[Bioc-devel] groHMM Bioconductor
Tulip Nandu
Tu||p@N@ndu @end|ng |rom UTSouthwe@tern@edu
Tue Mar 25 17:37:14 CET 2025
Hi,
Please can you add Pariksheet to the maintainer list for groHMM package. He would like to take a look at the error.
Regards,
Tulip.
________________________________
From: Nanda, Pariksheet <PAN79 using pitt.edu>
Sent: Monday, March 24, 2025 12:05 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Subject: Re: [Bioc-devel] groHMM Bioconductor
Hi Tulip, I don't know if you're still having trouble with this error? The branch will be frozen on March 31, so if you like, you can add me as a maintainer by e-mailing the Bioconductor mailing list and I can take a look to have it fixed before
Hi Tulip,
I don't know if you're still having trouble with this error?
The branch will be frozen on March 31, so if you like, you can add me as a maintainer by e-mailing the Bioconductor mailing list and I can take a look to have it fixed before then.
Pariksheet
Pariksheet Nanda, PhD
Postdoctoral Research Fellow
Shoemaker Laboratory
Department of Chemical Engineering
University of Pittsburgh
________________________________________
From: Nanda, Pariksheet <PAN79 using pitt.edu>
Sent: Friday, March 14, 2025 1:06 PM
To: Tulip Nandu
Subject: Re: [Bioc-devel] groHMM Bioconductor
The top line of the diff tells you the affected file. See https://urldefense.com/v3/__https://swcarpentry.github.io/git-novice/04-changes.html__;!!MznTZTSvDXGV0Co!Fj39n2xtjhxqdSvfUldatwzY2oCHQqtKiqoSis4zb77tu50_nzRN8-qj-Fwx0Dfb0O9QVSP1eEMblbxlzowDXGvS$
________________________________________
From: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Sent: Friday, March 14, 2025 12:24 PM
To: Nanda, Pariksheet
Subject: Re: [Bioc-devel] groHMM Bioconductor
Hi Pariksheet,
Where do I put this patch. Please can you elaborate?
Any help is appreciated.
Tulip.
________________________________
From: Nanda, Pariksheet <PAN79 using pitt.edu>
Sent: Friday, January 24, 2025 2:58 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] groHMM Bioconductor
Hi Tulip, Yes, per https: //cran. r-project. org/doc/manuals/r-devel/R-exts. html those interface macros functions now require R_ in front of them. Patch below fixes the source compilation. Pariksheet diff --git a/src/hmmMiscFunctions. c b/src/hmmMiscFunctions. c
Hi Tulip,
Yes, per https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-devel/R-exts.html__;!!MznTZTSvDXGV0Co!Fj39n2xtjhxqdSvfUldatwzY2oCHQqtKiqoSis4zb77tu50_nzRN8-qj-Fwx0Dfb0O9QVSP1eEMblbxlzgrxi7S7$<https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-devel/R-exts.html__;!!MznTZTSvDXGV0Co!FuAGf7ZBLarW_p1_SDCrWBlamPggJyziIyBBf3hOhjpIghswQcEeU-4qy16JA6_8JolF7JYuIpBLjPXC3So7-v-8$>those interface macros functions now require R_ in front of them. Patch below fixes the source compilation.
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 Jan 24, 2025, at 11:58 AM, Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu> 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’
>
> "
> ________________________________
> From: CoreTeam Bioconductor <bioconductorcoreteam using gmail.com>
> Sent: Friday, January 24, 2025 8:59 AM
> To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>; Lee Kraus <Lee.Kraus using UTSouthwestern.edu>
> Subject: groHMM Bioconductor
>
> Hello Package Maintainer, We would like to bring to your attention that your package is failing in both release and devel Bioconductor on all platforms. This is very problematic. Please fix the package in the next few weeks to avoid deprecation.
>
> Hello Package Maintainer,
>
> We would like to bring to your attention that your package is failing in both release and devel Bioconductor on all platforms. This is very problematic. Please fix the package in the next few weeks to avoid deprecation.
>
> https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/__;!!MznTZTSvDXGV0Co!Fj39n2xtjhxqdSvfUldatwzY2oCHQqtKiqoSis4zb77tu50_nzRN8-qj-Fwx0Dfb0O9QVSP1eEMblbxlznCtlx5L$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/__;!!MznTZTSvDXGV0Co!HyLGvx19vWGbTPEYEJ6kMU-mZOSFAyzw6D2Aq4jJTy1NGKVXuOqj4DeKiynwOdE0t0UPm8fgqnPfThLl5v3clQUntFcu2xxQ4eMDhg$><https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/__;!!MznTZTSvDXGV0Co!FuAGf7ZBLarW_p1_SDCrWBlamPggJyziIyBBf3hOhjpIghswQcEeU-4qy16JA6_8JolF7JYuIpBLjPXC3YpQExm5$>
>https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/__;!!MznTZTSvDXGV0Co!Fj39n2xtjhxqdSvfUldatwzY2oCHQqtKiqoSis4zb77tu50_nzRN8-qj-Fwx0Dfb0O9QVSP1eEMblbxlzgp-QvgM$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/__;!!MznTZTSvDXGV0Co!HyLGvx19vWGbTPEYEJ6kMU-mZOSFAyzw6D2Aq4jJTy1NGKVXuOqj4DeKiynwOdE0t0UPm8fgqnPfThLl5v3clQUntFcu2xw7_JAWnA$><https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/__;!!MznTZTSvDXGV0Co!FuAGf7ZBLarW_p1_SDCrWBlamPggJyziIyBBf3hOhjpIghswQcEeU-4qy16JA6_8JolF7JYuIpBLjPXC3d1d0-Vc$>
>
>If you have further questions or concerns please reach out on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
>
> We appreciate your quick attention to this matter
>
> Cheers,
> On behalf of the Bioconductor Core Team
>
> ________________________________
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
[cid:96ada66e-0f8a-4baf-8629-647b4e0f8d84 using namprd04.prod.outlook.com]
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