sigPathway.install

[Yikun]

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL sigPathway
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘sigPathway’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_probe_stat.c -o calc_probe_stat.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c calc_weights.c -o calc_weights.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c matrix_fn.c -o matrix_fn.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from sigPathway.h:18,
                 from matrix_fn.c:13:
matrix_fn.c: In function ‘matprod’:
matrix_fn.c:28:16: error: too few arguments to function ‘dgemm_’
   28 |       F77_CALL(dgemm)(transa, transb, &nrx, &ncy, &ncx, &one,
      |                ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
matrix_fn.c: In function ‘eigen’:
matrix_fn.c:65:12: error: too few arguments to function ‘dsyevr_’
   65 |   F77_CALL(dsyevr)(jobv, range, uplo, &n, rx, &n,
      |            ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:10: note: declared here
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:1: note: in expansion of macro ‘F77_NAME’
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      | ^~~~~~~~
matrix_fn.c:77:12: error: too few arguments to function ‘dsyevr_’
   77 |   F77_CALL(dsyevr)(jobv, range, uplo, &n, rx, &n,
      |            ^~~~~~
matrix_fn.c:77:3: note: in expansion of macro ‘F77_CALL’
   77 |   F77_CALL(dsyevr)(jobv, range, uplo, &n, rx, &n,
      |   ^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:10: note: declared here
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      |          ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/Lapack.h:1270:1: note: in expansion of macro ‘F77_NAME’
 1270 | F77_NAME(dsyevr)(const char* jobz, const char* range, const char* uplo,
      | ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:191: matrix_fn.o] Error 1
ERROR: compilation failed for package ‘sigPathway’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/sigPathway’

[martin-g]

Fails the same way on x86_64 - https://bioconductor.org/checkResults/3.17/bioc-LATEST/sigPathway/nebbiolo1-install.html

[martin-g]

The package is deprecated: https://code.bioconductor.org/browse/sigPathway/commit/97316df25499f4b156310472e9435e0398aa79bd and will be removed from Bioc in 3.18 (maybe earlier since it fails on 3.17)