Nothing
R/patchDVI.R
In patchDVI: Package to Patch '.dvi' or '.synctex' Files
Defines functions
patchDVI
setDVIspecials
DVIspecials
readDVI
SweaveDVI
knitDVI
SweaveMiktex
knitMiktex
Documented in
DVIspecials
knitDVI
knitMiktex
patchDVI
readDVI
setDVIspecials
SweaveDVI
SweaveMiktex
knitMiktex <- function(Rnw,
main,
cmd="texify",
options="--tex-option=-src-specials --tex-option=-interaction=nonstopmode",
includedir="--tex-option=--include-directory=",
stylepath=FALSE,
source.code=NULL,
make=1,
preview='yap "%s"',
patchLog = TRUE,
sleep = 0,
weave = knitr::knit,
...)
SweaveMiktex(Rnw = Rnw,
main = main,
cmd = cmd,
options = options,
includedir = includedir,
stylepath = stylepath,
source.code = source.code,
make = make,
preview = preview,
patchLog = patchLog,
sleep = sleep,
weave = weave,
...)
SweaveMiktex <- function(Rnw,
main,
cmd="texify",
options="--tex-option=-src-specials --tex-option=-interaction=nonstopmode",
includedir="--tex-option=--include-directory=",
stylepath=FALSE,
source.code=NULL,
make=1,
preview='yap "%s"',
patchLog = TRUE,
sleep = 0,
...) {
if (!is.null(source.code))
try(source(source.code, local=TRUE))
if (sub(".*\\.tex$", "TeX", Rnw, ignore.case = TRUE) == "TeX")
outputname <- Rnw
else
outputname <- SweaveAll(Rnw, make=make, stylepath=stylepath, ...)[1]
if (missing(main)) main <- outputname
cmd <- paste(cmd, " ", options, " ", includedir, Rtexinputs(),
" ", main, sep="")
cat(cmd, "\n")
consoleLog <- try(system(cmd, intern = TRUE))
status <- attr(consoleLog, "status")
if (patchLog && !inherits(consoleLog, "try-error")) {
tempLog <- tempfile(fileext = ".log")
writeLines(consoleLog, tempLog)
patchLog(tempLog)
consoleLog <- readLines(tempLog)
}
cat(consoleLog, sep = "\n")
if (!is.null(status) && status) Sys.sleep(sleep)
dvi <- sub("\\.tex$", ".dvi", main, ignore.case = TRUE)
message(patchDVI(dvi, patchLog = patchLog))
if (!is.null(preview)) {
cmd <- sprintf(preview, dvi)
cat(cmd, "\n")
system(cmd, wait=FALSE, invisible=FALSE)
}
}
knitDVI <- function( Rnw, main,
texinputs=NULL,
source.code=NULL,
make=1,
links=NULL,
preview=NULL,
patchLog = TRUE,
weave = knitr::knit,
... )
SweaveDVI( Rnw = Rnw,
main = main,
texinputs = texinputs,
source.code = source.code,
make = make,
links = links,
preview = preview,
patchLog = patchLog,
weave = weave,
...)
