From 4792fe2ea2a4984ed37a99c99c6534a1bfc248d1 Mon Sep 17 00:00:00 2001
From: Elliott Sales de Andrade <quantum.analyst@gmail.com>
Date: Jan 30 2020 08:12:52 +0000
Subject: Merge branch 'f30'


---

diff --git a/.gitignore b/.gitignore
index 0cece03..c77077c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@
 /data.table_1.12.2.tar.gz
 /data.table_1.12.4.tar.gz
 /data.table_1.12.6.tar.gz
+/data.table_1.12.8.tar.gz
diff --git a/0001-Fix-test-1729-on-ppc64le.patch b/0001-Fix-test-1729-on-ppc64le.patch
new file mode 100644
index 0000000..20813a4
--- /dev/null
+++ b/0001-Fix-test-1729-on-ppc64le.patch
@@ -0,0 +1,41 @@
+From f02279985b388aeb5d9c58f6fb82fea423fd477b Mon Sep 17 00:00:00 2001
+From: Elliott Sales de Andrade <quantum.analyst@gmail.com>
+Date: Wed, 13 Nov 2019 20:49:24 -0500
+Subject: [PATCH 1/3] Fix test 1729 on ppc64le.
+
+Signed-off-by: Elliott Sales de Andrade <quantum.analyst@gmail.com>
+---
+ inst/tests/tests.Rraw | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/inst/tests/tests.Rraw b/inst/tests/tests.Rraw
+index d287a398..de883b37 100644
+--- a/inst/tests/tests.Rraw
++++ b/inst/tests/tests.Rraw
+@@ -10342,7 +10342,7 @@ test(1729.05, nrow(DT), 507L)
+ 
+ options(datatable.verbose = FALSE) # capture.output() exact tests must not be polluted with verbosity
+ x = capture.output(fwrite(DT,na="NA"))[-1]   # -1 to remove the column name V1
+-y = capture.output(write.csv(DT,row.names=FALSE,quote=FALSE))[-1]
++y = gsub("\\.?0+e", "e", capture.output(write.csv(DT,row.names=FALSE,quote=FALSE))[-1])
+ # One mismatch that seems to be accuracy in base R's write.csv
+ # tmp = cbind(row=1:length(x), `fwrite`=x, `write.csv`=y)
+ # tmp[x!=y,]
+@@ -10388,12 +10388,12 @@ if (isTRUE(LD<-capabilities()["long.double"])) {  #3258
+   cat('Skipped test 1729.9 due to capabilities()["long.double"] ==', LD, '\n')
+ }
+ test(1729.10, fwrite(DT,na=""), output=ans)
+-test(1729.11, write.csv(DT,row.names=FALSE,quote=FALSE), output=ans)
++test(1729.11, gsub("\\.?0+e", "e", capture.output(write.csv(DT,row.names=FALSE,quote=FALSE))), ans)
+ DT = data.table(unlist(.Machine[c("double.eps","double.neg.eps","double.xmin","double.xmax")]))
+ #    double.eps double.neg.eps    double.xmin    double.xmax
+ #  2.220446e-16   1.110223e-16  2.225074e-308  1.797693e+308
+ test(1729.12, typeof(DT[[1L]]), "double")
+-test(1729.13, capture.output(fwrite(DT)), capture.output(write.csv(DT,row.names=FALSE,quote=FALSE)))
++test(1729.13, capture.output(fwrite(DT)), gsub("\\.?0+e", "e", capture.output(write.csv(DT,row.names=FALSE,quote=FALSE))))
+ 
+ if (test_bit64) {
+   test(1730.1, typeof(-2147483647L), "integer")
+-- 
+2.21.0
+
diff --git a/0002-Improve-fread-for-very-small-or-very-large-fp-number.patch b/0002-Improve-fread-for-very-small-or-very-large-fp-number.patch
new file mode 100644
index 0000000..12254ad
--- /dev/null
+++ b/0002-Improve-fread-for-very-small-or-very-large-fp-number.patch
@@ -0,0 +1,237 @@
+From f4334c4ac845f811b4be531c921cb50dc77007d1 Mon Sep 17 00:00:00 2001
+From: Elliott Sales de Andrade <quantum.analyst@gmail.com>
+Date: Thu, 9 Jan 2020 01:06:25 -0500
+Subject: [PATCH 2/3] Improve `fread` for very small or very large fp numbers.
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+On non-x86 architectures (armv7hl and ppc64le), test 1018 fails with a
+slightly differently parsed number. In base R, `R_strtod` handles small
+numbers by pre-dividing numerator and divsor before applying the
+exponent part (instead of dividing all together.) However, it does not
+use a lookup table.
+
+For `fread`, trim the exponent lookup table from ±350 to ±300, and if
