Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 908/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
groHMM 1.40.3 (landing page) Tulip Nandu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.40.3 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL groHMM |
StartedAt: 2024-12-19 16:02:04 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 16:02:54 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 50.7 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL groHMM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'groHMM' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AnnotateProbes.c -o AnnotateProbes.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DecayAlgorithm.c -o DecayAlgorithm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RegisterRRoutines.c -o RegisterRRoutines.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 '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; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:48: 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 -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-groHMM/00new/groHMM/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (groHMM)