Error running make

[cpsievert]

I see:

cpsievert@Carsons-MacBook-Pro:~/Desktop/github/local/plotly-test-table$ make
R --vanilla < table.R

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

  Natural language support but running in an English locale

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.

> require(plotly)
Loading required package: plotly
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Loading required package: ggplot2
> require(testthat)
Loading required package: testthat
> require(parallel)
Loading required package: parallel
> 
> data.dir <- normalizePath("data")
> 
> ## This file specifies the list of all the versions of the ggplotly
> ## code (not testing code) for which we want to run the current tests.
> code_commits <- read.csv("code_commits.csv", as.is=TRUE, comment.char="#")
> 
> ## Parse the first occurance of pattern from each of several strings
> ## using (named) capturing regular expressions, returning a matrix
> ## (with column names).
> str_match_perl <- function(string,pattern){
+   stopifnot(is.character(string))
+   stopifnot(is.character(pattern))
+   stopifnot(length(pattern)==1)
+   parsed <- regexpr(pattern,string,perl=TRUE)
+   captured.text <- substr(string,parsed,parsed+attr(parsed,"match.length")-1)
+   captured.text[captured.text==""] <- NA
+   captured.groups <- if(is.null(attr(parsed, "capture.start"))){
+     NULL
+   }else{
+     do.call(rbind,lapply(seq_along(string),function(i){
+       st <- attr(parsed,"capture.start")[i,]
+       if(is.na(parsed[i]) || parsed[i]==-1)return(rep(NA,length(st)))
+       substring(string[i],st,st+attr(parsed,"capture.length")[i,]-1)
+     }))
+   }
+   result <- cbind(captured.text,captured.groups)
+   colnames(result) <- c("",attr(parsed,"capture.names"))
+   result
+ }
> 
> ## Parse several occurances of pattern from each of several strings
> ## using (named) capturing regular expressions, returning a list of
> ## matrices (with column names).
> str_match_all_perl <- function(string,pattern){
+   stopifnot(is.character(string))
+   stopifnot(is.character(pattern))
+   stopifnot(length(pattern)==1)
+   parsed <- gregexpr(pattern,string,perl=TRUE)
+   lapply(seq_along(parsed),function(i){
+     r <- parsed[[i]]
+     full <- substring(string[i],r,r+attr(r,"match.length")-1)
+     starts <- attr(r,"capture.start")
+     if(is.null(starts)){
+       m <- cbind(full)
+       colnames(m) <- ""
+       m
+     }else{
+       if(r[1]==-1)return(matrix(nrow=0,ncol=1+ncol(starts)))
+       names <- attr(r,"capture.names")
+       lengths <- attr(r,"capture.length")
+       subs <- substring(string[i],starts,starts+lengths-1)
+       m <- matrix(c(full,subs),ncol=length(names)+1)
+       colnames(m) <- c("",names)
+       m
+     }
+   })
+ }
> 
> ### Named capture regular expression for parsing git log
> ### --pretty=format:'%H %ci %s' vis str_match_perl.
> commit.line.pattern <-
+   paste0("(?<SHA1>[0-9a-f]{40})",
+          " ",
+          "(?<datetime>",
+          "(?<year>[0-9]{4})",
+          "-",
+          "(?<month>[0-9]{2})",
+          "-",
+          "(?<day>[0-9]{2})",
+          " ",
+          "(?<hour>[0-9]{2})",
+          ":",
+          "(?<minute>[0-9]{2})",
+          ":",
+          "(?<second>[0-9]{2})",
+          ")",
+          " ",
+          "(?<gmt_offset_sign>[-+])",
+          "(?<gmt_offset_hours>[0-9]{2})",
+          "(?<gmt_offset_minutes>[0-9]{2})",
+          " ",
+          "(?<subject>.*)")
> 
> ### Parse a git log character vector, returning data.frame.
> commits <- function(git.lines){
+   stopifnot(is.character(git.lines))
+   m <- str_match_perl(git.lines, commit.line.pattern)
