void REvprintf(const char *format, va_list arg)
{
if(R_ErrorCon != 2) {
Rconnection con = getConnection_no_err(R_ErrorCon);
if(con == NULL) {
/* should never happen, but in case of corruption... */
R_ErrorCon = 2;
} else {
/* Parentheses added for FC4 with gcc4 and -D_FORTIFY_SOURCE=2 */
(con->vfprintf)(con, format, arg);
con->fflush(con);
return;
}
}
if(R_Consolefile) {
/* try to interleave stdout and stderr carefully */
if(R_Outputfile && (R_Outputfile != R_Consolefile)) {
fflush(R_Outputfile);
vfprintf(R_Consolefile, format, arg);
/* normally R_Consolefile is stderr and so unbuffered, but
it can be something else (e.g. stdout on Win9x) */
fflush(R_Consolefile);
} else vfprintf(R_Consolefile, format, arg);
} else {
char buf[BUFSIZE];
vsnprintf(buf, BUFSIZE, format, arg);
buf[BUFSIZE-1] = '\0';
R_WriteConsoleEx(buf, (int) strlen(buf), 1);
}
}
static void cat_cleanup(void *data)
{
cat_info *pci = (cat_info *) data;
Rconnection con = pci->con;
Rboolean wasopen = pci->wasopen;
int changedcon = pci->changedcon;
con->fflush(con);
if(changedcon) switch_stdout(-1, 0);
/* previous line might have closed it */
if(!wasopen && con->isopen) con->close(con);
#ifdef Win32
WinUTF8out = FALSE;
#endif
}
void Rvprintf(const char *format, va_list arg)
{
int i=0, con_num=R_OutputCon;
Rconnection con;
va_list argcopy;
static int printcount = 0;
if (++printcount > 100) {
R_CheckUserInterrupt();
printcount = 0 ;
}
do{
con = getConnection(con_num);
va_copy(argcopy, arg);
/* Parentheses added for Fedora with -D_FORTIFY_SOURCE=2 */
(con->vfprintf)(con, format, argcopy);
va_end(argcopy);
con->fflush(con);
con_num = getActiveSink(i++);
} while(con_num>0);
}
SEXP attribute_hidden do_readDCF(SEXP call, SEXP op, SEXP args, SEXP env)
{
int nwhat, nret, nc, nr, m, k, lastm, need;
Rboolean blank_skip, field_skip = FALSE;
int whatlen, dynwhat, buflen = 8096; // was 100, but that re-alloced often
char *line, *buf;
regex_t blankline, contline, trailblank, regline, eblankline;
regmatch_t regmatch[1];
SEXP file, what, what2, retval, retval2, dims, dimnames;
Rconnection con = NULL;
Rboolean wasopen, is_eblankline;
RCNTXT cntxt;
SEXP fold_excludes;
Rboolean field_fold = TRUE, has_fold_excludes;
const char *field_name;
int offset = 0; /* -Wall */
checkArity(op, args);
file = CAR(args);
con = getConnection(asInteger(file));
wasopen = con->isopen;
if(!wasopen) {
if(!con->open(con)) error(_("cannot open the connection"));
/* Set up a context which will close the connection on error */
begincontext(&cntxt, CTXT_CCODE, R_NilValue, R_BaseEnv, R_BaseEnv,
R_NilValue, R_NilValue);
cntxt.cend = &con_cleanup;
cntxt.cenddata = con;
}
if(!con->canread) error(_("cannot read from this connection"));
args = CDR(args);
PROTECT(what = coerceVector(CAR(args), STRSXP)); /* argument fields */
nwhat = LENGTH(what);
dynwhat = (nwhat == 0);
args = CDR(args);
PROTECT(fold_excludes = coerceVector(CAR(args), STRSXP));
has_fold_excludes = (LENGTH(fold_excludes) > 0);
buf = (char *) malloc(buflen);
if(!buf) error(_("could not allocate memory for 'read.dcf'"));
nret = 20;
/* it is easier if we first have a record per column */
PROTECT(retval = allocMatrixNA(STRSXP, LENGTH(what), nret));
/* These used to use [:blank:] but that can match \xa0 as part of
a UTF-8 character (and is nbspace on Windows). */
tre_regcomp(&blankline, "^[[:blank:]]*$", REG_NOSUB & REG_EXTENDED);
tre_regcomp(&trailblank, "[ \t]+$", REG_EXTENDED);
