Oliver Kullmann
2012-Oct-13 21:16 UTC
[Rd] installation of R (2.14.1 and 2.15.1) fails due to [reg-packages.Rout] Error
Hello, I'm trying to install R from sources on two Linux machines (both with Suse 12.2): 1.> uname -aLinux cs-wsok 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux 2.> uname -aLinux csltok.swansea.ac.uk 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux I am trying version 2.14.1 on first machine and 2.15.1 on second machine. On both machines I'm using gcc and gfortran, version 4.5.4. On both machines I get the same test-error (the example below is for 2.14.1, but the messages are identicall with 2.15.1): running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ...make[4]: *** [reg-packages.Rout] Error 1 make[4]: Leaving directory `/home/csoliver/OKplatform/ExternalSources/builds/R/R-2.14.1/tests' make[3]: *** [test-Reg] Error 2 make[3]: Leaving directory `/home/csoliver/OKplatform/ExternalSources/builds/R/R-2.14.1/tests' make[2]: *** [test-all-basics] Error 1 The error-log in reg-packages.Rout.fail is (again for 2.14.1, but it is identical for 2.15.1, except of the obvious differences): --- R version 2.14.1 (2011-12-22) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.> ## PR 1271 detach("package:base") crashes R. > try(detach("package:base"))Error in detach("package:base") : detaching "package:base" is not allowed> > > ## invalid 'lib.loc' > stopifnot(length(installed.packages("mgcv")) == 0) > ## gave a low-level error message > > > ## package.skeleton() with metadata-only code > ## work in current (= ./tests/ directory): > tmp <- tempfile() > writeLines(c('setClass("foo", contains="numeric")',+ 'setMethod("show", "foo",', + ' function(object) cat("I am a \\"foo\\"\\n"))'), + tmp)> if(file.exists("myTst")) unlink("myTst", recursive=TRUE) > package.skeleton("myTst", code_files = tmp)# with a file name warningCreating directories ... Creating DESCRIPTION ... Creating NAMESPACE ... Creating Read-and-delete-me ... Copying code files ... Making help files ... Done. Further steps are described in './myTst/Read-and-delete-me'. Warning message: In package.skeleton("myTst", code_files = tmp) : Invalid file name(s) for R code in ./myTst/R: 'file7da22fb20b64' are now renamed to 'z<name>.R'> file.copy(tmp, (tm2 <- paste(tmp,".R", sep="")))[1] TRUE> unlink("myTst", recursive=TRUE) > op <- options(warn=2) # *NO* "invalid file name" warning {failed in 2.7.[01]}: > package.skeleton("myTst", code_files = tm2, namespace=TRUE)Creating directories ... Creating DESCRIPTION ... Creating NAMESPACE ... Creating Read-and-delete-me ... Copying code files ... Making help files ... Done. Further steps are described in './myTst/Read-and-delete-me'.> options(op) > ##_2_ only a class, no generics/methods: > writeLines(c('setClass("DocLink",',+ 'representation(name="character",', + ' desc="character"))'), tmp)> if(file.exists("myTst2")) unlink("myTst2", recursive=TRUE) > package.skeleton("myTst2", code_files = tmp)Creating directories ... Creating DESCRIPTION ... Creating NAMESPACE ... Creating Read-and-delete-me ... Copying code files ... Making help files ... Done. Further steps are described in './myTst2/Read-and-delete-me'. Warning message: In package.skeleton("myTst2", code_files = tmp) : Invalid file name(s) for R code in ./myTst2/R: 'file7da22fb20b64' are now renamed to 'z<name>.R'> ##- end_2_ # failed in R 2.11.0 > stopifnot(1 == grep("setClass",+ readLines(list.files("myTst/R", full.names=TRUE))), + c("foo-class.Rd","show-methods.Rd") %in% list.files("myTst/man"))> ## failed for several reasons in R < 2.7.0 > ## > ## Part 2: -- build, install, load and "inspect" the package: > dir.exists <- function(x)+ is.character(x) && file.exists(x) && file.info(path.expand(x))$isdir> build.pkg <- function(dir) {+ stopifnot(dir.exists(dir)) + patt <- paste(basename(dir), ".