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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 902/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.41.0  (landing page)
Tulip Nandu , W. Lee Kraus
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/groHMM
git_branch: devel
git_last_commit: 8d0b05a
git_last_commit_date: 2024-12-03 18:09:10 -0500 (Tue, 03 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


BUILD results for groHMM on nebbiolo1

To the developers/maintainers of the groHMM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/groHMM.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: groHMM
Version: 1.41.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM
StartedAt: 2024-12-23 17:23:21 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 17:23:23 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 2.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM
###
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* checking for file ‘groHMM/DESCRIPTION’ ... OK
* preparing ‘groHMM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:43:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:146:13: warning: unused variable ‘II’ [-Wunused-variable]
  146 |         int II = 0;
      |             ^~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function ‘forward’:
hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  142 |       for(k=1; k<n; k++)
      |       ^~~
hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  145 |         for (k = 0; k<n; k++) {
      |         ^~~
In file included from hmmFwBw.c:45:
hmmHeader.h: At top level:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o
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
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’ [-Wunused-variable]
  384 |   double wi, *newEx;
      |          ^~
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’ [-Wunused-variable]
  417 |   double epsilon=0.00001;
      |          ^~~~~~~
In file included from hmmHeader.h:36,
                 from hmmMiscFunctions.c:43:
UsefulValues.h: At top level:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195: hmmMiscFunctions.o] Error 1
ERROR: compilation failed for package ‘groHMM’
* removing ‘/tmp/RtmpGDZrUK/Rinst63fe77e4686a4/groHMM’
      -----------------------------------
ERROR: package installation failed