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 <pa...@pitt.edu> Sent: Monday, March 24, 2025 12:05 PM To: Tulip Nandu <tulip.na...@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 <pa...@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.na...@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 <pa...@pitt.edu> Sent: Friday, January 24, 2025 2:58 PM To: Tulip Nandu <tulip.na...@utsouthwestern.edu>; bioc-devel@r-project.org <bioc-devel@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.na...@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 <bioconductorcoret...@gmail.com> > Sent: Friday, January 24, 2025 8:59 AM > To: Tulip Nandu <tulip.na...@utsouthwestern.edu>; Lee Kraus > <lee.kr...@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@r-project.org<mailto:bioc-devel@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. 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