[GitHub] [arrow] eddelbuettel edited a comment on issue #6435: CRAN package installation issues on Linux

[GitBox <gi...@apache.org>]

eddelbuettel edited a comment on issue #6435:
URL: https://github.com/apache/arrow/issues/6435#issuecomment-1065916683


   On Debian testing (fully current) with release 7.0.0 I can avoid the AVX issue on the old chipset by installing `libsnappy-dev`, and by (as before) unsetting `ccache` -- but builds still fail at the final loading stage and I would not know how to debug this:
   
   ```
   [...lots omitted...]
   g++  -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpMAMG47/R.INSTALL378f7d3f2336cf/arrow/libarrow/arrow-7.0.0/include  -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH
   _S3 -DARROW_R_WITH_JSON -I'/home/dirk/tmp/lib/cpp11/include'    -fpic  -g -O2 -Wall -pipe  -Wno-deprecated-declarations -Wno-parentheses -Wno-maybe-uninitialized -Wno-unused -Wno-sign-compare -Wno-ignored-attrib
   utes -Wno-nonnull -c threadpool.cpp -o threadpool.o 
   g++  -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpMAMG47/R.INSTALL378f7d3f2336cf/arrow/libarrow/arrow-7.0.0/include  -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH
   _S3 -DARROW_R_WITH_JSON -I'/home/dirk/tmp/lib/cpp11/include'    -fpic  -g -O2 -Wall -pipe  -Wno-deprecated-declarations -Wno-parentheses -Wno-maybe-uninitialized -Wno-unused -Wno-sign-compare -Wno-ignored-attrib
   utes -Wno-nonnull -c type_infer.cpp -o type_infer.o 
   g++ -std=gnu++11 -Wl,-S -shared -L/usr/lib/R/lib -Wl,-z,relro -o arrow.so RTasks.o altrep.o array.o array_to_vector.o arraydata.o arrowExports.o bridge.o buffer.o chunkedarray.o compression.o compute-exec.o comp
   ute.o config.o csv.o dataset.o datatype.o expression.o feather.o field.o filesystem.o imports.o io.o json.o memorypool.o message.o parquet.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o sca
   lar.o schema.o symbols.o table.o threadpool.o type_infer.o -L/tmp/RtmpMAMG47/R.INSTALL378f7d3f2336cf/arrow/libarrow/arrow-7.0.0/lib -larrow_dataset -lparquet -larrow -larrow /usr/lib/x86_64-linux-gnu/libbz2.so -
   pthread -larrow_bundled_dependencies -lsnappy -lbrotlidec -lbrotlienc -lbrotlicommon -lz -llz4 -lzstd -larrow -larrow_bundled_dependencies -larrow_dataset -lparquet -lssl -lcrypto -lcurl -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 0x7fc1c4914d73, 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 && !quietly)         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, nlines = 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’
   
   The downloaded source packages are in
           ‘/tmp/downloaded_packages’
   Warning message:
   In install.packages(pkgs, ...) :
     installation of package ‘arrow’ had non-zero exit status
   dirk@cloud-devel:~$ 
   ```
   
   I set `NOT_CRAN=true ARROW_R_DEV=true` and gave a target directory.   Debian testing, current -- i.e. a platform without RSPM support a fallback :-/  
   
   Any suggestions?
   
   PS Silly me. I just realized that this _is_ the AVX issue.  We're still getting an invalid code upsetting the cpu.  So no `arrow` for me on this older Xeon 5140.


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