tre_regcomp(&contline, "^[[:blank:]]+", REG_EXTENDED);
tre_regcomp(®line, "^[^:]+:[[:blank:]]*", REG_EXTENDED);
tre_regcomp(&eblankline, "^[[:space:]]+\\.[[:space:]]*$", REG_EXTENDED);
k = 0;
lastm = -1; /* index of the field currently being recorded */
blank_skip = TRUE;
void *vmax = vmaxget();
while((line = Rconn_getline2(con))) {
if(strlen(line) == 0 ||
tre_regexecb(&blankline, line, 0, 0, 0) == 0) {
/* A blank line. The first one after a record ends a new
* record, subsequent ones are skipped */
if(!blank_skip) {
k++;
if(k > nret - 1){
nret *= 2;
PROTECT(retval2 = allocMatrixNA(STRSXP, LENGTH(what), nret));
transferVector(retval2, retval);
UNPROTECT_PTR(retval);
retval = retval2;
}
blank_skip = TRUE;
lastm = -1;
field_skip = FALSE;
field_fold = TRUE;
}
} else {
blank_skip = FALSE;
if(tre_regexecb(&contline, line, 1, regmatch, 0) == 0) {
/* A continuation line: wrong if at the beginning of a
record. */
if((lastm == -1) && !field_skip) {
line[20] = '\0';
error(_("Found continuation line starting '%s ...' at begin of record."),
line);
}
if(lastm >= 0) {
need = (int) strlen(CHAR(STRING_ELT(retval,
lastm + nwhat * k))) + 2;
if(tre_regexecb(&eblankline, line, 0, NULL, 0) == 0) {
is_eblankline = TRUE;
} else {
is_eblankline = FALSE;
if(field_fold) {
offset = regmatch[0].rm_eo;
/* Also remove trailing whitespace. */
if((tre_regexecb(&trailblank, line, 1,
regmatch, 0) == 0))
line[regmatch[0].rm_so] = '\0';
} else {
offset = 0;
}
need += (int) strlen(line + offset);
}
if(buflen < need) {
char *tmp = (char *) realloc(buf, need);
if(!tmp) {
free(buf);
error(_("could not allocate memory for 'read.dcf'"));
} else buf = tmp;
buflen = need;
}
strcpy(buf,CHAR(STRING_ELT(retval, lastm + nwhat * k)));
strcat(buf, "\n");
if(!is_eblankline) strcat(buf, line + offset);
SET_STRING_ELT(retval, lastm + nwhat * k, mkChar(buf));
}
} else {
if(tre_regexecb(®line, line, 1, regmatch, 0) == 0) {
for(m = 0; m < nwhat; m++){
whatlen = (int) strlen(CHAR(STRING_ELT(what, m)));
if(strlen(line) > whatlen &&
line[whatlen] == ':' &&
strncmp(CHAR(STRING_ELT(what, m)),
line, whatlen) == 0) {
/* An already known field we are recording. */
lastm = m;
field_skip = FALSE;
field_name = CHAR(STRING_ELT(what, lastm));
if(has_fold_excludes) {
field_fold =
field_is_foldable_p(field_name,
fold_excludes);
}
if(field_fold) {
offset = regmatch[0].rm_eo;
/* Also remove trailing whitespace. */
if((tre_regexecb(&trailblank, line, 1,
regmatch, 0) == 0))
line[regmatch[0].rm_so] = '\0';
} else {
offset = 0;
}
SET_STRING_ELT(retval, m + nwhat * k,
mkChar(line + offset));
break;
} else {
/* This is a field, but not one prespecified */
lastm = -1;
field_skip = TRUE;
}
}
if(dynwhat && (lastm == -1)) {
/* A previously unseen field and we are
* recording all fields */
field_skip = FALSE;
PROTECT(what2 = allocVector(STRSXP, nwhat+1));
PROTECT(retval2 = allocMatrixNA(STRSXP,
nrows(retval)+1,
ncols(retval)));
if(nwhat > 0) {
copyVector(what2, what);
for(nr = 0; nr < nrows(retval); nr++){
for(nc = 0; nc < ncols(retval); nc++){
SET_STRING_ELT(retval2, nr+nc*nrows(retval2),
STRING_ELT(retval,
nr+nc*nrows(retval)));
}
}
}
UNPROTECT_PTR(retval);
UNPROTECT_PTR(what);
retval = retval2;
what = what2;
/* Make sure enough space was used */
need = (int) (Rf_strchr(line, ':') - line + 1);
if(buflen < need){
char *tmp = (char *) realloc(buf, need);
if(!tmp) {
free(buf);
error(_("could not allocate memory for 'read.dcf'"));
} else buf = tmp;
