New CRAN UBSAN issue(s)

[eddelbuettel]

Changes in r-devel last week lead to an email to Rcpp (see this issue) also mentions new UBSAN issues for nanotime 😿

See this log which I haven't tried to replicate yet.

[eddelbuettel]

Further email from Dortmund upon re-submission:

Thanks, we see with gcc-UBSAN still

est_nanoival.R............... 143 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:46:46:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:340:62:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 144 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 301 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 302 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 303 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 304 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 308 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const type', which requires 8 byte alignment
test_nanoival.R............... 309 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'union type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const union type', which requires 8 byte alignment
test_nanoival.R............... 310 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const type', which requires 8 byte alignment
test_nanoival.R............... 311 tests OK
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52:
runtime error: reference binding to misaligned address 0x000000000001 for type
'type', which requires 8 byte alignment
nanotime.Rcheck/tests/tinytest.Rout:/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75:
runtime error: reference binding to misaligned address 0x000000000001 for type
'const type', which requires 8 byte alignment

Please fix and resubmit.

Using the update (ie freshly pulled) container via docker pull rocker/r-devel-san I can repluicate by launching the container (with the repo mounted) and installing inside it

RDscript -e 'install.packages(c("bit64", "RcppCCTZ", "zoo", "Rcpp", "RcppDate", "tinytest", "data.table"))' 
RD CMD INSTALL nanotime_0.3.8.tar.gz
RDscript -e 'tinytest::test_package("nanotime")'

The issue is actually an Rcpp issue we are looking at but having open questions, see RcppCore/Rcpp#1310

I am therefore proposing the skip the offending tests for now as per this diff ensuring the tests still run at continuous integratin at GitHub, but not at CRAN:

modified   inst/tinytest/test_nanoival.R
@@ -2,6 +2,7 @@ library(nanotime)
 suppressMessages(library(bit64))
 
 isSolaris <- Sys.info()[["sysname"]] == "SunOS"
+extended_tests <- Sys.getenv("CI", "") != ""
 
 savedFormat <- NULL
 one_second  <- 1e9
@@ -555,12 +556,15 @@ expect_true(is.null(names(c_xy)))
 ## --------------------------------------------------------------------------
 
 ## time - interval
+## N=143
 
 ## test_intersect_time_interval_null_interval <- function() {
-i1 <- as.nanoival(NULL)
-s1 <- seq(nanotime("2015-01-01 12:00:00"), length.out=10, by=one_second)
-expect_identical(s1[i1], as.nanotime())
-expect_identical(s1 %in% i1, rep(FALSE, 10))
+if (extended_tests) {
+    i1 <- as.nanoival(NULL)
+    s1 <- seq(nanotime("2015-01-01 12:00:00"), length.out=10, by=one_second)
+    expect_identical(s1[i1], as.nanotime())
+    expect_identical(s1 %in% i1, rep(FALSE, 10))
+}
 
 ##test_intersect.idx_unsorted <- function() {
 a <- c(nanotime("2013-12-12 12:12:12"), nanotime("2012-12-12 12:12:12"))
@@ -1432,19 +1436,21 @@ expect_identical(nanoival.sopen(nanoival()), logical())
 expect_identical(nanoival.eopen(nanoival()), logical())
 
 ## set ops:
-expect_identical(union(nanoival(nanotime(1), nanotime(2)), nanoival()), nanoival(nanotime(1), nanotime(2)))
-expect_identical(intersect(nanoival(nanotime(1), nanotime(2)), nanoival()), nanoival())
-expect_identical(setdiff(nanoival(nanotime(1), nanotime(2)), nanoival()), nanoival(nanotime(1), nanotime(2)))
-expect_identical(setdiff.idx(nanotime(), nanoival()), numeric())
-expect_identical(setdiff.idx(nanotime(1), nanoival()), 1)
-expect_identical(setdiff.idx(nanotime(), nanoival(nanotime(1), nanotime(2))), numeric())
-expect_identical(intersect(nanotime(1), nanoival()), nanotime())
-expect_identical(intersect(nanotime(), nanoival(nanotime(1), nanotime(2))), nanotime())
-expect_identical(intersect.idx(nanotime(1), nanoival()), list(x=numeric(), y=numeric()))
-expect_identical(intersect.idx(nanotime(), nanoival(nanotime(1), nanotime(2))), list(x=numeric(), y=numeric()))
-expect_identical(nanotime() %in% nanoival(nanotime(1), nanotime(2)), logical(0))
-expect_identical(nanotime(1:10) %in% nanoival(), rep(FALSE, 10))
-expect_identical(is.na(as.nanoival()), logical())
+if (extended_tests) {
+    expect_identical(union(nanoival(nanotime(1), nanotime(2)), nanoival()), nanoival(nanotime(1), nanotime(2)))
+    expect_identical(intersect(nanoival(nanotime(1), nanotime(2)), nanoival()), nanoival())
+    expect_identical(setdiff(nanoival(nanotime(1), nanotime(2)), nanoival()), nanoival(nanotime(1), nanotime(2)))
+    expect_identical(setdiff.idx(nanotime(), nanoival()), numeric())
+    expect_identical(setdiff.idx(nanotime(1), nanoival()), 1)
+    expect_identical(setdiff.idx(nanotime(), nanoival(nanotime(1), nanotime(2))), numeric())
+    expect_identical(intersect(nanotime(1), nanoival()), nanotime())
+    expect_identical(intersect(nanotime(), nanoival(nanotime(1), nanotime(2))), nanotime())
+    expect_identical(intersect.idx(nanotime(1), nanoival()), list(x=numeric(), y=numeric()))
+    expect_identical(intersect.idx(nanotime(), nanoival(nanotime(1), nanotime(2))), list(x=numeric(), y=numeric()))
+    expect_identical(nanotime() %in% nanoival(nanotime(1), nanotime(2)), logical(0))
+    expect_identical(nanotime(1:10) %in% nanoival(), rep(FALSE, 10))
+    expect_identical(is.na(as.nanoival()), logical())
+}
 
 ## all.equal:
 expect_identical(all.equal(nanoival(nanotime(1), nanotime(2)), nanoival(nanotime(1), nanotime(2))), TRUE)

This has the desired effect:

root@2db179a00739:/work# RDscript -e 'tinytest::run_test_dir("inst/tinytest")'
test_data.frame.R.............   16 tests OK 0.8s
test_data.table.R.............   16 tests OK 0.1s
test_nanoduration.R...........  252 tests OK 0.4s
test_nanoival.R...............  304 tests OK 0.9s
test_nanoperiod.R.............  336 tests OK 0.2s
test_nanotime.R...............  267 tests OK 0.3s
test_ops.R....................   58 tests OK 91ms
test_xts.R....................    0 tests    2ms [Exited at #43: Skip xts tests for now]
test_zoo.R....................    1 tests OK 18ms
All ok, 1250 results (2.8s)
root@2db179a00739:/work#