Multiple platform build/check report for BioC 3.23 - INSTALL results for COMPASS on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4522
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"	2847
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 COMPASS on nebbiolo1

To the developers/maintainers of the COMPASS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COMPASS.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: COMPASS
Version: 1.49.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL COMPASS
StartedAt: 2026-03-09 15:09:51 -0400 (Mon, 09 Mar 2026)
EndedAt: 2026-03-09 15:10:45 -0400 (Mon, 09 Mar 2026)
EllapsedTime: 54.3 seconds
RetCode: 0
Status: OK
Command output

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###
### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL COMPASS
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘COMPASS’ ...
** this is package ‘COMPASS’ version ‘1.49.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c COMPASS_init.c -o COMPASS_init.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c CellCounts.cpp -o CellCounts.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c CellCounts_character.cpp -o CellCounts_character.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c digamma.c -o digamma.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c mat2vec.c -o mat2vec.o
mat2vec.c: In function ‘mat2vec’:
mat2vec.c:38:18: warning: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                  ^~~~~~~
mat2vec.c:45:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^
mat2vec.c:45:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^
mat2vec.c:45:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   45 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^
mat2vec.c:47:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^
mat2vec.c:47:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   47 |       HANDLE_CASE_MEMCPY(REAL, double);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |           ^
mat2vec.c:49:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
mat2vec.c:38:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   38 |           (char*)DATAPTR(elt), (char*)DATAPTR(x) + (i* nRow* sz), nRow* sz); \
      |                                ^
mat2vec.c:49:7: note: in expansion of macro ‘HANDLE_CASE_MEMCPY’
   49 |       HANDLE_CASE_MEMCPY(INTEGER, int);
      |       ^~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c melt_dataframe.c -o melt_dataframe.o
melt_dataframe.c: In function ‘stack_vector’:
melt_dataframe.c:57:21: warning: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                     ^~~~~~~
melt_dataframe.c:67:5: note: in expansion of macro ‘HANDLE_CASE’
   67 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |              ^
melt_dataframe.c:67:5: note: in expansion of macro ‘HANDLE_CASE’
   67 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                                                  ^
melt_dataframe.c:67:5: note: in expansion of macro ‘HANDLE_CASE’
   67 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |              ^
melt_dataframe.c:68:5: note: in expansion of macro ‘HANDLE_CASE’
   68 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                                                  ^
melt_dataframe.c:68:5: note: in expansion of macro ‘HANDLE_CASE’
   68 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |              ^
melt_dataframe.c:69:5: note: in expansion of macro ‘HANDLE_CASE’
   69 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:57:50: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   57 |       memcpy((char*)DATAPTR(out) + (i* len* sz), (char*)DATAPTR(x), len* sz); \
      |                                                  ^
melt_dataframe.c:69:5: note: in expansion of macro ‘HANDLE_CASE’
   69 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c: In function ‘melt_dataframe’:
melt_dataframe.c:147:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  147 |       memcpy((char*)DATAPTR(value_SEXP) + (i* nRow * sizeof(CTYPE)), \
      |              ^
melt_dataframe.c:160:5: note: in expansion of macro ‘HANDLE_CASE’
  160 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:148:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  148 |              (char*)DATAPTR(tmp),                                    \
      |              ^
melt_dataframe.c:160:5: note: in expansion of macro ‘HANDLE_CASE’
  160 |     HANDLE_CASE(INTSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:147:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  147 |       memcpy((char*)DATAPTR(value_SEXP) + (i* nRow * sizeof(CTYPE)), \
      |              ^
melt_dataframe.c:161:5: note: in expansion of macro ‘HANDLE_CASE’
  161 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:148:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  148 |              (char*)DATAPTR(tmp),                                    \
      |              ^
melt_dataframe.c:161:5: note: in expansion of macro ‘HANDLE_CASE’
  161 |     HANDLE_CASE(REALSXP, double);
      |     ^~~~~~~~~~~
melt_dataframe.c:147:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  147 |       memcpy((char*)DATAPTR(value_SEXP) + (i* nRow * sizeof(CTYPE)), \
      |              ^
melt_dataframe.c:162:5: note: in expansion of macro ‘HANDLE_CASE’
  162 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
melt_dataframe.c:148:14: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  148 |              (char*)DATAPTR(tmp),                                    \
      |              ^
melt_dataframe.c:162:5: note: in expansion of macro ‘HANDLE_CASE’
  162 |     HANDLE_CASE(LGLSXP, int);
      |     ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c melt_matrix.c -o melt_matrix.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c samplePuPs.cpp -o samplePuPs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c transpose_list.c -o transpose_list.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphas_Exp_MH.cpp -o updatealphas_Exp_MH.o
updatealphas_Exp_MH.cpp: In function ‘SEXPREC* updatealphas_Exp_MH(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
updatealphas_Exp_MH.cpp:26:10: warning: variable ‘psik’ set but not used [-Wunused-but-set-variable]
   26 |   double psik = 0.;
      |          ^~~~
updatealphas_Exp_MH.cpp:35:7: warning: variable ‘flagkk’ set but not used [-Wunused-but-set-variable]
   35 |   int flagkk = 0;
      |       ^~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphau.cpp -o updatealphau.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o COMPASS.so COMPASS_init.o CellCounts.o CellCounts_character.o RcppExports.o digamma.o mat2vec.o melt_dataframe.o melt_matrix.o samplePuPs.o transpose_list.o updatealphas_Exp.o updatealphas_Exp_MH.o updatealphau.o updatealphau_noPu_Exp.o updatealphau_noPu_Exp_MH.o updatebeta_RW.o updategammak_noPu.o utils.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-COMPASS/00new/COMPASS/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (COMPASS)