+anything is in that removed range, do two multiplications instead. This
+results in approximately the same effect as in base R.
+
+Removing some of the range from the lookup table also fixes several
+warnings such as:
+
+```
+freadLookups.h:57:1: warning: floating constant truncated to zero [-Woverflow]
+   57 | 1.0E-324L,
+      | ^~~~~~~~~
+freadLookups.h:690:1: warning: floating constant exceeds range of 'long double' [-Woverflow]
+  690 | 1.0E309L,
+      | ^~~~~~~~
+```
+
+See #3492 and #4032.
+
+Signed-off-by: Elliott Sales de Andrade <quantum.analyst@gmail.com>
+---
+ inst/tests/tests.Rraw |   3 +-
+ src/fread.c           |  26 ++++++++---
+ src/fread.h           |   2 +-
+ src/freadLookups.h    | 104 +-----------------------------------------
+ 5 files changed, 26 insertions(+), 111 deletions(-)
+
+diff --git a/inst/tests/tests.Rraw b/inst/tests/tests.Rraw
+index de883b37..06b6dc2c 100644
+--- a/inst/tests/tests.Rraw
++++ b/inst/tests/tests.Rraw
+@@ -2929,7 +2929,8 @@ test(1017.2, fread(f, integer64="character"), DT)
+ unlink(f)
+ 
+ # ERANGE errno handled, #4879
+-test(1018, identical(fread("1.46761e-313\n"), data.table(V1=1.46761e-313)))
++test(1018.1, identical(fread("1.46761e-313\n"), data.table(V1=1.46761e-313)))
++test(1018.2, identical(fread("1.46761e+313\n"), data.table(V1=1.46761e+313)))
+ test(1019, fread("A\n1.23456789123456789123456999\n"), data.table(A=1.234567891234568))
+ 
+ # crash assigning to row 0, #2754
+diff --git a/src/fread.c b/src/fread.c
+index 7d6e4f05..57cdfc83 100644
+--- a/src/fread.c
++++ b/src/fread.c
+@@ -644,9 +644,9 @@ static void StrtoI64(FieldParseContext *ctx)
+ // TODO: review ERANGE checks and tests; that range outside [1.7e-308,1.7e+308] coerces to [0.0,Inf]
+ /*
+ f = "~/data.table/src/freadLookups.h"
+-cat("const long double pow10lookup[701] = {\n", file=f, append=FALSE)
+-for (i in (-350):(349)) cat("1.0E",i,"L,\n", sep="", file=f, append=TRUE)
+-cat("1.0E350L\n};\n", file=f, append=TRUE)
++cat("const long double pow10lookup[601] = {\n", file=f, append=FALSE)
++for (i in (-300):(299)) cat("1.0E",i,"L,\n", sep="", file=f, append=TRUE)
++cat("1.0E300L\n};\n", file=f, append=TRUE)
+ */
+ 
+ 
+@@ -763,11 +763,23 @@ static void parse_double_regular(FieldParseContext *ctx)
+     }
+     e += Eneg? -E : E;
+   }
+-  e += 350; // lookup table is arranged from -350 (0) to +350 (700)
+-  if (e<0 || e>700) goto fail;
++  if (e<-350 || e>350) goto fail;
+ 
+-  double r = (double)((long double)acc * pow10lookup[e]);
+-  *target = neg? -r : r;
++  long double r = (long double)acc;
++  if (e < -300 || e > 300) {
++    // Handle extra precision by pre-multiplying the result by pow(10, extra),
++    // and then remove extra from e.
++    // This avoids having to store very small or very large constants that may
++    // fail to be encoded by the compiler, even though the values can actually
++    // be stored correctly.
++    int_fast8_t extra = e < 0 ? e + 300 : e - 300;
++    r *= pow10lookup[extra + 300];
++    e -= extra;
++  }
++  e += 300; // lookup table is arranged from -300 (0) to +300 (600)
++
++  r *= pow10lookup[e];
++  *target = (double)(neg? -r : r);
+   *(ctx->ch) = ch;
+   return;
+ 
+diff --git a/src/fread.h b/src/fread.h
+index ec230c69..64150d66 100644
+--- a/src/fread.h
++++ b/src/fread.h
+@@ -30,7 +30,7 @@ typedef enum {
+ 
+ extern int8_t typeSize[NUMTYPE];
+ extern const char typeName[NUMTYPE][10];
+-extern const long double pow10lookup[701];
++extern const long double pow10lookup[601];
+ extern const uint8_t hexdigits[256];
+ 
+ 
+diff --git a/src/freadLookups.h b/src/freadLookups.h
+index faeb4ade..bb736a60 100644
+--- a/src/freadLookups.h
