, 0.875, 1.125, 1.25, NaN, NaN), c(NA, NA, 1, 1.125, 1.25, NaN))