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This page was generated on 2022-10-19 13:23:56 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

INSTALL results for XDE on merida1


To the developers/maintainers of the XDE package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2128/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XDE 2.42.0  (landing page)
Robert Scharpf
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/XDE
git_branch: RELEASE_3_15
git_last_commit: 298e83e
git_last_commit_date: 2022-04-26 11:00:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: XDE
Version: 2.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XDE
StartedAt: 2022-10-18 15:49:08 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 15:50:59 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 110.8 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘XDE’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Cholesky.cpp -o Cholesky.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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: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;
        ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable]
  double x,y,tt,sum;
         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Update_v2.cpp -o Update_v2.o
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,
         ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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
        ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/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)