尝试使用 C5.0 CRAN 包训练具有大约 300 万行和 600 列数据集的模型时，出现以下错误：
粘贴错误(apply(x, 1, paste, collapse = ","), collapse = "\n") : 结果将超过 2^31-1 字节
从存储库所有者对类似问题的回答来看，这是由于字符串中字节数的R 限制，限制为 2^31 - 1。
1 回答
3
前面的答案很长：
因此，如问题所述，错误发生在C5.0中使用的Cubist包中makeDataFile函数的最后一行，它将所有行连接成一个字符串。由于需要这个字符串来将数据传递给 C 中的 C5.0 函数，但不需要在 R 中进行任何操作，并且 C 除了机器本身的内存限制之外没有内存限制，我采取的方法是而是在 C 中创建这样的字符串。为了做到这一点，R 代码将在一个字符向量中传递信息，该字符向量包含不超过长度限制的各种字符串，而不是一个，这样一旦在 C 中，这些元素就可以连接起来。
但是，我发现 strcat 函数非常慢，因此我选择创建另一个 R 函数（create_max_len_strings） ，而不是将所有行作为字符向量中的单独元素在循环中使用 strcat 连接起来在不达到内存限制的情况下将行连接成最长（~或接近~）的字符串，因此只需应用几次 strcat 即可连接这些较长的字符串。
因此，原始 makeDataFile() 函数的最后一行将被替换，以便将每一行单独保留为字符向量的一个元素，仅在每个字符串行的末尾添加一个换行符，以便在连接其中一些元素时使用 create_max_len_strings() 将它们分成更长的字符串，它们将被区分：
create_max_len_strings <- function(original_vector) {
vector_length = length(original_vector)
nchars = sum(nchar(original_vector, type = "chars"))
## Check if the length of the string would reach 1900000000, which is close to the memory limitation
if(nchars >= 1900000000){
## Calculate how many strings we could create of the maximum length
nchunks = 0
while(nchars > 0){
nchars = nchars - 1900000000
nchunks = nchunks + 1
}
## Get the number of rows that would be contained in each string
chunk_size = vector_length/nchunks
## Get the rounded number of rows in each string
chunk_size = floor(chunk_size)
index = chunk_size
## Create a vector with the indexes of the rows that delimit each string
indexes_vector = c()
indexes_vector = append(indexes_vector, 0)
n = nchunks
while(n > 0){
indexes_vector = append(indexes_vector, index)
index = index + chunk_size
n = n - 1
}
## Get the last few rows if the division had remainder
remainder = vector_length %% nchunks
if (remainder != 0){
indexes_vector = append(indexes_vector, vector_length)
nchunks = nchunks + 1
}
## Create the strings pasting together the rows from the indexes in the indexes vector
strings_vector = c()
i = 2
while (i <= length(indexes_vector)){
## Sum 1 to the index_init so that the next string does not contain the last row of the previous string
index_init = indexes_vector[i-1] + 1
index_end = indexes_vector[i]
## Paste the rows from the vector from index_init to index_end
string <- paste0(original_vector[index_init:index_end], collapse="")
## Create vector containing the strings that were created
strings_vector <- append(strings_vector, string)
i = i + 1
}
}else {
strings_vector = paste0(original_vector, collapse="")
}
strings_vector
}
makeDataFile <- function(x, y, w = NULL) {
## Previous code stays the same
...
x = apply(x, 1, paste, collapse = ",")
x = paste(x, "\n", sep="")
char_vec = create_max_len_strings(x)
}
调用 C5.0
现在，为了创建最终字符串以传递给 C 中的 c50() 函数，创建并调用了一个中间函数。为了做到这一点，在 R 中调用 c50() 的 .C() 语句被替换为调用此函数的 .Call() 语句，因为 .Call() 允许将向量等复杂对象传递给 C。此外，它允许在变量result中返回结果，而不必通过引用传回变量tree、rules和output。调用 C5.0 的结果将在字符向量结果中接收，其中包含与树、规则和前三个位置的输出对应的字符串：
C5.0.default <- function(x,
y,
trials = 1,
rules = FALSE,
weights = NULL,
control = C5.0Control(),
costs = NULL,
...) {
## Previous code stays the same
...