SweaveDVI <- function( Rnw, main,
texinputs=NULL,
source.code=NULL,
make=1,
links=NULL,
preview=NULL,
patchLog = TRUE,
... ) {
if (!is.null(source.code) && file.exists(source.code))
try(source(source.code, local=TRUE))
if (sub(".*\\.tex$", "TeX", Rnw, ignore.case = TRUE) == "TeX")
outputname <- Rnw
else
outputname <- SweaveAll(Rnw, make=make, ...)[1]
if (missing(main)) main <- outputname
consoleLog <- try(tools::texi2dvi(main, pdf=FALSE, texinputs=texinputs, links=links))
if (patchLog && !inherits(consoleLog, "try-error")) {
tempLog <- tempfile(fileext = ".log")
writeLines(consoleLog, tempLog)
patchLog(tempLog)
consoleLog <- readLines(tempLog)
}
cat(consoleLog, sep = "\n")
dvi <- sub("\\.tex$", ".dvi", main, ignore.case=TRUE)
message(patchDVI(dvi, patchLog = patchLog))
if (!is.null(preview)) {
cmd <- sprintf(preview, dvi)
cat(cmd, "\n")
system(cmd, wait=FALSE, invisible=FALSE)
}
}
readDVI <- function(f, show=c("bop", "special", "fntdef", "preamble")) {
size <- file.info(f)$size
con <- file(f, "rb")
bytes <- readBin(con, "raw", size)
close(con)
parmsizes <- c( rep(0, 128), 1:4, 8, 1:4, 8, # 0 to 137
0, 44, 0,0,0, 1:4, 0, 1:4, 0, # 138 to 152
1:4, 1:4, 0, 1:4, 0, 1:4, # 153 to 170
rep(0, 64), 1:4, 1:4, 15:18, # 171 to 246
14, 28, 5, 9, rep(NA, 5)) # 247 to 255
pos <- 0
opcode <- 0
while (pos < size) {
pos <- pos+1
opcode <- as.integer(bytes[pos])
parmsize <- parmsizes[opcode + 1]
if (opcode < 139L) { # do nothing
} else if (opcode == 139L && "bop" %in% show) { # bop
counters <- readBin(bytes[pos + 1:(parmsize-4)], "integer", n= 10, size=4, endian="big")
prev <- readBin(bytes[pos + 40 + 1:4], "integer", size=4, endian="big")
cat("bop at pos=", pos, ": counters=", paste(counters, collapse=" "), " prev=", prev, "\n")
} else if (opcode < 239L) { # do nothing
} else if (opcode < 243L) { # xxxi
k <- readBin(bytes[pos + (1:parmsize)], "integer", size=parmsize, endian="big")
if ("special" %in% show) {
special <- readChar(bytes[(pos + parmsize + 1):(pos + parmsize + k)], k)
cat("special at pos=", pos," is ", special, "\n")
}
parmsize <- parmsize + k
} else if (opcode < 247L) { # fnt def i
a <- as.integer(bytes[pos + parmsize ])
if ("fntdef" %in% show) {
fntname <- readChar(bytes[(pos + parmsize + 1):(pos + parmsize + a)], a)
cat("fnt def at pos=", pos, " is ", fntname, "\n")
}
parmsize <- parmsize + a
} else if (opcode == 247L) { # pre
k <- as.integer(bytes[pos + parmsize])
if ("preamble" %in% show) {
comment <- readChar(bytes[(pos + parmsize + 1):(pos + parmsize + k)], k)
cat("preamble at pos=", pos, " with comment ", comment, "\n")
}
parmsize <- parmsize + k
} else if (opcode == 249L) break
pos <- pos + parmsize
}
}
DVIspecials <- function(f) {
size <- file.info(f)$size
con <- file(f, "rb")
bytes <- readBin(con, "raw", size)
close(con)
.Call(C_dviSpecials, bytes)
}
setDVIspecials <- function(f, newspecials, newname=f) {
size <- file.info(f)$size
con <- file(f, "r+b")
on.exit(close(con))
bytes <- readBin(con, "raw", size)
bytes <- .Call(C_setDviSpecials, bytes, as.character(newspecials))
