Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2273/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
XDE 2.52.0 (landing page) Robert Scharpf
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the XDE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XDE.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: XDE |
Version: 2.52.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XDE |
StartedAt: 2024-11-19 15:38:26 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 15:39:42 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 76.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XDE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘XDE’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Cholesky.cpp -o Cholesky.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Matrix_v2.cpp -o Matrix_v2.o In file included from Matrix_v2.cpp:1: ./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ Matrix_v2.cpp:148:7: warning: variable 'signDet' set but not used [-Wunused-but-set-variable] int signDet = 1; ^ Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable] int k = 1; ^ Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable] int i,j,r; ^ 4 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Potential_v2.cpp -o Potential_v2.o Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison] if (theGene[k][i] == 1) include == 1; ~~~~~~~~^~~~ Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment if (theGene[k][i] == 1) include == 1; ^~ = 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Random_v2.cpp -o Random_v2.o Random_v2.cpp:12:16: warning: variable 'temp' set but not used [-Wunused-but-set-variable] unsigned int temp = UINT_MAX - 1; ^ Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable] double x,y,tt,sum; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rinterface_v2.cpp -o Rinterface_v2.o In file included from Rinterface_v2.cpp:2: In file included from ./Update_v2.h:8: ./Random.h:19:9: warning: 'PI' macro redefined [-Wmacro-redefined] #define PI 3.14159265 ^ /Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:39:9: note: previous definition is here #define PI M_PI ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Structure.cpp -o Structure.o Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable] char c; ^ Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable] int nRead = sscanf(var1,"%d",&value); ^ Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable] int nRead = sscanf(var2,"%le",&value); ^ Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable] char c; ^ Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable] char c; ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Update_v2.cpp -o Update_v2.o Update_v2.cpp:2314:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:2464:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3293:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3404:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable] double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta, ^ Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable] double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues, ^ Update_v2.cpp:4526:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ Update_v2.cpp:4657:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable] int nOn = 0; ^ 8 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Utility_v2.cpp -o Utility_v2.o Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable] double detPrior = inverse(var,varInv); ^ Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable] double detPosterior = 1.0 /inverse(varInv,var); ^ Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable] int s; ^ Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable] double detPrior = inverse(var,varInv); ^ Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable] double detPosterior = 1.0 / inverse(varInv,var); ^ Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable] int ngg = neighbour[gg].size(); ^ Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable] int ngg = neighbour[gg].size(); ^ Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable] map<int,double>::iterator itextra = VinvSparse[k].end(); ^ 8 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o In file included from diffExpressed_main.cpp:16: ./Random.h:19:9: warning: 'PI' macro redefined [-Wmacro-redefined] #define PI 3.14159265 ^ /Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:39:9: note: previous definition is here #define PI M_PI ^ In file included from diffExpressed_main.cpp:38: ./UpdateGamma2Gibbs.h:112:14: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ In file included from diffExpressed_main.cpp:42: ./UpdateXiGibbs.h:95:11: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ ./UpdateXiGibbs.h:162:15: warning: variable 'pot' set but not used [-Wunused-but-set-variable] double pot = - model->potential(ran); ^ 4 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-XDE/00new/XDE/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘qqplot’ in package ‘XDE’ ** 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 (XDE)