dataString <- makeDataFile(x, y, weights)
num_chars = sum(nchar(dataString, type = "chars"))
result <- .Call(
"call_C50",
as.character(namesString),
dataString,
as.character(num_chars), ## The length of the resulting string is passed as character because it is too long for an integer
as.character(costString),
as.logical(control$subset),
# -s "use the Subset option" var name: SUBSET
as.logical(rules),
# -r "use the Ruleset option" var name: RULES
## for the bands option, I'm not sure what the default should be.
as.integer(control$bands),
# -u "sort rules by their utility into bands" var name: UTILITY
## The documentation has two options for boosting:
## -b use the Boosting option with 10 trials
## -t trials ditto with specified number of trial
## I think we should use -t
as.integer(trials),
# -t : " ditto with specified number of trial", var name: TRIALS
as.logical(control$winnow),
# -w "winnow attributes before constructing a classifier" var name: WINNOW
as.double(control$sample),
# -S : use a sample of x% for training
# and a disjoint sample for testing var name: SAMPLE
as.integer(control$seed),
# -I : set the sampling seed value
as.integer(control$noGlobalPruning),
# -g: "turn off the global tree pruning stage" var name: GLOBAL
as.double(control$CF),
# -c: "set the Pruning CF value" var name: CF
## Also, for the number of minimum cases, I'm not sure what the
## default should be. The code looks like it dynamically sets the
## value (as opposed to a static, universal integer
as.integer(control$minCases),
# -m : "set the Minimum cases" var name: MINITEMS
as.logical(control$fuzzyThreshold),
# -p "use the Fuzzy thresholds option" var name: PROBTHRESH
as.logical(control$earlyStopping)
)
## Get the first three positions of the character vector that contain the tree, rules and output returned by C5.0 in C
result_tree = result[1]
result_rules = result[2]
result_output = result[3]
modelContent <- strsplit(
if (rules)
result_rules
else
result_tree, "\n"
)[[1]]
entries <- grep("^entries", modelContent, value = TRUE)
if (length(entries) > 0) {
actual <- as.numeric(substring(entries, 10, nchar(entries) - 1))
} else
actual <- trials
if (trials > 1) {
boostResults <- getBoostResults(result_output)
## This next line is here to avoid a false positive warning in R
## CMD check:
## * checking R code for possible problems ... NOTE
## C5.0.default: no visible binding for global variable 'Data'
Data <- NULL
size <-
if (!is.null(boostResults))
subset(boostResults, Data == "Training Set")$Size
else
NA
} else {
boostResults <- NULL
size <- length(grep("[0-9])$", strsplit(result_output, "\n")[[1]]))
}
out <- list(
names = namesString,
cost = costString,
costMatrix = costs,
caseWeights = !is.null(weights),
control = control,
trials = c(Requested = trials, Actual = actual),
rbm = rules,
boostResults = boostResults,
size = size,
dims = dim(x),
call = funcCall,
levels = levels(y),
output = result_output,
tree = result_tree,
predictors = colnames(x),
rules = result_rules
)
class(out) <- "C5.0"
out
}
现在进入 C 代码，函数 call_c50() 基本上充当 R 代码和 C 代码之间的中间体，连接 dataString 数组中的元素以获得 C 函数c50()所需的字符串，通过访问每个位置使用 CHAR(STRING_ELT(x, i)) 的数组并将它们连接在一起（strcat）。然后将其余变量强制转换为它们各自的类型，并调用文件 top.c 中的 c50() 函数（该函数也应该放置在其中）。调用 c50() 的结果将通过创建一个字符向量并将与tree、rules和output对应的字符串放置在每个位置来返回给 R 例程。
最后，c50() 函数基本上保持原样，除了变量treev、rulesv和outputv，因为这些值将由 .Call() 返回而不是通过引用传递，它们不再需要在函数的参数中。由于它们都是字符串，因此可以通过将每个字符串设置到数组c50_return中的位置来在单个数组中返回它们。
顶部.c：
SEXP call_C50(SEXP namesString, SEXP data_vec, SEXP datavec_len, SEXP costString, SEXP subset, SEXP rules, SEXP bands, SEXP trials, SEXP winnow, SEXP sample,
SEXP seed, SEXP noGlobalPruning, SEXP CF, SEXP minCases, SEXP fuzzyThreshold, SEXP earlyStopping){
char* string;
char* concat;
long n = 0;
long size;
int i;
char* eptr;
// Get the length of the data vector
n = length(data_vec);
// Get the string indicating the length of the final string
char* size_str = malloc((strlen(CHAR(STRING_ELT(datavec_len, 0)))+1)*sizeof(char));
strcpy(size_str, CHAR(STRING_ELT(datavec_len, 0)));
// Turn the string to long