close(con)
con <- file(newname, "wb")
writeBin(bytes, con)
}
patchDVI <- function(f, newname=f, patchLog = TRUE) {
specials <- DVIspecials(f)
concordind <- grep("^concordance:", specials)
concords <- specials[concordind]
parseConcord <- function(split) {
oldname <- split[2]
newname <- split[3]
if (length(split) == 4) {
ofs <- 0
vi <- 4
} else {
ofs <- as.integer(sub("^ofs ([0-9]+)", "\\1", split[4]))
vi <- 5
}
values <- as.integer(strsplit(split[vi], " ")[[1]])
firstline <- values[1]
rledata <- matrix(values[-1], nrow=2)
rle <- structure(list(lengths=rledata[1,], values=rledata[2,]), class="rle")
diffs <- inverse.rle(rle)
concord <- c(firstline, firstline + cumsum(diffs))
list(oldname=oldname, newname=newname, concord=concord, ofs=ofs)
}
concords <- strsplit(concords, ":")
concords <- lapply(concords, parseConcord)
names(concords) <- sapply(concords, function(x) x$oldname)
if (patchLog)
patchLog(paste0(tools::file_path_sans_ext(f), ".log"), concords = concords)
srcrefind <- grep("^src:", specials)
srcrefs <- specials[srcrefind]
linenums <- sub("^src:([0-9]+).*$", "\\1", srcrefs)
filenames <- substr(srcrefs, 5+nchar(linenums), 10000)
# \input{file} doesn't put .tex on it
noext <- !grepl("\\.", filenames)
filenames[noext] <- paste(filenames[noext], ".tex", sep="")
filenames <- myNormalizePath(filenames)
linenums <- as.integer(linenums)
changed <- rep(FALSE, length(filenames))
for (i in seq_along(concords)) {
n <- names(concords)[i]
ofs <- concords[[i]]$ofs
concord <- concords[[i]]$concord
subset <- (filenames == myNormalizePath(n)) & (linenums > ofs) & (linenums <= ofs + length(concord))
linenums[subset] <- concord[linenums[subset] - ofs]
filenames[subset] <- concords[[i]]$newname
changed[subset] <- TRUE
}
newrefs <- ifelse(changed, paste("src:", linenums, filenames, sep=""), srcrefs)
specials[srcrefind] <- newrefs
specials[concordind] <- NA
if (any(changed) || length(concordind))
setDVIspecials(f, specials, newname)
changes <- sum(changed) + length(concordind)
msg <- paste(changes, "patches made.")
if (!changes)
msg <- paste(msg, "Did you set \\SweaveOpts{concordance=TRUE}?")
msg
}
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patchDVI documentation built on May 5, 2020, 3 p.m.
R Package Documentation
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Defines functions patchDVI setDVIspecials DVIspecials readDVI SweaveDVI knitDVI SweaveMiktex knitMiktex
Documented in DVIspecials knitDVI knitMiktex patchDVI readDVI setDVIspecials SweaveDVI SweaveMiktex
knitMiktex <- function(Rnw,
main,
cmd="texify",
options="--tex-option=-src-specials --tex-option=-interaction=nonstopmode",
includedir="--tex-option=--include-directory=",
stylepath=FALSE,
source.code=NULL,
make=1,
preview='yap "%s"',
patchLog = TRUE,
sleep = 0,
weave = knitr::knit,
...)
SweaveMiktex(Rnw = Rnw,
main = main,
cmd = cmd,
options = options,
includedir = includedir,
stylepath = stylepath,
source.code = source.code,
make = make,
preview = preview,
patchLog = patchLog,
sleep = sleep,
weave = weave,
...)
