Check that build works on new machine
Closed this issue · 14 comments
@mwpennell -- can you try this
Rich, so i tried this. All the data files built perfectly but I encountered a few problems.
- make exited out because I did not have sowsear and pandoc installed. not a problem -- I just installed these but I think it would be useful if in the README file you stated that these need to be installed and wear to find them. Pandoc, I think people can figure out but people won't know where to find sowsear.
- I got the following error in creating the pdf:
pandoc: Error producing PDF from TeX source.
! Package pdftex.def Error: File `figure/fraction_phy_binomial1.png' not found.
See the pdftex.def package documentation for explanation.
Type H for immediate help.
...
l.543 ...aphics{figure/fraction_phy_binomial1.png}
make: *** [wood.pdf] Error 43
Not sure what this is. any suggestions?
For (1) - yes: I'll add that to the README file. Not sure which other packages we need, but I'll look into that too. There's a dependence on diversitree that might be only for drop.tip, and if so I'll try and drop that too.
For (2) - Hmm, no idea. That worked fine here. This is in processing the md -> html, I presume? That worked fine here, but it looks like you're missing files that you should have. Could you try it on a fresh clone perhaps?
ok this was on a fresh clone. it could have to do with some files i don't have on my computer. linux is weird. will try and figure this out to see if it specific to my machine or not.
Weird. I don't get a figure with a 1.png ending. could you email me the md and rmd files so I can see where that would have come from?
That's so weird. This section here:
``` {r fraction_phy_binomial,fig.cap="Woodiness percentage by order"}
fig.fraction.on.phylogeny(phy.o, res.b)
```
``` {r fraction_phy_hypergeometric,fig.cap="Woodiness percentage by order"}
fig.fraction.on.phylogeny(phy.o, res.h)
```
Is getting converted into this:
```r
fig.fraction.on.phylogeny(phy.o, res.b)
```
```r
fig.fraction.on.phylogeny(phy.o, res.h)
```
Which makes no sense. There are two options I see for this: (1) knitr, (2) linux/mac disagreement about devices.
What version of knitr do you have? I am using 1.5 (2013-09-28). That appears to be the most current version, so you probably have that.
Can you try deleting the line that says
on.exit(par(op))
The line is here, and see if that fixes it.
yes that is very strange.
i commented out this line but same error. I have the same version of knitr installed. Maybe get @wcornwell to try this on his mac to see if it is perhaps a system-specific thing (or perhaps just something weird in how i have my devices setup??).
I get this error:
Rscript R/make-output-dat.g.rds.R
Error in rbind(deparse.level, ...) :
numbers of columns of arguments do not match
Calls: load.woodiness.data.genus -> rbind -> rbind
Execution halted
make: *** [output/dat.g.rds] Error 1
@wcornwell - is that also on a clean clone? I don't get that error and @mwpennell presumably didn't either.
Reproducibility is hard, let's go shopping.
That was a dirty clone, trying again
OK, cool. I think I saw that error when I had dirty files in output hanging about as I changed which columns were retained.
*** caught segfault ***
address 0xa0, cause 'memory not mapped'
Traceback:
1: .Call(symbol)
2: Module(module, mustStart = TRUE, where = env)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
7: loadModule(module = "diversitree", what = TRUE, env = ns, loadNow = TRUE)
8: (function (ns) loadModule(module = "diversitree", what = TRUE, env = ns, loadNow = TRUE))()
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch((function (ns) loadModule(module = "diversitree", what = TRUE, env = ns, loadNow = TRUE))(), error = function(e) e)
13: eval(expr, envir, enclos)
14: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e), list(FUN = f, WHERE = where)), where)
15: .doLoadActions(where, attach)
16: methods:::cacheMetaData(ns, TRUE, ns)
17: loadNamespace(name)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(loadNamespace(name), error = function(e) stop(e))
22: getNamespace(ns)
23: asNamespace(pkg)
24: get(name, envir = asNamespace(pkg), inherits = FALSE)
25: diversitree:::mrca.tipset
26: build.order.tree(dat.g)
27: eval(expr, envir, enclos)
28: eval(call, envir, enclos)
29: withVisible(eval(call, envir, enclos))
30: withCallingHandlers(withVisible(eval(call, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: 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 msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
35: try(f, silent = TRUE)
36: handle(ev <- withCallingHandlers(withVisible(eval(call, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
37: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler)
38: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L)
39: in_dir(opts_knit$get("root.dir") %n% input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L))
40: block_exec(params)
41: call_block(x)
42: process_group.block(group)
43: process_group(group)
44: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
45: process_file(text, output)
46: knit("wood.Rmd")
aborting ...
make: *** [wood.md] Segmentation fault: 11
Probably a Rcpp vs R vs gcc vs apple vs clang issue. My suggestion is to reinstall Rcpp and diversitree, but that's a PITA at the moment. If you have a working compiler toolchain, do
install.packages(c("Rcpp", "diversitree"), type="source")
I'm going to work out if dropping diversitree makes sense at this point (see #5). I need to do a new CRAN release soon, but things are a gong show with the Mavericks changing compilers.