size = strtol(size_str, &eptr, 10);
// Allocate memory for the number of characters indicated by datavec_len
string = malloc((size+1)*sizeof(char));
// Copy the first element of data_vec into the string variable
strcpy(string, CHAR(STRING_ELT(data_vec, 0)));
// Loop over the data vector until all elements are concatenated in the string variable
for (i = 1; i < n; i++) {
strcat(string, CHAR(STRING_ELT(data_vec, i)));
}
// Copy the value of namesString into a char*
char* namesv = malloc((strlen(CHAR(STRING_ELT(namesString, 0)))+1)*sizeof(char));
strcpy(namesv, CHAR(STRING_ELT(namesString, 0)));
// Copy the value of costString into a char*
char* costv = malloc((strlen(CHAR(STRING_ELT(costString, 0)))+1)*sizeof(char));
strcpy(costv, CHAR(STRING_ELT(costString, 0)));
// Call c50() function casting the rest of arguments into their respective C types
char** c50_return = c50(namesv, string, costv, asLogical(subset), asLogical(rules), asInteger(bands), asInteger(trials), asLogical(winnow), asReal(sample), asInteger(seed), asInteger(noGlobalPruning), asReal(CF), asInteger(minCases), asLogical(fuzzyThreshold), asLogical(earlyStopping));
free(string);
free(namesv);
free(costv);
// Create a character vector to be returned to the C5.0 R function
SEXP out = PROTECT(allocVector(STRSXP, 3));
SET_STRING_ELT(out, 0, mkChar(c50_return[0]));
SET_STRING_ELT(out, 1, mkChar(c50_return[1]));
SET_STRING_ELT(out, 2, mkChar(c50_return[2]));
UNPROTECT(1);
return out;
}
static char** c50(char *namesv, char *datav, char *costv, int subset,
int rules, int utility, int trials, int winnow,
double sample, int seed, int noGlobalPruning, double CF,
int minCases, int fuzzyThreshold, int earlyStopping) {
int val; /* Used by setjmp/longjmp for implementing rbm_exit */
char ** c50_return = malloc(3 * sizeof(char*));
// Initialize the globals to the values that the c50
// program would have at the start of execution
initglobals();
// Set globals based on the arguments. This is analogous
// to parsing the command line in the c50 program.
setglobals(subset, rules, utility, trials, winnow, sample, seed,
noGlobalPruning, CF, minCases, fuzzyThreshold, earlyStopping,
costv);
// Handles the strbufv data structure
rbm_removeall();
// Deallocates memory allocated by NewCase.
// Not necessary since it's also called at the end of this function,
// but it doesn't hurt, and I'm feeling paranoid.
FreeCases();
// XXX Should this be controlled via an option?
// Rprintf("Calling setOf\n");
setOf();
// Create a strbuf using *namesv as the buffer.
// Note that this is a readonly strbuf since we can't
// extend *namesv.
STRBUF *sb_names = strbuf_create_full(namesv, strlen(namesv))
// Register this strbuf using the name "undefined.names"
if (rbm_register(sb_names, "undefined.names", 0) < 0) {
error("undefined.names already exists");
}
// Create a strbuf using *datav and register it as "undefined.data"
STRBUF *sb_datav = strbuf_create_full(datav, strlen(datav));
// XXX why is sb_datav copied? was that part of my debugging?
// XXX or is this the cause of the leak?
if (rbm_register(strbuf_copy(sb_datav), "undefined.data", 0) < 0) {
error("undefined data already exists");
}
// Create a strbuf using *costv and register it as "undefined.costs"
if (strlen(costv) > 0) {
// Rprintf("registering cost matrix: %s", *costv);
STRBUF *sb_costv = strbuf_create_full(costv, strlen(costv));
// XXX should sb_costv be copied?
if (rbm_register(sb_costv, "undefined.costs", 0) < 0) {
error("undefined.cost already exists");
}
} else {
// Rprintf("no cost matrix to register\n");
}
/*
* We need to initialize rbm_buf before calling any code that
* might call exit/rbm_exit.
*/
if ((val = setjmp(rbm_buf)) == 0) {
// Real work is done here
c50main();
if (rules == 0) {
// Get the contents of the the tree file
STRBUF *treebuf = rbm_lookup("undefined.tree");
if (treebuf != NULL) {
char *treeString = strbuf_getall(treebuf);
c50_return[0] = R_alloc(strlen(treeString) + 1, 1);
strcpy(c50_return[0], treeString);
c50_return[1] = "";
} else {
// XXX Should *treev be assigned something in this case?