++++ b/src/freadLookups.h
+@@ -27,57 +27,7 @@ const uint8_t hexdigits[256] = {
+ };
+ 
+ 
+-const long double pow10lookup[701] = {
+-1.0E-350L,
+-1.0E-349L,
+-1.0E-348L,
+-1.0E-347L,
+-1.0E-346L,
+-1.0E-345L,
+-1.0E-344L,
+-1.0E-343L,
+-1.0E-342L,
+-1.0E-341L,
+-1.0E-340L,
+-1.0E-339L,
+-1.0E-338L,
+-1.0E-337L,
+-1.0E-336L,
+-1.0E-335L,
+-1.0E-334L,
+-1.0E-333L,
+-1.0E-332L,
+-1.0E-331L,
+-1.0E-330L,
+-1.0E-329L,
+-1.0E-328L,
+-1.0E-327L,
+-1.0E-326L,
+-1.0E-325L,
+-1.0E-324L,
+-1.0E-323L,
+-1.0E-322L,
+-1.0E-321L,
+-1.0E-320L,
+-1.0E-319L,
+-1.0E-318L,
+-1.0E-317L,
+-1.0E-316L,
+-1.0E-315L,
+-1.0E-314L,
+-1.0E-313L,
+-1.0E-312L,
+-1.0E-311L,
+-1.0E-310L,
+-1.0E-309L,
+-1.0E-308L,
+-1.0E-307L,
+-1.0E-306L,
+-1.0E-305L,
+-1.0E-304L,
+-1.0E-303L,
+-1.0E-302L,
+-1.0E-301L,
++const long double pow10lookup[601] = {
+ 1.0E-300L,
+ 1.0E-299L,
+ 1.0E-298L,
+@@ -678,57 +628,7 @@ const long double pow10lookup[701] = {
+ 1.0E297L,
+ 1.0E298L,
+ 1.0E299L,
+-1.0E300L,
+-1.0E301L,
+-1.0E302L,
+-1.0E303L,
+-1.0E304L,
+-1.0E305L,
+-1.0E306L,
+-1.0E307L,
+-1.0E308L,
+-1.0E309L,
+-1.0E310L,
+-1.0E311L,
+-1.0E312L,
+-1.0E313L,
+-1.0E314L,
+-1.0E315L,
+-1.0E316L,
+-1.0E317L,
+-1.0E318L,
+-1.0E319L,
+-1.0E320L,
+-1.0E321L,
+-1.0E322L,
+-1.0E323L,
+-1.0E324L,
+-1.0E325L,
+-1.0E326L,
+-1.0E327L,
+-1.0E328L,
+-1.0E329L,
+-1.0E330L,
+-1.0E331L,
+-1.0E332L,
+-1.0E333L,
+-1.0E334L,
+-1.0E335L,
+-1.0E336L,
+-1.0E337L,
+-1.0E338L,
+-1.0E339L,
+-1.0E340L,
+-1.0E341L,
+-1.0E342L,
+-1.0E343L,
+-1.0E344L,
+-1.0E345L,
+-1.0E346L,
+-1.0E347L,
+-1.0E348L,
+-1.0E349L,
+-1.0E350L
++1.0E300L
+ };
+ 
+ #endif
+-- 
+2.21.0
+
diff --git a/0003-Use-consistent-types-with-fwriteMainArgs.nrow.patch b/0003-Use-consistent-types-with-fwriteMainArgs.nrow.patch
new file mode 100644
index 0000000..08bd403
--- /dev/null
+++ b/0003-Use-consistent-types-with-fwriteMainArgs.nrow.patch
@@ -0,0 +1,99 @@
+From 79911aaf7cd877c0d25fccd5aaecdecd9a5d0204 Mon Sep 17 00:00:00 2001
+From: Elliott Sales de Andrade <quantum.analyst@gmail.com>
+Date: Thu, 30 Jan 2020 01:26:50 -0500
+Subject: [PATCH 3/3] Use consistent types with fwriteMainArgs.nrow.
+
+On armv7hl, test 1737.5 fails due to garbage in the column length
+mismatch error message. This is because the message tries to format
+`args.nrow` (an `int64_t`) using `%d` (i.e., `int`). Strangely, this
+does not fail on any other architectures, but this is likely a fluke.
+
+In all the other formatting calls, remove the unnecessary `(int64_t)`
+type cast, since `fwriteMainArgs.nargs` already is one.
+
+Signed-off-by: Elliott Sales de Andrade <quantum.analyst@gmail.com>
+---
+ src/fwrite.c  |  6 +++---
+ src/fwriteR.c | 13 +++++++------
+ 2 files changed, 10 insertions(+), 9 deletions(-)
+
+diff --git a/src/fwrite.c b/src/fwrite.c
+index b5ff08cd..93cbaf62 100644
+--- a/src/fwrite.c
++++ b/src/fwrite.c
+@@ -620,7 +620,7 @@ void fwriteMain(fwriteMainArgs args)
+       for (int j=args.ncol-10; j<args.ncol; j++) DTPRINT("%d ", args.whichFun[j]);
+     }
+     DTPRINT("\nargs.doRowNames=%d args.rowNames=%d doQuote=%d args.nrow=%"PRId64" args.ncol=%d eolLen=%d\n",
+-          args.doRowNames, args.rowNames, doQuote, (int64_t)args.nrow, args.ncol, eolLen);
++          args.doRowNames, args.rowNames, doQuote, args.nrow, args.ncol, eolLen);
+   }
+ 
+   // Calculate upper bound for line length. Numbers use a fixed maximum (e.g. 12 for integer) while strings find the longest
+@@ -777,7 +777,7 @@ void fwriteMain(fwriteMainArgs args)
+   if (numBatches < nth) nth = numBatches;
+   if (verbose) {
+     DTPRINT("Writing %"PRId64" rows in %d batches of %d rows (each buffer size %dMB, showProgress=%d, nth=%d)\n",