buflen = need;
}
strncpy(buf, line, Rf_strchr(line, ':') - line);
buf[Rf_strchr(line, ':') - line] = '\0';
SET_STRING_ELT(what, nwhat, mkChar(buf));
nwhat++;
/* lastm uses C indexing, hence nwhat - 1 */
lastm = nwhat - 1;
field_name = CHAR(STRING_ELT(what, lastm));
if(has_fold_excludes) {
field_fold =
field_is_foldable_p(field_name,
fold_excludes);
}
offset = regmatch[0].rm_eo;
if(field_fold) {
/* Also remove trailing whitespace. */
if((tre_regexecb(&trailblank, line, 1,
regmatch, 0) == 0))
line[regmatch[0].rm_so] = '\0';
}
SET_STRING_ELT(retval, lastm + nwhat * k,
mkChar(line + offset));
}
} else {
/* Must be a regular line with no tag ... */
line[20] = '\0';
error(_("Line starting '%s ...' is malformed!"), line);
}
}
}
}
vmaxset(vmax);
if(!wasopen) {endcontext(&cntxt); con->close(con);}
free(buf);
tre_regfree(&blankline);
tre_regfree(&contline);
tre_regfree(&trailblank);
tre_regfree(®line);
tre_regfree(&eblankline);
if(!blank_skip) k++;
/* and now transpose the whole matrix */
PROTECT(retval2 = allocMatrixNA(STRSXP, k, LENGTH(what)));
copyMatrix(retval2, retval, 1);
PROTECT(dimnames = allocVector(VECSXP, 2));
PROTECT(dims = allocVector(INTSXP, 2));
INTEGER(dims)[0] = k;
INTEGER(dims)[1] = LENGTH(what);
SET_VECTOR_ELT(dimnames, 1, what);
setAttrib(retval2, R_DimSymbol, dims);
setAttrib(retval2, R_DimNamesSymbol, dimnames);
UNPROTECT(6);
return(retval2);
}
static void con_cleanup(void *data)
{
Rconnection con = data;
if(con->isopen) con->close(con);
}
/* "do_parse" - the user interface input/output to files.
The internal R_Parse.. functions are defined in ./gram.y (-> gram.c)
.Internal( parse(file, n, text, prompt, srcfile, encoding) )
If there is text then that is read and the other arguments are ignored.
*/
SEXP attribute_hidden do_parse(SEXP call, SEXP op, SEXP args, SEXP env)
{
SEXP text, prompt, s, source;
Rconnection con;
Rboolean wasopen, old_latin1 = known_to_be_latin1,
old_utf8 = known_to_be_utf8, allKnown = TRUE;
int ifile, num, i;
const char *encoding;
ParseStatus status;
checkArity(op, args);
R_ParseError = 0;
R_ParseErrorMsg[0] = '\0';
ifile = asInteger(CAR(args)); args = CDR(args);
con = getConnection(ifile);
wasopen = con->isopen;
num = asInteger(CAR(args)); args = CDR(args);
if (num == 0)
return(allocVector(EXPRSXP, 0));
PROTECT(text = coerceVector(CAR(args), STRSXP));
if(length(CAR(args)) && !length(text))
errorcall(call, _("coercion of 'text' to character was unsuccessful"));
args = CDR(args);
prompt = CAR(args); args = CDR(args);
source = CAR(args); args = CDR(args);
if(!isString(CAR(args)) || LENGTH(CAR(args)) != 1)
error(_("invalid '%s' value"), "encoding");
encoding = CHAR(STRING_ELT(CAR(args), 0)); /* ASCII */
known_to_be_latin1 = known_to_be_utf8 = FALSE;
/* allow 'encoding' to override declaration on 'text'. */
if(streql(encoding, "latin1")) {
known_to_be_latin1 = TRUE;
allKnown = FALSE;
} else if(streql(encoding, "UTF-8")) {
known_to_be_utf8 = TRUE;
allKnown = FALSE;
} else if(!streql(encoding, "unknown") && !streql(encoding, "native.enc"))
warning(_("argument '%s = \"%s\"' will be ignored"), "encoding", encoding);
if (prompt == R_NilValue)
PROTECT(prompt);
else
PROTECT(prompt = coerceVector(prompt, STRSXP));
if (length(text) > 0) {
/* If 'text' has known encoding then we can be sure it will be
correctly re-encoded to the current encoding by
translateChar in the parser and so could mark the result in
a Latin-1 or UTF-8 locale.