// XXX Throw an error?
}
} else {
// Get the contents of the the rules file
STRBUF *rulesbuf = rbm_lookup("undefined.rules");
if (rulesbuf != NULL) {
char *rulesString = strbuf_getall(rulesbuf);
c50_return[1] = R_alloc(strlen(rulesString) + 1, 1);
strcpy(c50_return[1], rulesString);
c50_return[0] = "";
} else {
// XXX Should *rulesv be assigned something in this case?
// XXX Throw an error?
}
}
} else {
Rprintf("c50 code called exit with value %d\n", val - JMP_OFFSET);
}
// Close file object "Of", and return its contents via argument outputv
char *outputString = closeOf();
c50_return[2] = R_alloc(strlen(outputString) + 1, 1);
strcpy(c50_return[2], outputString);
// Deallocates memory allocated by NewCase
FreeCases();
// We reinitialize the globals on exit out of general paranoia
initglobals();
return c50_return;
}
***重要提示：如果创建的字符串长于 2147483647，您还需要更改 strbuf.c 中函数 strbuf_gets() 中变量 i 和 j 的定义。这个函数基本上遍历字符串的每个位置，因此试图将它们的值增加到超过 INT 限制以访问数组中的这些位置将导致分段错误。我建议将声明类型更改为 long 以避免此问题。
C5.0 预测
但是，由于 makeDataFile 函数不仅用于创建模型，还用于将数据传递给predictions()函数，因此也必须修改此函数。就像之前一样，predict.C5.0()中用于调用 predictions() 的 .C() 语句将被替换为 .Call() 语句，以便能够将字符向量传递给 C，然后将结果将在结果变量中返回，而不是通过引用传递：
predict.C5.0 <- function (object,
newdata = NULL,
trials = object$trials["Actual"],
type = "class",
na.action = na.pass,
...) {
## Previous code stays the same
...
caseString <- makeDataFile(x = newdata, y = NULL)
num_chars = sum(nchar(caseString, type = "chars"))
## When passing trials to the C code, convert to
## zero if the original version of trials is used
if (trials <= 0)
stop("'trials should be a positive integer", call. = FALSE)
if (trials == object$trials["Actual"])
trials <- 0
## Add trials (not object$trials) as an argument
results <- .Call(
"call_predictions",
caseString,
as.character(num_chars),
as.character(object$names),
as.character(object$tree),
as.character(object$rules),
as.character(object$cost),
pred = integer(nrow(newdata)),
confidence = double(length(object$levels) * nrow(newdata)),
trials = as.integer(trials)
)
predictions = as.numeric(unlist(results[1]))
confidence = as.numeric(unlist(results[2]))
output = as.character(results[3])
if(any(grepl("Error limit exceeded", output)))
stop(output, call. = FALSE)
if (type == "class") {
out <- factor(object$levels[predictions], levels = object$levels)
} else {
out <-
matrix(confidence,
ncol = length(object$levels),
byrow = TRUE)
if (!is.null(rownames(newdata)))
rownames(out) <- rownames(newdata)
colnames(out) <- object$levels
}
out
}
在文件 top.c 中，predictions()函数将被修改为接收 .Call() 语句传递的变量，这样就像之前一样，caseString 数组将被连接成一个字符串，其余的变量铸造成各自的类型。在这种情况下，变量pred和confidence也将作为整数和双精度类型的向量接收，因此需要将它们转换为 int* 和 double*。函数的其余部分保持原样，以便创建预测，结果变量predv、confidencev和输出变量将分别放置在向量的前三个位置。
顶部.c：
SEXP call_predictions(SEXP caseString, SEXP case_len, SEXP names, SEXP tree, SEXP rules, SEXP cost, SEXP pred, SEXP confidence, SEXP trials){
char* casev;
char* outputv = "";
char* eptr;
char* size_str = malloc((strlen(CHAR(STRING_ELT(case_len, 0)))+1)*sizeof(char));
strcpy(size_str, CHAR(STRING_ELT(case_len, 0)));
long size = strtol(size_str, &eptr, 10);
casev = malloc((size+1)*sizeof(char));
strcpy(casev, CHAR(STRING_ELT(caseString, 0)));
int n = length(caseString);
for (int i = 1; i < n; i++) {
strcat(casev, CHAR(STRING_ELT(caseString, i)));
}
char* namesv = malloc((strlen(CHAR(STRING_ELT(names, 0)))+1)*sizeof(char));
strcpy(namesv, CHAR(STRING_ELT(names, 0)));
