From owner-freebsd-ports-bugs@freebsd.org Mon Jul 31 16:38:07 2017 Return-Path: Delivered-To: freebsd-ports-bugs@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id EC58ADB3D87 for ; Mon, 31 Jul 2017 16:38:07 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2001:1900:2254:206a::16:76]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id CFECD835C4 for ; Mon, 31 Jul 2017 16:38:07 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from bugs.freebsd.org ([127.0.1.118]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id v6VGc7DN062339 for ; Mon, 31 Jul 2017 16:38:07 GMT (envelope-from bugzilla-noreply@freebsd.org) From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 221127] math/R: cannot install packages from CRAN Date: Mon, 31 Jul 2017 16:38:07 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Only Me X-Bugzilla-Who: rs.os@t-online.de X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: jrm@freebsd.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter flagtypes.name Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated MIME-Version: 1.0 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 31 Jul 2017 16:38:08 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D221127 Bug ID: 221127 Summary: math/R: cannot install packages from CRAN Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: jrm@freebsd.org Reporter: rs.os@t-online.de Flags: maintainer-feedback?(jrm@freebsd.org) Assignee: jrm@freebsd.org Hello, recently I discovered an issue by installing a new package from CRAN: `install.packages("roxygen2")` results in a segfault: ``` ... trying URL 'https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz' *** caught segfault *** address 0x7fffdfdfe000, cause 'invalid permissions' Traceback: 1: download.file(url, destfile, method, mode =3D "wb", ...) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch(expr, error =3D function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch)))=20= =20=20=20=20=20=20=20 call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type =3D "w") + nchar(sm[1L], type =3D "w") if (is.na(w= ))=20=20=20=20=20=20 w <- 14L + nchar(dcall, type =3D "b") + nchar(sm[1L], = type =3D "b") if (w > LONG) prefix <- paste0(prefix, "\n ") = }=20=20 else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\= n")=20 .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file =3D outFile) .Internal(printDeferredWarnings()) }=20=20=20 invisible(structure(msg, class =3D "try-error", condition =3D e))}) 6: try(download.file(url, destfile, method, mode =3D "wb", ...)) 7: download.packages(pkgs, destdir =3D tmpd, available =3D available,=20= =20=20=20 contriburl =3D contriburl, method =3D method, type =3D "source", quiet = =3D quiet, ...) 8: install.packages("roxygen2") ``` I tried to install various packages from CRAN. Segfault occurs after downloading a bunch of dependencies (there is not a certain dependency that throws this error). I tried the R package from the quarterly branch as well= as the package from the latest branch without any luck. Does this affect more people? Are there any workarounds? Best --=20 You are receiving this mail because: You are the assignee for the bug.=