A small complication is that different elements could have
different encodings, but all that matters is that all
non-ASCII elements have known encoding.
*/
for(i = 0; i < length(text); i++)
if(!ENC_KNOWN(STRING_ELT(text, i)) &&
!IS_ASCII(STRING_ELT(text, i))) {
allKnown = FALSE;
break;
}
if(allKnown) {
known_to_be_latin1 = old_latin1;
known_to_be_utf8 = old_utf8;
}
if (num == NA_INTEGER) num = -1;
s = R_ParseVector(text, num, &status, source);
if (status != PARSE_OK) parseError(call, R_ParseError);
}
else if (ifile >= 3) {/* file != "" */
if (num == NA_INTEGER) num = -1;
try {
if(!wasopen && !con->open(con))
error(_("cannot open the connection"));
if(!con->canread) error(_("cannot read from this connection"));
s = R_ParseConn(con, num, &status, source);
if(!wasopen) con->close(con);
} catch (...) {
if (!wasopen && con->isopen)
con->close(con);
throw;
}
if (status != PARSE_OK) parseError(call, R_ParseError);
}
else {
if (num == NA_INTEGER) num = 1;
s = R_ParseBuffer(&R_ConsoleIob, num, &status, prompt, source);
if (status != PARSE_OK) parseError(call, R_ParseError);
}
UNPROTECT(2);
known_to_be_latin1 = old_latin1;
known_to_be_utf8 = old_utf8;
return s;
}
SEXP writetable(SEXP call, SEXP op, SEXP args, SEXP env)
{
SEXP x, sep, rnames, eol, na, dec, quote, xj;
int nr, nc, i, j, qmethod;
Rboolean wasopen, quote_rn = FALSE, *quote_col;
Rconnection con;
const char *csep, *ceol, *cna, *sdec, *tmp=NULL /* -Wall */;
char cdec;
SEXP *levels;
R_StringBuffer strBuf = {NULL, 0, MAXELTSIZE};
wt_info wi;
RCNTXT cntxt;
args = CDR(args);
x = CAR(args); args = CDR(args);
/* this is going to be a connection open or openable for writing */
if(!inherits(CAR(args), "connection"))
error(_("'file' is not a connection"));
con = getConnection(asInteger(CAR(args))); args = CDR(args);
if(!con->canwrite)
error(_("cannot write to this connection"));
wasopen = con->isopen;
if(!wasopen) {
strcpy(con->mode, "wt");
if(!con->open(con)) error(_("cannot open the connection"));
}
nr = asInteger(CAR(args)); args = CDR(args);
nc = asInteger(CAR(args)); args = CDR(args);
rnames = CAR(args); args = CDR(args);
sep = CAR(args); args = CDR(args);
eol = CAR(args); args = CDR(args);
na = CAR(args); args = CDR(args);
dec = CAR(args); args = CDR(args);
quote = CAR(args); args = CDR(args);
qmethod = asLogical(CAR(args));
if(nr == NA_INTEGER) error(_("invalid '%s' argument"), "nr");
if(nc == NA_INTEGER) error(_("invalid '%s' argument"), "nc");
if(!isNull(rnames) && !isString(rnames))
error(_("invalid '%s' argument"), "rnames");
if(!isString(sep)) error(_("invalid '%s' argument"), "sep");
if(!isString(eol)) error(_("invalid '%s' argument"), "eol");
if(!isString(na)) error(_("invalid '%s' argument"), "na");
if(!isString(dec)) error(_("invalid '%s' argument"), "dec");
if(qmethod == NA_LOGICAL) error(_("invalid '%s' argument"), "qmethod");
csep = translateChar(STRING_ELT(sep, 0));
