[R] make check fails -- how to debug
Barris, Wes
We@@B@rr|@ @end|ng |rom cobb-v@ntre@@@com
Wed Feb 12 15:20:55 CET 2020
Thanks Ivan. Here is the contents of reg-packages.Rout.fail. I'm not sure exactly what part of this is the fatal error:
R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> .R_LIBS <- function(libp = .libPaths()) { # (>> in utils?)
+ libp <- libp[! libp %in% .Library]
+ if(length(libp))
+ paste(libp, collapse = .Platform$path.sep)
+ else "" # character(0) is invalid for Sys.setenv()
+ }
> Sys.setenv(R_LIBS = .R_LIBS() # for build.pkg() & install.packages()
+ , R_BUILD_ENVIRON = "nothing" # avoid ~/.R/build.environ which might set R_LIBS
+ , R_ENVIRON = "none"
+ , R_PROFILE = "none"
+ )
>
> ## PR 1271 detach("package:base") crashes R.
> tools::assertError(detach("package:base"))
>
>
> ## 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 warning
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'.
Warning message:
In package.skeleton("myTst", code_files = tmp) :
Invalid file name(s) for R code in ./myTst/R:
'file62e012b0d16'
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)
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:
'file62e012b0d16'
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:
> build.pkg <- function(dir) {
+ stopifnot(dir.exists(dir), file.exists(DESC <- file.path(dir, "DESCRIPTION")))
+ pkgName <- sub("^[A-Za-z]+: ", "", grep("^Package: ", readLines(DESC), value=TRUE))
+ patt <- paste(pkgName, ".*tar\\.gz$", sep="_")
+ unlink(dir('.', pattern = patt))
+ Rcmd <- paste(shQuote(file.path(R.home("bin"), "R")), "CMD")
+ r <- system(paste(Rcmd, "build --keep-empty-dirs", shQuote(dir)),
+ intern = TRUE)
+ ## return name of tar file built
+ structure(dir('.', pattern = patt), log3 = r)
+ }
> build.pkg("myTst")
[1] "myTst_1.0.tar.gz"
attr(,"log3")
[1] "* checking for file 'myTst/DESCRIPTION' ... OK"
[2] "* preparing 'myTst':"
[3] "* checking DESCRIPTION meta-information ... OK"
[4] "* installing the package to process help pages"
[5] "* saving partial Rd database"
[6] "* checking for LF line-endings in source and make files and shell scripts"
[7] "* checking for empty or unneeded directories"
[8] "* building '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' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
Warning: /usr/local/src/stats/R-3.6.2/CentOS/tests/myTst/man/myTst-package.Rd:27: All text must be in a section
Warning: /usr/local/src/stats/R-3.6.2/CentOS/tests/myTst/man/myTst-package.Rd:28: All text must be in a section
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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 License License_is_FOSS
myTst NA "What license is it under?" NA
License_restricts_use OS_type MD5sum NeedsCompilation Built
myTst NA NA NA NA "3.6.2"
> stopifnot(require("myTst",lib = "myLib"))
Loading required package: myTst
> sm <- findMethods(show, where= as.environment("package:myTst"))
> stopifnot(names(sm using names) == "foo")
> unlink("myTst_*")
>
> ## getPackageName() for "package:foo":
> require('methods')
> library(tools)
> oo <- options(warn=2)
> detach("package:tools", unload=TRUE)
> options(oo)
> ## gave warning (-> Error) about creating package name
>
>
> ## More building & installing packages
> ## NB: tests were added here for 2.11.0.
> ## NB^2: do not do this in the R sources (but in a build != src directory!)
> ## and this testdir is not installed.
> if(interactive() && Sys.getenv("USER") == "maechler")
+ Sys.setenv(SRCDIR = normalizePath("~/R/D/r-devel/R/tests"))
> (pkgSrcPath <- file.path(Sys.getenv("SRCDIR"), "Pkgs"))# e.g., -> "../../R/tests/Pkgs"
[1] "../../tests/Pkgs"
> if(!file_test("-d", pkgSrcPath) && !interactive()) {
+ unlink("myTst", recursive=TRUE)
+ print(proc.time())
+ q("no")
+ }
> ## else w/o clause:
>
> do.cleanup <- !nzchar(Sys.getenv("R_TESTS_NO_CLEAN"))
> isWIN <- .Platform$OS.type == "windows"
> has.symlink <- !isWIN
> ## Installing "on to" a package existing as symlink in the lib.loc
> ## -- used to fail with misleading error message (#PR 16725):
>
> if(has.symlink && !unlink("myLib_2", recursive=TRUE) && dir.create("myLib_2") &&
+ file.rename("myLib/myTst", "myLib_2/myTst") &&
+ file.symlink("../myLib_2/myTst", "myLib/myTst"))
+ install.packages("myTst", lib = "myLib", repos=NULL, type = "source")
* installing *source* package 'myTst' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
Warning: /usr/local/src/stats/R-3.6.2/CentOS/tests/myTst/man/myTst-package.Rd:27: All text must be in a section
Warning: /usr/local/src/stats/R-3.6.2/CentOS/tests/myTst/man/myTst-package.Rd:28: All text must be in a section
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (myTst)
> ## In R <= 3.3.2 gave error with *misleading* error message:
> ## ERROR: 'myTst' is not a legal package name
>
> if(isWIN) { # (has no symlinks anyway)
+ file.copy(pkgSrcPath, tempdir(), recursive = TRUE)
+ } else { # above file.copy() not useful as it replaces symlink by copy