char* treev = malloc((strlen(CHAR(STRING_ELT(tree, 0)))+1)*sizeof(char));
strcpy(treev, CHAR(STRING_ELT(tree, 0)));
char* rulesv = malloc((strlen(CHAR(STRING_ELT(rules, 0)))+1)*sizeof(char));
strcpy(rulesv, CHAR(STRING_ELT(rules, 0)));
char* costv = malloc((strlen(CHAR(STRING_ELT(cost, 0)))+1)*sizeof(char));
strcpy(costv, CHAR(STRING_ELT(cost, 0)));
int variable;
int* predv = &variable;
int npred = length(pred);
predv = malloc((npred+1)*sizeof(int));
for (int i = 0; i < npred; i++) {
predv[i] = INTEGER(pred)[i];
}
double variable1;
double* confidencev = &variable1;
int nconf = length(confidence);
confidencev = malloc((nconf+1)*sizeof(double));
for (int i = 0; i < nconf; i++) {
confidencev[i] = REAL(confidence)[i];
}
int* trialsv = &variable;
*trialsv = asInteger(trials);
/* Original code for predictions starts */
int val;
// Announce ourselves for testing
// Rprintf("predictions called\n");
// Initialize the globals
initglobals();
// Handles the strbufv data structure
rbm_removeall();
// XXX Should this be controlled via an option?
// Rprintf("Calling setOf\n");
setOf();
STRBUF *sb_cases = strbuf_create_full(casev, strlen(casev));
if (rbm_register(sb_cases, "undefined.cases", 0) < 0) {
error("undefined.cases already exists");
}
STRBUF *sb_names = strbuf_create_full(namesv, strlen(namesv));
if (rbm_register(sb_names, "undefined.names", 0) < 0) {
error("undefined.names already exists");
}
if (strlen(treev)) {
STRBUF *sb_treev = strbuf_create_full(treev, strlen(treev));
if (rbm_register(sb_treev, "undefined.tree", 0) < 0) {
error("undefined.tree already exists");
}
} else if (strlen(rulesv)) {
STRBUF *sb_rulesv = strbuf_create_full(rulesv, strlen(rulesv));
if (rbm_register(sb_rulesv, "undefined.rules", 0) < 0) {
error("undefined.rules already exists");
}
setrules(1);
} else {
error("either a tree or rules must be provided");
}
// Create a strbuf using *costv and register it as "undefined.costs"
if (strlen(costv) > 0) {
// Rprintf("registering cost matrix: %s", *costv);
STRBUF *sb_costv = strbuf_create_full(costv, strlen(costv));
// XXX should sb_costv be copied?
if (rbm_register(sb_costv, "undefined.costs", 0) < 0) {
error("undefined.cost already exists");
}
} else {
// Rprintf("no cost matrix to register\n");
}
if ((val = setjmp(rbm_buf)) == 0) {
// Real work is done here
// Rprintf("\n\nCalling rpredictmain\n");
rpredictmain(trialsv, predv, confidencev);
// Rprintf("predict finished\n\n");
} else {
// Rprintf("predict code called exit with value %d\n\n", val - JMP_OFFSET);
}
// Close file object "Of", and return its contents via argument outputv
char *outputString = closeOf();
char *output = R_alloc(strlen(outputString) + 1, 1);
strcpy(output, outputString);
// We reinitialize the globals on exit out of general paranoia
initglobals();
/* Original code for predictions ends */
free(namesv);
free(treev);
free(rulesv);
free(costv);
SEXP predx = PROTECT(allocVector(INTSXP, npred));
for (int i = 0; i < npred; i++) {
INTEGER(predx)[i] = predv[i];
}
SEXP confidencex = PROTECT(allocVector(REALSXP, nconf));
for (int i = 0; i < npred; i++) {
REAL(confidencex)[i] = confidencev[i];
}
SEXP outputx = PROTECT(allocVector(STRSXP, 1));
SET_STRING_ELT(outputx, 0, mkChar(output));
SEXP vector = PROTECT(allocVector(VECSXP, 3));
SET_VECTOR_ELT(vector, 0, predx);
SET_VECTOR_ELT(vector, 1, confidencex);
SET_VECTOR_ELT(vector, 2, outputx);
UNPROTECT(4);
free(predv);
free(confidencev);
return vector;
}
于 2021-06-25T00:33:19.827 回答