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This page was generated on 2024-03-28 11:40:16 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 2256/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XDE 2.49.0  (landing page)
Robert Scharpf
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/XDE
git_branch: devel
git_last_commit: b2cd139
git_last_commit_date: 2023-10-24 09:39:19 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for XDE on lconway


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.

raw results


Summary

Package: XDE
Version: 2.49.0
Command: rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.49.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XDE.buildbin-libdir
StartedAt: 2024-03-28 01:51:24 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:52:26 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 61.2 seconds
RetCode: 0
Status:   OK  
PackageFile: XDE_2.49.0.tgz
PackageFileSize: 2.25 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.49.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XDE.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XDE.buildbin-libdir XDE_2.49.0.tar.gz'
>>>>>>> 

* 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++11 -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++11 -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++11 -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++11 -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++11 -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++11 -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++11 -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++11 -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++11 -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++11 -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 /Users/biocbuild/bbs-3.19-bioc/meat/XDE.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR XDE.buildbin-libdir/XDE/libs/XDE.so
>>>>>>> 

>>>>>>> Paths before fix:
XDE.buildbin-libdir/XDE/libs/XDE.so:
	XDE.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so"

>>>>>>> Paths after fix:
XDE.buildbin-libdir/XDE/libs/XDE.so:
	XDE.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)