+   stopifnot(!is.na(m[,1]))
+   commit.time <- strptime(m[,"datetime"], "%Y-%m-%d %H:%M:%S", "GMT") + 0
+   gmt.offset.sign <- ifelse(m[,"gmt_offset_sign"]=="+", 1, -1)
+   gmt.offset.hours <- as.numeric(m[,"gmt_offset_hours"])
+   minutes.only <- as.numeric(m[,"gmt_offset_minutes"])
+   gmt.offset.minutes <- minutes.only + gmt.offset.hours * 60
+   gmt.offset.seconds <- gmt.offset.minutes * 60
+   gmt.offset <- gmt.offset.sign * gmt.offset.seconds
+   gmt.time <- commit.time - gmt.offset
+   subject <- m[, "subject"]
+   SHA1 <- m[, "SHA1"]
+   abbrev <- substr(subject, 1, 18)
+   commits <- data.frame(SHA1, subject, abbrev, gmt.time,
+                         stringsAsFactors = FALSE)
+   rownames(commits) <- commits$SHA1
+   class(commits) <- c("commits", "data.frame")
+   stopifnot(nrow(commits) == length(git.lines))
+   commits
+ }
> 
> ### Print commits 80 characters per line.
> print.commits <- function(commits){
+   print(as.data.frame(commits)[, c("gmt.time", "abbrev")])
+ }
> 
> ### Use convert on the command line to convert file.png to
> ### file-thumb.png.
> thumb <- function(png.file){
+   stopifnot(is.character(png.file))
+   stopifnot(length(png.file) == 1)
+   if(file.exists(png.file)){
+     thumb.file <- sub("[.]png$", "-thumb.png", png.file)
+     if(!file.exists(thumb.file)){
+       ##mcparallel({
+       cmd <- paste("convert", png.file, "-resize 230", thumb.file)
+       cat("\n", cmd, "\n", sep="")
+       system(cmd)
+       ##})
+     }
+     thumb.file
+   }else{
+     NA
+   }
+ }
> 
> ### Run all tests in test.file, defining save_outputs in a way which
> ### just saves ggplots.
> test.ggplots <- function(test.file){
+   result.list <- list()
+   save_outputs <- function(gg, name, ...) {
+     filesystem_name <- gsub(' ', '-', name)
+     fs.png <- paste0(filesystem_name, ".png")
+     gg.png.file <- file.path(data.dir, "ggplot2", fs.png)
+     ggplot.dir <- dirname(gg.png.file)
+     dir.create(ggplot.dir, showWarnings = FALSE, recursive = TRUE)
+     if(!file.exists(gg.png.file)){
+       cat(sprintf("\npng(%s)\n", gg.png.file)) 
+       png(gg.png.file, width=700, h=500, type="cairo")
+       print(gg)
+       dev.off()
+     }
+     result.list[[name]] <<- name
+   }
+   e <- new.env()
+   tryCatch({
+     testthat:::test_file(test.file, env=e)
+   }, error=function(e){
+     cat("\nError in testthat::test_file\n")
+     print(e)
+   })
+   as.character(do.call(c, result.list))
+ }
> 
> ## Assume plotly repos is in the same directory as plotly-test-table
> ## repos.
> plotly.pkg <- file.path("..", "plotly")
> testthat.dir <- file.path(plotly.pkg, "tests", "testthat")
> test.files <- Sys.glob(file.path(testthat.dir, "test-*.R"))
> 
> ## get the SHA1 of the tests on the current branch; and the SHA1,
> ## time, and subjects of all commits.
> old.wd <- setwd(testthat.dir)
> test.SHA1 <- system("git rev-parse HEAD", intern=TRUE)
> all.cmd <- "git log --pretty=format:'%H %ci %s' --all"
> all.txt <- system(all.cmd, intern=TRUE)
> all.commits <- commits(all.txt)
> setwd(old.wd)
> 
> ## Load database which records test SHA1, test files, and test names.
> load("testfileDB.RData")
> 
> ## Need to initialize elements as lists, in case there are single
> ## elements in the result of test.ggplots.
> if(is.null(testfileDB[[test.SHA1]])){
+   testfileDB[[test.SHA1]] <- list()
+ }
> 
> ## For every test-*.R file, run it and see what ggplots are produced.
> for(test.file in test.files){
+   test.base <- basename(test.file)
+   if(is.null(testfileDB[[test.SHA1]][[test.base]])){
+     result <- test.ggplots(test.file)
+     testfileDB[[test.SHA1]][[test.base]] <- result
+   }
+ }
Abline : ......

Area : .......

