[package - main-amd64-default][math/R-cran-XLConnect] Failed for R-cran-XLConnect-1.0.5 in stage
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Date: Wed, 05 Oct 2022 01:35:14 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://beefy18.nyi.freebsd.org/data/main-amd64-default/p73caab237543_sab9293239c/logs/R-cran-XLConnect-1.0.5.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=p73caab237543_sab9293239c
Log:
=>> Building math/R-cran-XLConnect
build started at Wed Oct 5 01:34:57 UTC 2022
port directory: /usr/ports/math/R-cran-XLConnect
package name: R-cran-XLConnect-1.0.5
building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400072 amd64
maintained by: thierry@FreeBSD.org
Makefile ident:
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Host OSVERSION: 1400063
Jail OSVERSION: 1400072
Job Id: 10
!!! Jail is newer than host. (Jail: 1400072, Host: 1400063) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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--PLIST_SUB--
JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" R_MOD_DIR=lib/R/library/XLConnect OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/XLConnect" EXAMPLESDIR="share/examples/XLConnect" DATADIR="share/XLConnect" WWWDIR="www/XLConnect" ETCDIR="etc/XLConnect"
--End PLIST_SUB--
--SUB_LIST--
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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-amd64-default-job-10] Installing pkg-1.18.4...
[main-amd64-default-job-10] 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-amd64-default-job-10] Installing R-cran-rJava-1.0.6...
[main-amd64-default-job-10] `-- Installing R-4.2.1...
<snip>
The alsa-lib port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
=====
Message from libinotify-20211018:
--
You might want to consider increasing the kern.maxfiles tunable if you plan
to use this library for applications that need to monitor activity of a lot
of files.
=====
Message from openjdk8-8.342.07.1_1:
--
This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and
procfs(5) mounted on /proc.
If you have not done it yet, please do the following:
mount -t fdescfs fdesc /dev/fd
mount -t procfs proc /proc
To make it permanent, you need the following lines in /etc/fstab:
fdesc /dev/fd fdescfs rw 0 0
proc /proc procfs rw 0 0
===> R-cran-XLConnect-1.0.5 depends on package: R-cran-rJava>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on file: /usr/local/openjdk8/bin/java - found
===> R-cran-XLConnect-1.0.5 depends on file: /usr/local/bin/R - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for R-cran-XLConnect-1.0.5
===========================================================================
=======================<phase: build >============================
===========================================================================
=======================<phase: run-depends >============================
===> R-cran-XLConnect-1.0.5 depends on package: R-cran-rJava>0 - found
===> R-cran-XLConnect-1.0.5 depends on package: apache-poi>0 - not found
===> Installing existing package /packages/All/apache-poi-4.1.2.pkg
[main-amd64-default-job-10] Installing apache-poi-4.1.2...
[main-amd64-default-job-10] Extracting apache-poi-4.1.2: .......... done
=====
Message from apache-poi-4.1.2:
--
===> NOTICE:
The apache-poi port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> R-cran-XLConnect-1.0.5 depends on package: apache-poi>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on package: SparseBitSet>0 - not found
===> Installing existing package /packages/All/SparseBitSet-1.2.pkg
[main-amd64-default-job-10] Installing SparseBitSet-1.2...
[main-amd64-default-job-10] Extracting SparseBitSet-1.2: .... done
===> R-cran-XLConnect-1.0.5 depends on package: SparseBitSet>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on package: apache-xmlbeans>0 - not found
===> Installing existing package /packages/All/apache-xmlbeans-3.1.0.pkg
[main-amd64-default-job-10] Installing apache-xmlbeans-3.1.0...
[main-amd64-default-job-10] Extracting apache-xmlbeans-3.1.0: .......... done
=====
Message from apache-xmlbeans-3.1.0:
--
To use XMLBeans you might have to define the following variables:
export XMLBEANS_HOME=/usr/local/share/java/classes
export CLASSPATH=/usr/local/share/java/classes/xmlbeans.jar:$CLASSPATH
===> R-cran-XLConnect-1.0.5 depends on package: apache-xmlbeans>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-math>0 - not found
===> Installing existing package /packages/All/apache-commons-math-3.6.1_1.pkg
[main-amd64-default-job-10] Installing apache-commons-math-3.6.1_1...
[main-amd64-default-job-10] Extracting apache-commons-math-3.6.1_1: ........ done
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-math>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-codec>0 - not found
===> Installing existing package /packages/All/apache-commons-codec-1.15.pkg
[main-amd64-default-job-10] Installing apache-commons-codec-1.15...
[main-amd64-default-job-10] Extracting apache-commons-codec-1.15: .......... done
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-codec>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-compress>0 - not found
===> Installing existing package /packages/All/apache-commons-compress-1.21.pkg
[main-amd64-default-job-10] Installing apache-commons-compress-1.21...
[main-amd64-default-job-10] Extracting apache-commons-compress-1.21: .......... done
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-compress>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-collections4>0 - not found
===> Installing existing package /packages/All/apache-commons-collections4-4.4.pkg
[main-amd64-default-job-10] Installing apache-commons-collections4-4.4...
[main-amd64-default-job-10] Extracting apache-commons-collections4-4.4: .......... done
===> R-cran-XLConnect-1.0.5 depends on package: apache-commons-collections4>0 - found
===> Returning to build of R-cran-XLConnect-1.0.5
===> R-cran-XLConnect-1.0.5 depends on file: /usr/local/openjdk8/bin/java - found
===> R-cran-XLConnect-1.0.5 depends on file: /usr/local/bin/R - found
===========================================================================
=======================<phase: stage >============================
===> Staging for R-cran-XLConnect-1.0.5
===> Generating temporary packing list
* 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/RtmplKumTd/file2872424d7713': No such file or directory
Error in file(con, "rb") : cannot open the connection
* removing '/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