Hi Tulip,
The R NEWS file says "Strict R headers are now the default. This
removes the legacy definitions of PI, Calloc, Realloc and Free: use
M_PI, R_Calloc, R_Realloc or R_Free instead" here:
https://cran.r-project.org/doc/manuals/r-devel/NEWS.html so the patch
below fixes the source compilation of groHMM.
NB: Resending in plain text because the mailing list list rejected my
previous message with "The message's content type was not explicitly
allowed" for some reason.
Pariksheet
---
diff --git a/src/hmmMiscFunctions.c b/src/hmmMiscFunctions.c
index 68d2359..85e1a29 100755
--- a/src/hmmMiscFunctions.c
+++ b/src/hmmMiscFunctions.c
@@ -271,8 +271,8 @@ extern void SStatsGamma_p1(int state, int emis_indx,
void* ss, fwbk_t fwbk) {
}
extern void UpdateGamma(int state, void* ss, hmm_t *hmm) {
ssGamma *SS = (ssGamma*)ss;
- double *shape= (double*)Calloc(1, double);
- double *scale= (double*)Calloc(1, double);
+ double *shape= (double*)R_Calloc(1, double);
+ double *scale= (double*)R_Calloc(1, double);
int updateRetVal= MLEGamma(SS[0].N, SS[0].sumPiXi, SS[0].sumLogPiXi,
shape, scale);
if(updateRetVal == 0) {
@@ -284,8 +284,8 @@ extern void UpdateGamma(int state, void* ss, hmm_t
*hmm) {
due to instibility! Using Shape: %f; Scale: %f\n",
state, hmm[0].em_args[state][0], hmm[0].em_args[state][1]);
}
- Free(shape);
- Free(scale);
+ R_Free(shape);
+ R_Free(scale);
}
// Used to fit a constrained gamma, where E[x] = 1, and shape=1/scale.
extern void UpdateGamma_SHAPEeq1overSCALE(int state, void* ss, hmm_t
*hmm) {
On 1/24/25 11:58 AM, Tulip Nandu wrote:
Hi,
Can anyone please help with this error. I solved one error of dgeTests now this
one cropped up. THis wan all working fine before. Has anything changed.
Please let me know. Any help is appreciated.
Regards,
Tulip.
"
hmmMiscFunctions.c: In function ‘SStatsGamma’:
hmmMiscFunctions.c:235:37: warning: format ‘%d’ expects argument of type ‘int’,
but argument 2 has type ‘double’ [-Wformat=]
235 | if(!(logPP <= epsilon)) Rprintf("[SSallocGamma] -- \
| ^~~~~~~~~~~~~~~~~~~~
236 | Assertion about to fail! logPP= %d\n", logPP);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~
| |
| double
hmmMiscFunctions.c: In function ‘UpdateGamma’:
hmmMiscFunctions.c:274:27: warning: implicit declaration of function ‘Calloc’;
did you mean ‘calloc’? [-Wimplicit-function-declaration]
274 | double *shape= (double*)Calloc(1, double);
| ^~~~~~
| calloc
hmmMiscFunctions.c:274:37: error: expected expression before ‘double’
274 | double *shape= (double*)Calloc(1, double);
| ^~~~~~
hmmMiscFunctions.c:275:37: error: expected expression before ‘double’
275 | double *scale= (double*)Calloc(1, double);
| ^~~~~~
hmmMiscFunctions.c:287:3: warning: implicit declaration of function ‘Free’; did
you mean ‘free’? [-Wimplicit-function-declaration]
287 | Free(shape);
| ^~~~
| free
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195:
hmmMiscFunctions.o] Error 1
ERROR: compilation failed for package ‘groHMM’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/groHMM’
"
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