:) 
bar : .................

Boxplot : .........

You rock! 
Build function : ...

categorical data on the axes : .......

Contour : ...

Woot! 
date : ..............

Probability density : .....

Density2d : ...

geom_errorbarh : .....

Errorbar : ...

Facets : ...............

Heatmap : ....

:) 
Histogram : .......stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
.............

Hline : ....................

labels : ......

legends : .....

line : .........

names : ..

path : ..............................

polygon : .....................................................

ribbon : .....

segment : ..

size : .......

You are a coding rockstar! 
Stack : .......

Step : ............

Text : ...........

ggplot themes : .....................

ggplot ticks : ..........................................................................................................

Vline : .................

means and error bars : ................................Loading required package: plyr
......................................

Filename : .

get_figure : ......

rotated ticks : 

Unimplemented geoms : ....

Warning messages:
1: In layer2traces(L, df, misc) : Converting violin plot into boxplot:

            probability density estimation is not supported in Plotly yet.
2: In layer2traces(L, df, misc) : You may want to use geom_histogram.
3: In layer2traces(L, df, misc) :
  Conversion not implemented for geom_unimplemented (basic geom_unimplemented), ignoring. Please open an issue with your example code at https://github.com/ropensci/plotly/issues
> 
> ## Save the testfileDB to avoid having to re-run these tests just to
> ## find out which plots are produced.
> save(testfileDB, file="testfileDB.RData")
> 
> ### After having installed the version of plotly specified in
> ### code_commits.csv, and run all of the tests and save the generated
> ### plotlys to disk.
> test.plotlys <- function(test.file){
+   ## This is run from within the plotly/tests/testthat directory, so
+   ## data.dir should be a full path.
+   save_outputs <- function(gg, name, ...) {
+     filesystem_name <- gsub(' ', '-', name)
+     fs.png <- paste0(filesystem_name, ".png")
+     plotly.png.file <- file.path(data.dir, SHA1, fs.png)
+     SHA1.dir <- dirname(plotly.png.file)
+     dir.create(SHA1.dir, showWarnings = FALSE, recursive = TRUE)
+     if(!file.exists(plotly.png.file)){
+       ##mcparallel({
+         py <- plotly("TestBot", "r1neazxo9w")
+         kwargs <-
+           list(filename=paste0("ggplot2/", SHA1, "/", name),
+                fileopt="overwrite",
+                auto_open=FALSE)
+         u <- py$ggplotly(gg, kwargs=kwargs)
+         plotly.png.url <- paste0(u$response$url, ".png")
+         cat(sprintf("\ndownloading %s -> %s\n",
+                     plotly.png.url, plotly.png.file))
+         pngdata <- getURLContent(plotly.png.url)
+         writeBin(as.raw(pngdata), plotly.png.file)
+       ##})
+     }
+   }
+   e <- new.env()
+   tryCatch({
+     test_file(test.file, env=e)
+   }, error=function(e){
+     cat("\nError in testthat::test_file\n")
+     print(e)
+   })
+ }
> 
> ## Check to see if we need to run any of the tests, by checking to see
> ## if the PNG files exist. If not, run the test and make the plotlys.
> test.info <- testfileDB[[test.SHA1]]
> for(commit.i in 1:nrow(code_commits)){
+   code_commit <- code_commits[commit.i, ]
+   SHA1 <- code_commit$SHA1
+   commit.dir <- file.path("data", SHA1)
+   commit.files <- dir(commit.dir)
+   to.run <- list()
+   for(test.base in names(test.info)){
+     test.names <- test.info[[test.base]]
+     if(length(test.names)){
+       test.pngs <- paste0(test.names, ".png")
+       if(!all(test.pngs %in% commit.files)){
+         to.run[[test.base]] <- test.base
+       }
+     }
+   }
+   if(length(to.run)){
+     install.str <- paste0(code_commit$user, "/plotly@", SHA1)
+     devtools::install_github(install.str)
+   }
+   for(test.base in to.run){
+     test.file <- file.path(testthat.dir, test.base)
+     test.plotlys(test.file)
+   }
+ }
Downloading github repo cpsievert/plotly@05d29e763e3984501535998de9a1aef21d86902f
Installing plotly
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
  '/private/var/folders/wc/zv89d1fx5nxdljsysq40m6vr0000gn/T/Rtmp9XUlWo/devtoolsd0941a8230f1/cpsievert-plotly-05d29e7'  \
  --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library'  \
  --install-tests 