+ system(paste('cp -R', shQuote(pkgSrcPath), shQuote(tempdir())))
+ }
> pkgPath <- file.path(tempdir(), "Pkgs")
> if(!dir.exists(pkgPath)) {
+ message("No valid 'pkgPath' (from 'pkgSrcPath') - exit this test")
+ if(!interactive()) q("no")
+ }
>
> ## pkgB tests an empty R directory
> dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE,
+ showWarnings = FALSE)
> p.lis <- c(if("Matrix" %in% row.names(installed.packages(.Library)))
+ c("pkgA", "pkgB", "pkgC"),
+ "exNSS4", "exSexpr")
> InstOpts <- list("exSexpr" = "--html")
> pkgApath <- file.path(pkgPath, "pkgA")
> if("pkgA" %in% p.lis && !dir.exists(d <- pkgApath)) {
+ cat("symlink 'pkgA' does not exist as directory ",d,"; copying it\n", sep='')
+ file.copy(file.path(pkgPath, "xDir", "pkg"), to = d, recursive=TRUE)
+ ## if even the copy failed (NB: pkgB, pkgC depend on pkgA)
+ if(!dir.exists(d)) p.lis <- p.lis[!(p.lis %in% c("pkgA", "pkgB", "pkgC"))]
+ }
> dir2pkg <- function(dir) ifelse(dir == "pkgC", "PkgC", dir)
> if(is.na(match("myLib", .lP <- .libPaths()))) {
+ .libPaths(c("myLib", .lP)) # PkgC needs pkgA from there
+ .lP <- .libPaths()
+ }
> Sys.setenv(R_LIBS = .R_LIBS(.lP)) # for build.pkg() & install.packages()
> for(p in p.lis) {
+ p. <- dir2pkg(p) # 'p' is sub directory name; 'p.' is package name
+ cat("building package", p., "...\n")
+ r <- build.pkg(file.path(pkgPath, p))
+ if(!length(r)) # so some sort of failure, show log
+ cat(attr(r, "log3"), sep = "\n")
+ if(!isTRUE(file.exists(r)))
+ stop("R CMD build failed (no tarball) for package ", p)
+ ## otherwise install the tar file:
+ cat("installing package", p., "using built file", r, "...\n")
+ ## "FIXME": want to catch warnings in the "console output" of this:
+ install.packages(r, lib = "myLib", repos=NULL, type = "source",
+ INSTALL_opts = InstOpts[[p.]])
+ stopifnot(require(p., lib = "myLib", character.only=TRUE))
+ detach(pos = match(p., sub("^package:","", search())))
+ }
building package pkgA ...
installing package pkgA using built file pkgA_1.2.tar.gz ...
* installing *source* package 'pkgA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgA)
Loading required package: pkgA
Attaching package: 'pkgA'
The following object is masked from 'package:base':
search
building package pkgB ...
installing package pkgB using built file pkgB_1.0.tar.gz ...
* installing *source* package 'pkgB' ...
** using staged installation
** help
No man pages found in package 'pkgB'
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgB)
Loading required package: pkgB
building package PkgC ...
installing package PkgC using built file PkgC_1.0-0.tar.gz ...
* installing *source* package 'PkgC' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
>From .checkSubclasses(): subclass "classApp" of class "classA" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x4886478>, where2=<environment: namespace:PkgC>]
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PkgC)
Loading required package: PkgC
building package exNSS4 ...
installing package exNSS4 using built file exNSS4_1.1.tar.gz ...
* installing *source* package 'exNSS4' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package 'exNSS4'
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (exNSS4)
Loading required package: exNSS4
building package exSexpr ...
Converting Rd files to LaTeX
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
pdflatex is not available
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
pdflatex is not available
Error in running tools::texi2pdf()
* checking for file '/tmp/Rtmp5m0Zx8/Pkgs/exSexpr/DESCRIPTION' ... OK
* preparing 'exSexpr':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* building the PDF package manual
Hmm ... looks like a package
Creating pdf output from LaTeX ...
Error: R CMD build failed (no tarball) for package exSexpr
In addition: Warning message:
In system(paste(Rcmd, "build --keep-empty-dirs", shQuote(dir)), :
running command ''/usr/local/src/stats/R-3.6.2/CentOS/bin/R' CMD build --keep-empty-dirs '/tmp/Rtmp5m0Zx8/Pkgs/exSexpr'' had status 1
Execution halted
--
Wes
-----Original Message-----
From: Ivan Krylov <krylov.r00t using gmail.com>
Sent: Wednesday, February 12, 2020 3:37 AM
To: Barris, Wes <Wes.Barris using cobb-vantress.com>
Cc: r-help using r-project.org
Subject: [EXTERNAL] - Re: [R] make check fails -- how to debug
On Tue, 11 Feb 2020 21:26:33 +0000
"Barris, Wes" <Wes.Barris using cobb-vantress.com> wrote:
> running code in '../../tests/reg-packages.R' ...make[3]: ***
> [reg-packages.Rout] Error 1
tests/Makefile.common has the following in the .R.Rout rule:
@$(ECHO) $(ECHO_N) "running code in '$<' ...$(ECHO_C)" > $@.log
@$(R) < $< > $@.fail 2>&1 || (cat $@.log && rm $@.log && exit 1)
> How can I troubleshoot this to find out what is wrong?
Take a look at tests/reg-packages.Rout.fail, it should contain all output produced by tests/reg-packages.R when it ran.
--
Best regards,
Ivan
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