[Bioc-devel] groHMM Bioconductor

[Tulip Nandu]

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://bioconductor.org/checkResults/release/bioc-LATEST/<https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/__;!!MznTZTSvDXGV0Co!HyLGvx19vWGbTPEYEJ6kMU-mZOSFAyzw6D2Aq4jJTy1NGKVXuOqj4DeKiynwOdE0t0UPm8fgqnPfThLl5v3clQUntFcu2xxQ4eMDhg$>
https://bioconductor.org/checkResults/devel/bioc-LATEST/<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/__;!!MznTZTSvDXGV0Co!HyLGvx19vWGbTPEYEJ6kMU-mZOSFAyzw6D2Aq4jJTy1NGKVXuOqj4DeKiynwOdE0t0UPm8fgqnPfThLl5v3clQUntFcu2xw7_JAWnA$>

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.

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