* installing *source* package ‘plotly’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (plotly)
Reloading installed plotly
Abline : ......
downloading https://plot.ly/~TestBot/1182.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/abline.png

Area : .....
downloading https://plot.ly/~TestBot/1183.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/area.png
..
downloading https://plot.ly/~TestBot/1184.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/area-fillcolor.png

bar : .......
downloading https://plot.ly/~TestBot/1185.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/bar-dodge.png
...
downloading https://plot.ly/~TestBot/1186.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/bar-stack.png
...
downloading https://plot.ly/~TestBot/1187.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/bar-identity.png
....
downloading https://plot.ly/~TestBot/1188.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/bar-dates.png

Boxplot : ...
downloading https://plot.ly/~TestBot/1189.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/boxplot.png
...
downloading https://plot.ly/~TestBot/1190.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/violin.png
...
downloading https://plot.ly/~TestBot/1191.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/boxplot-datetime.png

categorical data on the axes : ..
downloading https://plot.ly/~TestBot/1192.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/bar-factor-category.png
.....
downloading https://plot.ly/~TestBot/1193.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/bar-category-names.png

Contour : ...
downloading https://plot.ly/~TestBot/1194.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/contour.png

date : ....
downloading https://plot.ly/~TestBot/1195.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/date-strings.png
...
downloading https://plot.ly/~TestBot/1196.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/date-class-Date.png
.......
downloading https://plot.ly/~TestBot/1197.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/date-irregular-time-series.png

Probability density : .....
downloading https://plot.ly/~TestBot/1198.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/density.png

Density2d : ...
downloading https://plot.ly/~TestBot/1199.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/density2d.png

geom_errorbarh : .....
downloading https://plot.ly/~TestBot/1200.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/errorbar-horizontal.png

Errorbar : ...
downloading https://plot.ly/~TestBot/1201.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/errorbar.png

Facets : ...
downloading https://plot.ly/~TestBot/1202.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/facet_wrap_free.png
..
downloading https://plot.ly/~TestBot/1203.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/facet_wrap_free_y.png
..
downloading https://plot.ly/~TestBot/1204.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/facet_wrap_free_x.png
..
downloading https://plot.ly/~TestBot/1205.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/facet_grid_free.png
..
downloading https://plot.ly/~TestBot/1206.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/facet_grid_free_y.png
..
downloading https://plot.ly/~TestBot/1207.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/facet_grid_free_x.png
..

Heatmap : ....
downloading https://plot.ly/~TestBot/1208.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/heatmap.png

:) 
Histogram : .....
downloading https://plot.ly/~TestBot/1209.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/histogram-barmodestack.png
..
downloading https://plot.ly/~TestBot/1210.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/histogram-binwidth.png
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
.....stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.

downloading https://plot.ly/~TestBot/1211.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/histogram-dates.png
....
downloading https://plot.ly/~TestBot/1212.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/histogram-POSIXt-bins.png
....
downloading https://plot.ly/~TestBot/1213.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/histogram-Date-bins.png

Hline : ........
downloading https://plot.ly/~TestBot/1214.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/hline.png
..........
downloading https://plot.ly/~TestBot/1215.png -> /Users/cpsievert/Desktop/github/local/plotly-test-table/data/05d29e763e3984501535998de9a1aef21d86902f/hline-multiple.png
..
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labels : .
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.
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legends : .
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line : ..
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names : ..
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path : ....
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polygon : .......
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1..
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1. Error: filled polygons become several traces --------------------------------
Gateway Timeout

