BUG: install.packages("lambda.r") fails in R-devel w/ _R_CHECK_LENGTH_1_LOGIC2_=true #37
Comments
HenrikBengtsson
added a commit
to ccagc/QDNAseq
that referenced
this issue
Aug 31, 2019
…with _R_CHECK_LENGTH_1_LOGIC2_=true
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Hi @muxspace, is this repos/package still maintained? I haven't seen any activity in a while and I wonder if there's any chance this issue to get resolved. It's kind of a blocker downstream, e.g. when you try to run strict |
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@HenrikBengtsson I didn't see this issue until now. I'll take a look and see about resolving it. |
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Awesome. Thxs. |
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Here are some more troubleshooting details: $ _R_CHECK_LENGTH_1_LOGIC2_=verbose Rscript --vanilla -e 'install.packages("futile.logger", repos="https://cloud.r-project.org")'
Installing package into ‘/home/alice/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz'
Content type 'application/x-gzip' length 17456 bytes (17 KB)
==================================================
downloaded 17 KB
* installing *source* package ‘futile.logger’ ...
** package ‘futile.logger’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
lambda.r
--- call from context ---
NULL
--- call from argument ---
!is.na(line <- it()) && line$token != "SPECIAL"
--- R stacktrace ---
where 1: parse_fun(it)
where 2: describe(fn, idx, raw = FALSE) %when% {
raw
} %:=% {
class(fn) <- NULL
print(fn)
}
where 3: eval(exprs[i], envir)
where 4: eval(exprs[i], envir)
where 5: sys.source(codeFile, env, keep.source = keep.source, keep.parse.data = keep.parse.data)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: 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)[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))
})
where 10: try(sys.source(codeFile, env, keep.source = keep.source, keep.parse.data = keep.parse.data))
where 11: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
where 12: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
where 13: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source,
keep.parse.data = keep.parse.data, partial = TRUE)
where 14: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
where 15: suppressPackageStartupMessages(loadNamespace(package = package,
lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data,
partial = TRUE))
where 16: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,
keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir)
where 17: tools:::makeLazyLoading("futile.logger", "/home/alice/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-futile.logger/00new",
keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/home/alice/R/x86_64-pc-linux-gnu-library/3.6/futile.logger")
--- value of length: 9 type: logical ---
line1 col1 line2 col2 id parent token terminal text
2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
--- function from context ---
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Error in !is.na(line <- it()) && line$token != "SPECIAL" :
'length(x) = 9 > 1' in coercion to 'logical(1)'
Error: unable to load R code in package ‘lambda.r’
Execution halted
ERROR: lazy loading failed for package ‘futile.logger’
* removing ‘/home/alice/R/x86_64-pc-linux-gnu-library/3.6/futile.logger’
* restoring previous ‘/home/alice/R/x86_64-pc-linux-gnu-library/3.6/futile.logger’
The downloaded source packages are in
‘/tmp/alice/Rtmpr1kUbz/downloaded_packages’
Warning message:
In install.packages("futile.logger", repos = "https://cloud.r-project.org") :
installation of package ‘futile.logger’ had non-zero exit status |
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Hi @HenrikBengtsson I pushed a fix to master. Can you check on your end that it works? If so, I'll submit it to CRAN. |
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LGTM. Confirming. Thanks :) |
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It's on CRAN now |
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Great. Thanks
…On Fri, Sep 20, 2019, 07:28 Brian Lee Yung Rowe ***@***.***> wrote:
It's on CRAN now
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No problem. Thanks for making enough noise so I could address it :) |
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In R-devel, there are now optional checks asserting that
x && yis not called withlength(x) > 1orlength(y) > 1. These checks can be enabled with_R_CHECK_LENGTH_1_LOGIC2_=true- I'll assume they'll eventually will be on by default. I guess that CRAN will enable them before that. I know that the CRAN incomin checks already have it enabled.lambda.r produces:
already when installed.
Example
Session info
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