ceol = translateChar(STRING_ELT(eol, 0));
cna = translateChar(STRING_ELT(na, 0));
sdec = translateChar(STRING_ELT(dec, 0));
if(strlen(sdec) != 1)
error(_("'dec' must be a single character"));
cdec = sdec[0];
quote_col = (Rboolean *) R_alloc(nc, sizeof(Rboolean));
for(j = 0; j < nc; j++) quote_col[j] = FALSE;
for(i = 0; i < length(quote); i++) { /* NB, quote might be NULL */
int this = INTEGER(quote)[i];
if(this == 0) quote_rn = TRUE;
if(this > 0) quote_col[this - 1] = TRUE;
}
R_AllocStringBuffer(0, &strBuf);
PrintDefaults();
wi.savedigits = R_print.digits; R_print.digits = DBL_DIG;/* MAX precision */
wi.con = con;
wi.wasopen = wasopen;
wi.buf = &strBuf;
begincontext(&cntxt, CTXT_CCODE, call, R_BaseEnv, R_BaseEnv,
R_NilValue, R_NilValue);
cntxt.cend = &wt_cleanup;
cntxt.cenddata = &wi;
if(isVectorList(x)) { /* A data frame */
/* handle factors internally, check integrity */
levels = (SEXP *) R_alloc(nc, sizeof(SEXP));
for(j = 0; j < nc; j++) {
xj = VECTOR_ELT(x, j);
if(LENGTH(xj) != nr)
error(_("corrupt data frame -- length of column %d does not not match nrows"), j+1);
if(inherits(xj, "factor")) {
levels[j] = getAttrib(xj, R_LevelsSymbol);
} else levels[j] = R_NilValue;
}
for(i = 0; i < nr; i++) {
if(i % 1000 == 999) R_CheckUserInterrupt();
if(!isNull(rnames))
Rconn_printf(con, "%s%s",
EncodeElement2(rnames, i, quote_rn, qmethod,
&strBuf, cdec), csep);
for(j = 0; j < nc; j++) {
xj = VECTOR_ELT(x, j);
if(j > 0) Rconn_printf(con, "%s", csep);
if(isna(xj, i)) tmp = cna;
else {
if(!isNull(levels[j])) {
/* We do not assume factors have integer levels,
although they should. */
if(TYPEOF(xj) == INTSXP)
tmp = EncodeElement2(levels[j], INTEGER(xj)[i] - 1,
quote_col[j], qmethod,
&strBuf, cdec);
else if(TYPEOF(xj) == REALSXP)
tmp = EncodeElement2(levels[j],
(int) (REAL(xj)[i] - 1),
quote_col[j], qmethod,
&strBuf, cdec);
else
error("column %s claims to be a factor but does not have numeric codes", j+1);
} else {
tmp = EncodeElement2(xj, i, quote_col[j], qmethod,
&strBuf, cdec);
}
/* if(cdec) change_dec(tmp, cdec, TYPEOF(xj)); */
}
Rconn_printf(con, "%s", tmp);
}
Rconn_printf(con, "%s", ceol);
}
} else { /* A matrix */
if(!isVectorAtomic(x))
UNIMPLEMENTED_TYPE("write.table, matrix method", x);
/* quick integrity check */
if(LENGTH(x) != nr * nc)
error(_("corrupt matrix -- dims not not match length"));
for(i = 0; i < nr; i++) {
if(i % 1000 == 999) R_CheckUserInterrupt();
if(!isNull(rnames))
Rconn_printf(con, "%s%s",
EncodeElement2(rnames, i, quote_rn, qmethod,
&strBuf, cdec), csep);
for(j = 0; j < nc; j++) {
if(j > 0) Rconn_printf(con, "%s", csep);
if(isna(x, i + j*nr)) tmp = cna;
else {
tmp = EncodeElement2(x, i + j*nr, quote_col[j], qmethod,
&strBuf, cdec);
/* if(cdec) change_dec(tmp, cdec, TYPEOF(x)); */
}
Rconn_printf(con, "%s", tmp);
}
Rconn_printf(con, "%s", ceol);
}
}
endcontext(&cntxt);
wt_cleanup(&wi);
return R_NilValue;
}
