Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 902/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
groHMM 1.41.0 (landing page) Tulip Nandu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. |
Package: groHMM |
Version: 1.41.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL groHMM |
StartedAt: 2024-12-23 15:15:39 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 15:15:41 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 2.6 seconds |
RetCode: 1 |
Status: ERROR |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL groHMM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * 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 ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/groHMM’ * restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/groHMM’