eddelbuettel commented on issue #6435:
URL: https://github.com/apache/arrow/issues/6435#issuecomment-663879003
Just FYI I am continuing to have issues with Arrow, both 0.17.1 and 1.0.0.
I use a rather plain and pristine Debian testing machine for all reverse
dependency checking I do for my packages, and there arrow just segfaults on
load. Happened for weeks with 0.17.1 (so I now added Arrow to a list of
packages to skip) and continues with 1.0.0. I have no idea why.
The second required build to actual obtain Arrow dies on shown below. It
_looks_ good but then it blows up. Could it be that one of the pre-made
libraries you download bites?
```
R> arrow::install_arrow()
Installing package into ‘/home/dirk/tmp/lib’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/arrow_1.0.0.tar.gz'
Content type 'application/x-gzip' length 274139 bytes (267 KB)
==================================================
downloaded 267 KB
* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** Using centos-8 binary for debian-11
*** Successfully
retrieved C++ binaries for centos-8
PKG_CFLAGS=-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW
PKG_LIBS=-L/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/lib
-larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies
-larrow_dataset -lparquet
** libs
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c array.cpp -o array.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c array_from_vector.cpp -o
array_from_vector.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c array_to_vector.cpp -o array_to_vector.o
ccache g++ -std=gnu++11
-I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c arraydata.cpp -o arraydata.o
ccache g++ -std=gnu++11
-I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_A
RROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c arrowExports.cpp -o arrowExports.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c buffer.cpp -o buffer.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c chunkedarray.cpp -o chunkedarray.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c compression.cpp -o compression.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c compute.cpp -o compute.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c csv.cpp -o csv.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c dataset.cpp -o dataset.o
In file included from
/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include/arrow/dataset/api.h:27,
from dataset.cpp:22:
/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include/arrow/dataset/file_parquet.h:42:2:
warning: extra ‘;’ [-Wpedantic]
42 | }; // namespace arrow
| ^
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c datatype.cpp -o datatype.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c expression.cpp -o expression.o
In file included from
/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include/arrow/dataset/api.h:27,
from expression.cpp:22:
/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include/arrow/dataset/file_parquet.h:42:2:
warning: extra ‘;’ [-Wpedantic]
42 | }; // namespace arrow
| ^
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c feather.cpp -o feather.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c field.cpp -o field.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c filesystem.cpp -o filesystem.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c imports.cpp -o imports.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c io.cpp -o io.o
ccache g++ -std=gnu++11
-I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c json.cpp -o json.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c memorypool.cpp -o memorypool.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c message.cpp -o message.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c parquet.cpp -o parquet.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c py-to-r.cpp -o py-to-r.o
ccache g++ -std=gnu++11
-I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c recordbatch.cpp -o recordbatch.o
ccache g++ -std=gnu++11
-I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_A
RROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c recordbatchreader.cpp -o
recordbatchreader.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c recordbatchwriter.cpp -o
recordbatchwriter.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c scalar.cpp -o scalar.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c schema.cpp -o schema.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c symbols.cpp -o symbols.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c table.cpp -o table.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/include
-DARROW_R_WITH_ARROW -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic
-g -O2 -Wall -pipe -pedantic -c threadpool.cpp -o threadpool.o
ccache g++ -std=gnu++11 -Wl,-S -shared -L/usr/lib/R/lib -Wl,-z,relro -o
arrow.so array.o array_from_vector.o array_to_vector.o arraydata.o
arrowExports.o buffer.o chunkedarray.o compression.o compute.o csv.o dat
aset.o datatype.o expression.o feather.o field.o filesystem.o imports.o io.o
json.o memorypool.o message.o parquet.o py-to-r.o recordbatch.o
recordbatchreader.o recordbatchwriter.o scalar.o schema.o symbols.o ta
ble.o threadpool.o
-L/tmp/Rtmpm3tGKI/R.INSTALL7ce377c95737/arrow/libarrow/arrow-1.0.0/lib
-larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies
-larrow_dataset -lparquet -L/usr/lib/R/lib -lR
installing to /home/dirk/tmp/lib/00LOCK-arrow/00new/arrow/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** caught illegal operation ***
address 0x7f442e6c2917, cause 'illegal operand'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <-
loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps,
exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <-
conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <-
gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e)) if (logical.return)
message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE,
domain = NA)})
8: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return =
TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c)
tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if
(!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <-
paste("Error in", dcall, ": ") LONG <- 75L sm <-
strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type =
"w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L +
nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if
(w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <-
"Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent &&
isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
.Internal(printDeferredWarnings()) } invisible(structure(msg, class =
"try-error", condition = e))})
15: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE)))
16: tools:::.test_load_package("arrow",
"/home/dirk/tmp/lib/00LOCK-arrow/00new")
An irrecoverable exception occurred. R is aborting now ...
Illegal instruction
ERROR: loading failed
* removing ‘/home/dirk/tmp/lib/arrow’
* restoring previous ‘/home/dirk/tmp/lib/arrow’
The downloaded source packages are in
‘/tmp/RtmpHlrGzt/downloaded_packages’
Attaching package: ‘arrow’
The following object is masked from ‘package:utils’:
timestamp
Warning message:
In install.packages("arrow", repos = arrow_repos(repos, nightly), :
installation of package ‘arrow’ had non-zero exit status
R> q()
Save workspace image? [y/n/c]: n
```
R 4.0.2, Debian testing, all Debian packages current, all R packages current
to CRAN.
Iif there is an alternate build way you'd want to test let me know. Else if
I need Arrow I may just rely on an RSPM build.
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