*tar\\.gz$", sep="_") + unlink(dir('.', pattern = patt)) + Rcmd <- paste(file.path(R.home("bin"), "R"), "CMD") + r <- tail(system(paste(Rcmd, "build --keep-empty-dirs", dir), + intern = TRUE), 3) + ## return name of tar file built + dir('.', pattern = patt) + }> build.pkg("myTst")[1] "myTst_1.0.tar.gz"> ## clean up any previous attempt (which might have left a 00LOCK) > unlink("myLib", recursive = TRUE) > dir.create("myLib") > install.packages("myTst", lib = "myLib", repos=NULL, type = "source") # with warnings* installing *source* package 'myTst' ... ** R ** preparing package for lazy loading ** help Warning: /home/csoliver/OKplatform/ExternalSources/builds/R/R-2.14.1/tests/myTst/man/myTst-package.Rd:34: All text must be in a section Warning: /home/csoliver/OKplatform/ExternalSources/builds/R/R-2.14.1/tests/myTst/man/myTst-package.Rd:35: All text must be in a section *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (myTst)> print(installed.packages(lib.loc= "myLib", priority= "NA"))## (PR#13332)Package LibPath Version Priority Depends Imports LinkingTo Suggests myTst "myTst" "myLib" "1.0" NA "methods" NA NA NA Enhances OS_type License Built myTst NA NA "What license is it under?" "2.14.1"> stopifnot(require("myTst",lib = "myLib"))Loading required package: myTst> sm <- findMethods(show, where= as.environment("package:myTst")) > stopifnot(names(sm at names) == "foo") > unlink("myTst_*") > > ## More building & installing packages > ## NB: tests were added here for 2.11.0. > ## NB^2: do not do this in the R sources! > ## and this testdir is not installed. > pkgSrcPath <- file.path(Sys.getenv("SRCDIR"), "Pkgs") > if(file_test("-d", pkgSrcPath)) {+ ## could use file.copy(recursive = TRUE) + system(paste('cp -r', shQuote(pkgSrcPath), shQuote(tempdir()))) + pkgPath <- file.path(tempdir(), "Pkgs") + # op <- options(warn = 2) # There should be *NO* warnings here! + ## pkgB tests an empty R directory + dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE, + showWarnings = FALSE) + p.lis <- c("pkgA", "pkgB", "exNSS4") + for(p. in p.lis) { + cat("building package", p., "...\n") + r <- build.pkg(file.path(pkgPath, p.)) + cat("installing package", p., "using file", r, "...\n") + ## we could install the tar file ... (see build.pkg()'s definition) + install.packages(r, lib = "myLib", repos=NULL, type = "source") + stopifnot(require(p.,lib = "myLib", character.only=TRUE)) + detach(pos = match(p., sub("^package:","", search()))) + } + ## TODO: not just print, but check the "list": + res <- installed.packages(lib.loc = "myLib", priority = "NA") + print(res) + # options(op) + unlink("myLib", recursive = TRUE) + unlink(file.path(pkgPath), recursive = TRUE) + } building package pkgA ... installing package pkgA using file pkgA_1.1.tar.gz ... Error in untar2(tarfile, files, list, exdir) : unsupported entry type 'x' Loading required package: pkgA Error: require(p., lib = "myLib", character.only = TRUE) is not TRUE In addition: Warning messages: 1: In install.packages(r, lib = "myLib", repos = NULL, type = "source") : installation of package 'pkgA_1.1.tar.gz' had non-zero exit status 2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'pkgA' Execution halted --- Unfortunatly the above says nothing to me, and I didn't find information on the Internet. I hope somebody can help. In the past the build-process worked (at least for R-version 2.14.1) with Suse 11.2 and gcc version 4.5.3. Thanks for your attention. Oliver
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