SweaveMiktex <- function(Rnw,
main,
cmd="texify",
options="--tex-option=-src-specials --tex-option=-interaction=nonstopmode",
includedir="--tex-option=--include-directory=",
stylepath=FALSE,
source.code=NULL,
make=1,
preview='yap "%s"',
patchLog = TRUE,
sleep = 0,
...) {
if (!is.null(source.code))
try(source(source.code, local=TRUE))
if (sub(".*\\.tex$", "TeX", Rnw, ignore.case = TRUE) == "TeX")
outputname <- Rnw
else
outputname <- SweaveAll(Rnw, make=make, stylepath=stylepath, ...)[1]
if (missing(main)) main <- outputname
cmd <- paste(cmd, " ", options, " ", includedir, Rtexinputs(),
" ", main, sep="")
cat(cmd, "\n")
consoleLog <- try(system(cmd, intern = TRUE))
status <- attr(consoleLog, "status")
if (patchLog && !inherits(consoleLog, "try-error")) {
tempLog <- tempfile(fileext = ".log")
writeLines(consoleLog, tempLog)
patchLog(tempLog)
consoleLog <- readLines(tempLog)
}
cat(consoleLog, sep = "\n")
if (!is.null(status) && status) Sys.sleep(sleep)
dvi <- sub("\\.tex$", ".dvi", main, ignore.case = TRUE)
message(patchDVI(dvi, patchLog = patchLog))
if (!is.null(preview)) {
cmd <- sprintf(preview, dvi)
cat(cmd, "\n")
system(cmd, wait=FALSE, invisible=FALSE)
}
}
knitDVI <- function( Rnw, main,
texinputs=NULL,
source.code=NULL,
make=1,
links=NULL,
preview=NULL,
patchLog = TRUE,
weave = knitr::knit,
... )
SweaveDVI( Rnw = Rnw,
main = main,
texinputs = texinputs,
source.code = source.code,
make = make,
links = links,
preview = preview,
patchLog = patchLog,
weave = weave,
...)
SweaveDVI <- function( Rnw, main,
texinputs=NULL,
source.code=NULL,
make=1,
links=NULL,
preview=NULL,
patchLog = TRUE,
... ) {
if (!is.null(source.code) && file.exists(source.code))
try(source(source.code, local=TRUE))
if (sub(".*\\.tex$", "TeX", Rnw, ignore.case = TRUE) == "TeX")
outputname <- Rnw
else
outputname <- SweaveAll(Rnw, make=make, ...)[1]
if (missing(main)) main <- outputname
consoleLog <- try(tools::texi2dvi(main, pdf=FALSE, texinputs=texinputs, links=links))
if (patchLog && !inherits(consoleLog, "try-error")) {
tempLog <- tempfile(fileext = ".log")
writeLines(consoleLog, tempLog)
patchLog(tempLog)
consoleLog <- readLines(tempLog)
}
cat(consoleLog, sep = "\n")
dvi <- sub("\\.tex$", ".dvi", main, ignore.case=TRUE)
message(patchDVI(dvi, patchLog = patchLog))
if (!is.null(preview)) {
cmd <- sprintf(preview, dvi)
cat(cmd, "\n")
system(cmd, wait=FALSE, invisible=FALSE)
}
}
readDVI <- function(f, show=c("bop", "special", "fntdef", "preamble")) {
size <- file.info(f)$size
con <- file(f, "rb")
bytes <- readBin(con, "raw", size)
close(con)
parmsizes <- c( rep(0, 128), 1:4, 8, 1:4, 8, # 0 to 137
0, 44, 0,0,0, 1:4, 0, 1:4, 0, # 138 to 152
1:4, 1:4, 0, 1:4, 0, 1:4, # 153 to 170
rep(0, 64), 1:4, 1:4, 15:18, # 171 to 246
14, 28, 5, 9, rep(NA, 5)) # 247 to 255
pos <- 0
opcode <- 0
while (pos < size) {
pos <- pos+1
opcode <- as.integer(bytes[pos])
parmsize <- parmsizes[opcode + 1]
if (opcode < 139L) { # do nothing
} else if (opcode == 139L && "bop" %in% show) { # bop
counters <- readBin(bytes[pos + 1:(parmsize-4)], "integer", n= 10, size=4, endian="big")
prev <- readBin(bytes[pos + 40 + 1:4], "integer", size=4, endian="big")
cat("bop at pos=", pos, ": counters=", paste(counters, collapse=" "), " prev=", prev, "\n")
} else if (opcode < 239L) { # do nothing
} else if (opcode < 243L) { # xxxi
k <- readBin(bytes[pos + (1:parmsize)], "integer", size=parmsize, endian="big")
