Tulip Nandu
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/groHMM |
| git_branch: RELEASE_3_20 |
| git_last_commit: 65aef09 |
| git_last_commit_date: 2024-12-09 15:20:46 -0500 (Mon, 09 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -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: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.40.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R groHMM.buildbin-libdir |
| StartedAt: 2024-12-21 15:09:06 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 15:09:49 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 43.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: groHMM_1.40.3.tgz |
| PackageFileSize: 4.266 MiB |
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### Running command:
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### rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.40.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R groHMM.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=groHMM.buildbin-libdir groHMM_1.40.3.tar.gz'
>>>>>>>
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MLEfit.c -o MLEfit.o
MLEfit.c:260:25: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
int maxn = 2*n_x+1, cnt=0;
^
In file included from MLEfit.c:43:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Windowing.c -o Windowing.o
Windowing.c:146:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmFwBw.c:45:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c:236:49: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
Assertion about to fail! logPP= %d\n", logPP);
~~ ^~~~~
%f
hmmMiscFunctions.c:384:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c:417:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:48:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/groHMM.buildbin-libdir/00LOCK-groHMM/00new/groHMM/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (groHMM)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR groHMM.buildbin-libdir/groHMM/libs/groHMM.so
>>>>>>>
>>>>>>> Paths before fix:
groHMM.buildbin-libdir/groHMM/libs/groHMM.so:
groHMM.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"
>>>>>>> Paths after fix:
groHMM.buildbin-libdir/groHMM/libs/groHMM.so:
groHMM.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)