[package - main-arm64-default][math/R-cran-XLConnect] Failed for R-cran-XLConnect-1.0.5 in stage
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Date: Wed, 12 Oct 2022 10:15:07 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: thierry@FreeBSD.org
Log URL: http://ampere2.nyi.freebsd.org/data/main-arm64-default/pd20a3cf7e848_s91a84eb5ba/logs/R-cran-XLConnect-1.0.5.log
Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=pd20a3cf7e848_s91a84eb5ba
Log:
=>> Building math/R-cran-XLConnect
build started at Wed Oct 12 10:13:49 UTC 2022
port directory: /usr/ports/math/R-cran-XLConnect
package name: R-cran-XLConnect-1.0.5
building for: FreeBSD main-arm64-default-job-04 14.0-CURRENT FreeBSD 14.0-CURRENT 1400072 arm64
maintained by: thierry@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> R-cran-XLConnect-1.0.5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-arm64-default-job-04] Installing pkg-1.18.4...
[main-arm64-default-job-04] Extracting pkg-1.18.4: .......... done
===> R-cran-XLConnect-1.0.5 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-XLConnect-1.0.5
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-XLConnect-1.0.5 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-XLConnect-1.0.5 for building
=> SHA256 Checksum OK for XLConnect_1.0.5.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-XLConnect-1.0.5 for building
===> Extracting for R-cran-XLConnect-1.0.5
=> SHA256 Checksum OK for XLConnect_1.0.5.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for R-cran-XLConnect-1.0.5
===> Applying FreeBSD patches for R-cran-XLConnect-1.0.5 from /usr/ports/math/R-cran-XLConnect/files
===========================================================================
=======================<phase: build-depends >============================
===> R-cran-XLConnect-1.0.5 depends on package: R-cran-rJava>0 - not found
===> Installing existing package /packages/All/R-cran-rJava-1.0.6.pkg
[main-arm64-default-job-04] Installing R-cran-rJava-1.0.6...
[main-arm64-default-job-04] `-- Installing R-4.2.1...
[main-arm64-default-job-04] | `-- Installing cairo-1.17.4_2,3...
<snip>
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .jinit(parameters = parameters)
2: .jpackage(name = pkgname, jars = "*", morePaths = sharedPaths)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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)})
14: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
15: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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))})
21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
22: tools:::.test_load_package("XLConnect", "/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library")
An irrecoverable exception occurred. R is aborting now ...
** testing if installed package keeps a record of temporary installation path
Warning in file(con, "rb") :
cannot open file '/tmp/Rtmp8UsTgo/filef1e5a42dc61': No such file or directory
Error in file(con, "rb") : cannot open the connection
** installing *source* package 'XLConnect' ...
file 'R/onLoad.R' has the wrong MD5 checksum
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
OpenJDK 64-Bit Server VM warning: Attempt to allocate stack guard pages failed.
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .jinit(parameters = parameters)
2: .jpackage(name = pkgname, jars = "*", morePaths = sharedPaths)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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)})
14: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
15: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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))})
21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
22: tools:::.test_load_package("XLConnect", "/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library/00LOCK-XLConnect/00new")
An irrecoverable exception occurred. R is aborting now ...
** testing if installed package can be loaded from final location
OpenJDK 64-Bit Server VM warning: Attempt to allocate stack guard pages failed.
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .jinit(parameters = parameters)
2: .jpackage(name = pkgname, jars = "*", morePaths = sharedPaths)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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)})
14: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
15: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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))})
21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
22: tools:::.test_load_package("XLConnect", "/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library")
An irrecoverable exception occurred. R is aborting now ...
** testing if installed package keeps a record of temporary installation path
Warning in file(con, "rb") :
cannot open file '/tmp/Rtmp8UsTgo/filef1e3ec2e7bf': No such file or directory
Error in file(con, "rb") : cannot open the connection
** installing *source* package 'XLConnect' ...
file 'R/onLoad.R' has the wrong MD5 checksum
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
OpenJDK 64-Bit Server VM warning: Attempt to allocate stack guard pages failed.
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .jinit(parameters = parameters)
2: .jpackage(name = pkgname, jars = "*", morePaths = sharedPaths)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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)})
14: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
15: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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))})
21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
22: tools:::.test_load_package("XLConnect", "/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library/00LOCK-XLConnect/00new")
An irrecoverable exception occurred. R is aborting now ...
** testing if installed package can be loaded from final location
OpenJDK 64-Bit Server VM warning: Attempt to allocate stack guard pages failed.
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .jinit(parameters = parameters)
2: .jpackage(name = pkgname, jars = "*", morePaths = sharedPaths)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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)})
14: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
15: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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))})
21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
22: tools:::.test_load_package("XLConnect", "/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library")
An irrecoverable exception occurred. R is aborting now ...
** testing if installed package keeps a record of temporary installation path
Warning in file(con, "rb") :
cannot open file '/tmp/Rtmp8UsTgo/filef1e65d6fc26': No such file or directory
Error in file(con, "rb") : cannot open the connection
** installing *source* package 'XLConnect' ...
file 'R/onLoad.R' has the wrong MD5 checksum
mv: rename /wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library/XLConnect to /wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library/00LOCK-XLConnect/XLConnect/XLConnect: Directory not empty
ERROR: cannot remove earlier installation, is it in use?
* removing '/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library/XLConnect'
* restoring previous '/wrkdirs/usr/ports/math/R-cran-XLConnect/work/stage/usr/local/lib/R/library/XLConnect'
*** Error code 1
Stop.
make: stopped in /usr/ports/math/R-cran-XLConnect