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This page was generated on 2025-01-11 11:44 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 1809/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtreemix 1.69.0  (landing page)
Jasmina Bogojeska
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025)
git_url: https://git.bioconductor.org/packages/Rtreemix
git_branch: devel
git_last_commit: 45c317f
git_last_commit_date: 2024-10-29 09:28:26 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

INSTALL results for Rtreemix on lconway

To the developers/maintainers of the Rtreemix package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rtreemix.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: Rtreemix
Version: 1.69.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rtreemix
StartedAt: 2025-01-10 15:26:38 -0500 (Fri, 10 Jan 2025)
EndedAt: 2025-01-10 15:26:40 -0500 (Fri, 10 Jan 2025)
EllapsedTime: 2.4 seconds
RetCode: 1
Status:   ERROR  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Rtreemix’ ...
** using staged installation
** libs
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  -DR_NO_REMAP -c Rtreemix.cc -o Rtreemix.o
Rtreemix.cc:145:11: error: use of undeclared identifier 'length'
  int L = length(R_events);
          ^
Rtreemix.cc:155:22: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'?
  PROTECT(R_events = coerceVector(R_events, STRSXP));
                     ^~~~~~~~~~~~
                     Rf_coerceVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here
SEXP Rf_coerceVector(SEXP, SEXPTYPE);
     ^
Rtreemix.cc:191:15: error: use of undeclared identifier 'getAttrib'; did you mean 'Rf_getAttrib'?
  SEXP Rdim = getAttrib(R_mat, R_DimSymbol);
              ^~~~~~~~~
              Rf_getAttrib
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:538:6: note: 'Rf_getAttrib' declared here
SEXP Rf_getAttrib(SEXP, SEXP);
     ^
Rtreemix.cc:201:19: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'?
  PROTECT(R_mat = coerceVector(R_mat,INTSXP));
                  ^~~~~~~~~~~~
                  Rf_coerceVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here
SEXP Rf_coerceVector(SEXP, SEXPTYPE);
     ^
Rtreemix.cc:217:21: error: use of undeclared identifier 'getAttrib'; did you mean 'Rf_getAttrib'?
      C_mat[i][j] = R_INT_MATRIX(R_mat, i, j);
                    ^
Rtreemix.cc:45:49: note: expanded from macro 'R_INT_MATRIX'
#define R_INT_MATRIX(m,i,j) (INTEGER(m)[INTEGER(getAttrib(m, R_DimSymbol))[0] * j + i ]);
                                                ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:538:6: note: 'Rf_getAttrib' declared here
SEXP Rf_getAttrib(SEXP, SEXP);
     ^
Rtreemix.cc:245:19: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
  PROTECT(R_mat = allocMatrix(INTSXP, C_mat.dim1(), C_mat.dim2()));
                  ^~~~~~~~~~~
                  Rf_allocMatrix
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
SEXP Rf_allocMatrix(SEXPTYPE, int, int);
     ^
Rtreemix.cc:301:19: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
  PROTECT(R_mat = allocMatrix(REALSXP, C_mat.dim1(), C_mat.dim2()));
                  ^~~~~~~~~~~
                  Rf_allocMatrix
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
SEXP Rf_allocMatrix(SEXPTYPE, int, int);
     ^
Rtreemix.cc:333:19: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  PROTECT(R_vec = allocVector(REALSXP, v.size()));
                  ^~~~~~~~~~~
                  Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
Rtreemix.cc:359:17: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  PROTECT(ans = allocVector(STRSXP, 1));
                ^~~~~~~~~~~
                Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
Rtreemix.cc:365:28: error: use of undeclared identifier 'mkChar'
    SET_STRING_ELT(ans, 0, mkChar(v));
                           ^
Rtreemix.cc:475:20: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  PROTECT(result = allocVector(VECSXP, 4));
                   ^~~~~~~~~~~
                   Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
Rtreemix.cc:479:24: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  PROTECT(list_names = allocVector(STRSXP, 4));
                       ^~~~~~~~~~~
                       Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
Rtreemix.cc:481:33: error: use of undeclared identifier 'mkChar'
  SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
                                ^
Rtreemix.cc:483:33: error: use of undeclared identifier 'mkChar'
  SET_STRING_ELT(list_names, 1, mkChar("resp")); // the responsibilities
                                ^
Rtreemix.cc:485:33: error: use of undeclared identifier 'mkChar'
  SET_STRING_ELT(list_names, 2, mkChar("pat.hat")); // the complete sample matrix (if there were some missing data)
                                ^
Rtreemix.cc:487:33: error: use of undeclared identifier 'mkChar'
  SET_STRING_ELT(list_names, 3, mkChar("graphs.mixture")); // the list of the graphs each for every tree component
                                ^
Rtreemix.cc:491:3: error: use of undeclared identifier 'setAttrib'; did you mean 'Rf_setAttrib'?
  setAttrib(result, R_NamesSymbol, list_names);
  ^~~~~~~~~
  Rf_setAttrib
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:580:6: note: 'Rf_setAttrib' declared here
SEXP Rf_setAttrib(SEXP, SEXP, SEXP);
     ^
Rtreemix.cc:509:31: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
    SET_VECTOR_ELT(result, 2, allocMatrix(REALSXP, 0, 0));      
                              ^~~~~~~~~~~
                              Rf_allocMatrix
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
SEXP Rf_allocMatrix(SEXPTYPE, int, int);
     ^
Rtreemix.cc:515:25: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  PROTECT(list_graphs = allocVector(VECSXP, K));
                        ^~~~~~~~~~~
                        Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [Rtreemix.o] Error 1
ERROR: compilation failed for package ‘Rtreemix’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rtreemix’