+-            (int64_t)args.nrow, numBatches, rowsPerBatch, args.buffMB, args.showProgress, nth);
++            args.nrow, numBatches, rowsPerBatch, args.buffMB, args.showProgress, nth);
+   }
+   t0 = wallclock();
+ 
+@@ -905,7 +905,7 @@ void fwriteMain(fwriteMainArgs args)
+               if (verbose && !hasPrinted) DTPRINT("\n");
+               DTPRINT("\rWritten %.1f%% of %"PRId64" rows in %d secs using %d thread%s. "
+                       "maxBuffUsed=%d%%. ETA %d secs.      ",
+-                       (100.0*end)/args.nrow, (int64_t)args.nrow, (int)(now-startTime), nth, nth==1?"":"s",
++                       (100.0*end)/args.nrow, args.nrow, (int)(now-startTime), nth, nth==1?"":"s",
+                        maxBuffUsedPC, ETA);
+               // TODO: use progress() as in fread
+               nextTime = now+1;
+diff --git a/src/fwriteR.c b/src/fwriteR.c
+index 8040631d..e3d36606 100644
+--- a/src/fwriteR.c
++++ b/src/fwriteR.c
+@@ -26,7 +26,7 @@ const int getStringLen(SEXP *col, int64_t row) {
+ const int getMaxStringLen(const SEXP *col, const int64_t n) {
+   int max=0;
+   SEXP last=NULL;
+-  for (int i=0; i<n; ++i) {
++  for (int64_t i=0; i<n; ++i) {
+     SEXP this = *col++;
+     if (this==last) continue; // no point calling LENGTH() again on the same string; LENGTH is unlikely as fast as single pointer compare
+     int thisnchar = LENGTH(this);
+@@ -90,17 +90,17 @@ void writeList(SEXP *col, int64_t row, char **pch) {
+ const int getMaxListItemLen(const SEXP *col, const int64_t n) {
+   int max=0;
+   SEXP last=NULL;
+-  for (int i=0; i<n; ++i) {
++  for (int64_t i=0; i<n; ++i) {
+     SEXP this = *col++;
+     if (this==last) continue; // no point calling LENGTH() again on the same string; LENGTH is unlikely as fast as single pointer compare
+     int32_t wf = whichWriter(this);
+     if (TYPEOF(this)==VECSXP || wf==INT32_MIN || isFactor(this)) {
+-      error("Row %d of list column is type '%s' - not yet implemented. fwrite() can write list columns containing items which are atomic vectors of" \
++      error("Row %"PRId64" of list column is type '%s' - not yet implemented. fwrite() can write list columns containing items which are atomic vectors of" \
+             " type logical, integer, integer64, double, complex and character.", i+1, isFactor(this) ? "factor" : type2char(TYPEOF(this)));
+     }
+     int width = writerMaxLen[wf];
+     if (width==0) {
+-      if (wf!=WF_String) STOP("Internal error: row %d of list column has no max length method implemented", i+1); // # nocov
++      if (wf!=WF_String) STOP("Internal error: row %"PRId64" of list column has no max length method implemented", i+1); // # nocov
+       const int l = LENGTH(this);
+       for (int j=0; j<l; ++j) width+=LENGTH(STRING_ELT(this, j));
+     } else {
+@@ -230,8 +230,9 @@ SEXP fwriteR(
+   int firstListColumn = 0;
+   for (int j=0; j<args.ncol; j++) {
+     SEXP column = VECTOR_ELT(DFcoerced, j);
+-    if (args.nrow != length(column))
+-      error("Column %d's length (%d) is not the same as column 1's length (%d)", j+1, length(column), args.nrow);
++    if (args.nrow != length(column)) {
++      error("Column %d's length (%d) is not the same as column 1's length (%"PRId64")", j+1, length(column), args.nrow);
++    }
+     int32_t wf = whichWriter(column);
+     if (wf<0) {
+       error("Column %d's type is '%s' - not yet implemented in fwrite.", j+1, type2char(TYPEOF(column)));
+-- 
+2.21.0
+
diff --git a/R-data.table.spec b/R-data.table.spec
index 722c4df..b9af09a 100644
--- a/R-data.table.spec
+++ b/R-data.table.spec
@@ -7,13 +7,19 @@
 %global with_loop 0
 