1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: save_outputs(gg, "polygons-dashed") at test-ggplot-polygons.R:77
5: getURLContent(plotly.png.url)
6: stop.if.HTTP.error(http.header)

ribbon : .....
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segment : ..
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size : ..
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Stack : .......
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You are a coding rockstar! 
Step : ..
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Text : ....
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ggplot themes : ..
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ggplot ticks : 
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.
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Vline : ........
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Warning messages:
1: In layer2traces(L, df, misc) : Converting violin plot into boxplot:

            probability density estimation is not supported in Plotly yet.
2: In layer2traces(L, df, misc) : Converting violin plot into boxplot:

            probability density estimation is not supported in Plotly yet.
3: In layer2traces(L, df, misc) : You may want to use geom_histogram.
4: In layer2traces(L, df, misc) : You may want to use geom_histogram.
> 
> ## Make test table with one row for every element of current
> ## testfileDB (test.info) and one column for every line in
> ## code_commits.csv.
> test.names <- as.character(unlist(test.info))
> rev.commits <- code_commits[nrow(code_commits):1, ]
> columns.df <- with(rev.commits, {
+   data.frame(dir=c("ggplot2", SHA1), label=c("ggplot2", label))
+ })
> td.mat <- 
+   matrix(NA, length(test.names), nrow(columns.df))
> rownames(td.mat) <- test.names
> colnames(td.mat) <- columns.df$label
> png.mat <- big.mat <- td.mat
> 
> table.dir <- file.path("tables", test.SHA1)
> dir.create(table.dir, recursive=TRUE)
> ## First go to the directory where we will be making the table, so
> ## thumb() works fine.
> old.wd <- setwd(table.dir)
> for(column.i in 1:nrow(columns.df)){
+   column.info <- columns.df[column.i, ]
+   png.file <-
+     file.path("..", "..", "data", column.info$dir, paste0(test.names, ".png"))
+   thumb.file <- png.file
+   for(thumb.i in seq_along(thumb.file)){
+     thumb.file[[thumb.i]] <- thumb(thumb.file[[thumb.i]])
+   }
+   td.mat[, column.i] <-
+     sprintf('<a href="%s"><img src="%s" /></a>', png.file, thumb.file)
+   png.mat[, column.i] <-
+     sprintf('<img src="%s" />', png.file)
+   big.mat[, column.i] <-
+     sprintf('<img src="%s" />', png.file)
+ }

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> setwd(old.wd)
> 
> library(xtable)
> for(test.name in rownames(td.mat)){
+   img.tag <- png.mat[test.name, ]
+   df <- data.frame(label=names(img.tag), img.tag)
+   xt <- xtable(t(df))
+   html.file <- file.path(table.dir, paste0(test.name, ".html"))
+   print(xt, type="html", file=html.file, sanitize.text.function=identity,
+         include.rownames=FALSE, include.colnames=FALSE)
+ }
> ## Make big.html which shows big images directly.
> big.df <-
+   data.frame(test=rownames(td.mat),
+              big.mat)
> xt <- xtable(big.df)
> print(xt, type="html", file=file.path(table.dir, "big.html"),
+       sanitize.text.function=identity,
+       include.rownames=FALSE)
> ## Make index.html which shows small -thumb.png images and links to
> ## the bigger ones.
> td.df <-
+   data.frame(test=sprintf('<a href="%s.html">%s</a>',
+                test.names, test.names),
+              td.mat)
> xt <- xtable(td.df)
> print(xt, type="html", file=file.path(table.dir, "index.html"),
+       sanitize.text.function=identity,
+       include.rownames=FALSE)
> 
> table.SHA1 <- dir("tables")
> table.commits <- all.commits[table.SHA1, ]
> index <- paste0("tables/", table.SHA1, "/index.html")
> th.pattern <-
+   paste0("<TH> ",
+          "(?<label>[^ <]+)")
> column.labels <- c()
> for(index.file in index){
+   ilines <- readLines(index.file)
+   th.line <- grep("<TH>", ilines, value=TRUE)
+   label.mat <- str_match_all_perl(th.line, th.pattern)[[1]]
+   label <- label.mat[-1, "label"]
+   label <- label[label != "ggplot2"]
+   column.labels[[index.file]] <- paste(label, collapse = "<br />")
+ }
Error in str_match_all_perl(th.line, th.pattern)[[1]] : 
  subscript out of bounds
Execution halted
make: *** [table.html] Error 1

[cpsievert]

Let me know if you'd like to see any more output...

[cpsievert]

I've got another reason for you to love R versioning @tdhock ;)

I'm pretty sure this error is due to a difference in xtable 1.7-3 & 1.7-4. If you look at the top of the NEWS file, HTML tags were changed to be lowercase. You are assuming uppercase here and here

[tdhock]

haha, another problem due to the versionless R packaging system! glad you were able to figure it out though. I will update xtable and then update the regular expression the next time I run the code.