if ("special" %in% show) {
special <- readChar(bytes[(pos + parmsize + 1):(pos + parmsize + k)], k)
cat("special at pos=", pos," is ", special, "\n")
}
parmsize <- parmsize + k
} else if (opcode < 247L) { # fnt def i
a <- as.integer(bytes[pos + parmsize ])
if ("fntdef" %in% show) {
fntname <- readChar(bytes[(pos + parmsize + 1):(pos + parmsize + a)], a)
cat("fnt def at pos=", pos, " is ", fntname, "\n")
}
parmsize <- parmsize + a
} else if (opcode == 247L) { # pre
k <- as.integer(bytes[pos + parmsize])
if ("preamble" %in% show) {
comment <- readChar(bytes[(pos + parmsize + 1):(pos + parmsize + k)], k)
cat("preamble at pos=", pos, " with comment ", comment, "\n")
}
parmsize <- parmsize + k
} else if (opcode == 249L) break
pos <- pos + parmsize
}
}
DVIspecials <- function(f) {
size <- file.info(f)$size
con <- file(f, "rb")
bytes <- readBin(con, "raw", size)
close(con)
.Call(C_dviSpecials, bytes)
}
setDVIspecials <- function(f, newspecials, newname=f) {
size <- file.info(f)$size
con <- file(f, "r+b")
on.exit(close(con))
bytes <- readBin(con, "raw", size)
bytes <- .Call(C_setDviSpecials, bytes, as.character(newspecials))
close(con)
con <- file(newname, "wb")
writeBin(bytes, con)
}
patchDVI <- function(f, newname=f, patchLog = TRUE) {
specials <- DVIspecials(f)
concordind <- grep("^concordance:", specials)
concords <- specials[concordind]
parseConcord <- function(split) {
oldname <- split[2]
newname <- split[3]
if (length(split) == 4) {
ofs <- 0
vi <- 4
} else {
ofs <- as.integer(sub("^ofs ([0-9]+)", "\\1", split[4]))
vi <- 5
}
values <- as.integer(strsplit(split[vi], " ")[[1]])
firstline <- values[1]
rledata <- matrix(values[-1], nrow=2)
rle <- structure(list(lengths=rledata[1,], values=rledata[2,]), class="rle")
diffs <- inverse.rle(rle)
concord <- c(firstline, firstline + cumsum(diffs))
list(oldname=oldname, newname=newname, concord=concord, ofs=ofs)
}
concords <- strsplit(concords, ":")
concords <- lapply(concords, parseConcord)
names(concords) <- sapply(concords, function(x) x$oldname)
if (patchLog)
patchLog(paste0(tools::file_path_sans_ext(f), ".log"), concords = concords)
srcrefind <- grep("^src:", specials)
srcrefs <- specials[srcrefind]
linenums <- sub("^src:([0-9]+).*$", "\\1", srcrefs)
filenames <- substr(srcrefs, 5+nchar(linenums), 10000)
# \input{file} doesn't put .tex on it
noext <- !grepl("\\.", filenames)
filenames[noext] <- paste(filenames[noext], ".tex", sep="")
filenames <- myNormalizePath(filenames)
linenums <- as.integer(linenums)
changed <- rep(FALSE, length(filenames))
for (i in seq_along(concords)) {
n <- names(concords)[i]
ofs <- concords[[i]]$ofs
concord <- concords[[i]]$concord
subset <- (filenames == myNormalizePath(n)) & (linenums > ofs) & (linenums <= ofs + length(concord))
linenums[subset] <- concord[linenums[subset] - ofs]
filenames[subset] <- concords[[i]]$newname
changed[subset] <- TRUE
}
newrefs <- ifelse(changed, paste("src:", linenums, filenames, sep=""), srcrefs)
specials[srcrefind] <- newrefs
specials[concordind] <- NA
if (any(changed) || length(concordind))
setDVIspecials(f, specials, newname)
changes <- sum(changed) + length(concordind)
msg <- paste(changes, "patches made.")
if (!changes)
msg <- paste(msg, "Did you set \\SweaveOpts{concordance=TRUE}?")
msg
}
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R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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