 Name:             R-%{packname}
-Version:          1.12.6
+Version:          1.12.8
 Release:          1%{?dist}
 Summary:          Extension of `data.frame`
 
 License:          MPLv2.0
 URL:              https://CRAN.R-project.org/package=%{packname}
 Source0:          https://cran.r-project.org/src/contrib/%{packname}_%{version}.tar.gz
+# https://github.com/Rdatatable/data.table/issues/4032
+Patch0001:        0001-Fix-test-1729-on-ppc64le.patch
+# https://github.com/Rdatatable/data.table/pull/4165
+Patch0002:        0002-Improve-fread-for-very-small-or-very-large-fp-number.patch
+# https://github.com/Rdatatable/data.table/pull/4213
+Patch0003:        0003-Use-consistent-types-with-fwriteMainArgs.nrow.patch
 
 # Here's the R view of the dependencies world:
 # Depends:
@@ -46,6 +52,14 @@ natural and flexible syntax, for faster development.
 %prep
 %setup -q -c -n %{packname}
 
+pushd %{packname}
+bunzip2 inst/tests/tests.Rraw.bz2
+%patch0001 -p1
+%patch0002 -p1
+%patch0003 -p1
+bzip2 inst/tests/tests.Rraw
+popd
+
 
 %build
 
@@ -83,6 +97,9 @@ _R_CHECK_FORCE_SUGGESTS_=0 %{_bindir}/R CMD check %{packname}
 
 
 %changelog
+* Mon Jan 06 2020 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.12.8-1
+- Update to latest version
+
 * Mon Oct 21 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.12.6-1
 - Update to latest version
 
diff --git a/sources b/sources
index 47d8a15..98658a7 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (data.table_1.12.6.tar.gz) = 468a2728d9f2ae8f14ed7675f04c7526ef3b55123f84a9693bfdbec00355f4ebc75a6b3a45e0c451ef590ed6b8db716f61a973e8240c38908c4ac62edbce9cba
+SHA512 (data.table_1.12.8.tar.gz) = 04ffe5e2b5c7ad221dc8d48fb51f2b6717cece14926b71186177f7a3aba31fcb47441dbded0a6f298e434a18baa96d372b30ee16bfb8bd6f6e59c49edeea2b39