Multiple platform build/check report for BioC 3.21 - INSTALL results for genoCN on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4704
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4467
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4478
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 genoCN on palomino7

To the developers/maintainers of the genoCN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genoCN.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: genoCN

Version: 1.59.0

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL genoCN

StartedAt: 2025-02-02 15:33:34 -0500 (Sun, 02 Feb 2025)

EndedAt: 2025-02-02 15:33:37 -0500 (Sun, 02 Feb 2025)

EllapsedTime: 3.7 seconds

RetCode: 1

Status: ERROR

Command output

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL genoCN
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'genoCN' ...
** this is package 'genoCN' version '1.59.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c tnorm_mle.c -o tnorm_mle.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c utility.c -o utility.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
  317 |   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
      |                         ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
  317 |   int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
      |                ^
xCNV.c: In function 'viterbi':
xCNV.c:449:25: warning: implicit declaration of function 'Calloc'; did you mean 'calloc'? [-Wimplicit-function-declaration]
  449 |     trans1 = (double**) Calloc(N, double*);
      |                         ^~~~~~
      |                         calloc
xCNV.c:449:35: error: expected expression before 'double'
  449 |     trans1 = (double**) Calloc(N, double*);
      |                                   ^~~~~~
xCNV.c:450:39: error: expected expression before 'double'
  450 |     trans1[0] = (double*) Calloc(N*N, double);
      |                                       ^~~~~~
xCNV.c:455:33: error: expected expression before 'double'
  455 |     v_old = (double *)Calloc(N, double);
      |                                 ^~~~~~
xCNV.c:456:33: error: expected expression before 'double'
  456 |     v_new = (double *)Calloc(N, double);
      |                                 ^~~~~~
xCNV.c:458:32: error: expected expression before 'int'
  458 |     path_m = (int**) Calloc(L, int*);
      |                                ^~~
xCNV.c:459:36: error: expected expression before 'int'
  459 |     path_m[0] = (int*) Calloc(L*N, int);
      |                                    ^~~
xCNV.c:464:31: error: expected expression before 'double'
  464 |     tmp = (double *)Calloc(N, double);
      |                               ^~~~~~
xCNV.c:532:5: warning: implicit declaration of function 'Free'; did you mean 'free'? [-Wimplicit-function-declaration]
  532 |     Free(v_old);
      |     ^~~~
      |     free
xCNV.c: In function 'forward':
xCNV.c:579:29: error: expected expression before 'double'
  579 |     v = (double *)Calloc(N, double);
      |                             ^~~~~~
xCNV.c:581:35: error: expected expression before 'double'
  581 |     trans1 = (double**) Calloc(N, double*);
      |                                   ^~~~~~
xCNV.c:582:39: error: expected expression before 'double'
  582 |     trans1[0] = (double*) Calloc(N*N, double);
      |                                       ^~~~~~
xCNV.c: In function 'backward':
xCNV.c:652:29: error: expected expression before 'double'
  652 |     v = (double *)Calloc(N, double);
      |                             ^~~~~~
xCNV.c:654:35: error: expected expression before 'double'
  654 |     trans1 = (double**) Calloc(N, double*);
      |                                   ^~~~~~
xCNV.c:655:39: error: expected expression before 'double'
  655 |     trans1[0] = (double*) Calloc(N*N, double);
      |                                       ^~~~~~
xCNV.c: In function 'baum_welch':
xCNV.c:878:34: error: expected expression before 'double'
  878 |   dis    = (double *)Calloc(L-1, double);
      |                                  ^~~~~~
xCNV.c:879:34: error: expected expression before 'double'
  879 |   vjk    = (double *)Calloc(L-1, double);
      |                                  ^~~~~~
xCNV.c:880:33: error: expected expression before 'double'
  880 |   vjk0   = (double *)Calloc(LS, double);
      |                                 ^~~~~~
xCNV.c:881:32: error: expected expression before 'double'
  881 |   lvjk   = (double *)Calloc(N, double);
      |                                ^~~~~~
xCNV.c:882:34: error: expected expression before 'double'
  882 |   lvjk_j = (double *)Calloc(N-1, double);
      |                                  ^~~~~~
xCNV.c:883:32: error: expected expression before 'double'
  883 |   ps     = (double *)Calloc(L, double);
      |                                ^~~~~~
xCNV.c:886:30: error: expected expression before 'double'
  886 |   rUS  = (double *)Calloc(N, double);
      |                              ^~~~~~
xCNV.c:887:30: error: expected expression before 'double'
  887 |   pPS  = (double *)Calloc(N, double);
      |                              ^~~~~~
xCNV.c:888:30: error: expected expression before 'double'
  888 |   rNcb = (double *)Calloc(L, double);
      |                              ^~~~~~
xCNV.c:891:33: error: expected expression before 'double'
  891 |   rUS_cn  = (double *)Calloc(N, double);
      |                                 ^~~~~~
xCNV.c:892:33: error: expected expression before 'double'
  892 |   pPS_cn  = (double *)Calloc(N, double);
      |                                 ^~~~~~
xCNV.c:895:31: error: expected expression before 'double'
  895 |   bUS   = (double *)Calloc(N, double);
      |                               ^~~~~~
xCNV.c:896:28: error: expected expression before 'int'
  896 |   Omiga = (int *)Calloc(L, int);
      |                            ^~~
xCNV.c:897:31: error: expected expression before 'double'
  897 |   BAF01 = (double *)Calloc(L, double);
      |                               ^~~~~~
xCNV.c:898:31: error: expected expression before 'double'
  898 |   bNcb  = (double *)Calloc(L, double);
      |                               ^~~~~~
xCNV.c:904:30: error: expected expression before 'double'
  904 |   rU  = (double**) Calloc(L, double*);
      |                              ^~~~~~
xCNV.c:905:33: error: expected expression before 'double'
  905 |   rU[0] = (double*) Calloc(L*N, double);
      |                                 ^~~~~~
xCNV.c:914:30: error: expected expression before 'double'
  914 |   rN  = (double**) Calloc(L, double*);
      |                              ^~~~~~
xCNV.c:915:33: error: expected expression before 'double'
  915 |   rN[0] = (double*) Calloc(L*N, double);
      |                                 ^~~~~~
xCNV.c:922:30: error: expected expression before 'double'
  922 |   bU  = (double**) Calloc(L, double*);
      |                              ^~~~~~
xCNV.c:923:33: error: expected expression before 'double'
  923 |   bU[0] = (double*) Calloc(L*N, double);
      |                                 ^~~~~~
xCNV.c:930:30: error: expected expression before 'double'
  930 |   bN  = (double**) Calloc(L, double*);
      |                              ^~~~~~
xCNV.c:931:34: error: expected expression before 'double'
  931 |   bN[0] = (double*) Calloc(L*MM, double);
      |                                  ^~~~~~
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
  787 |   double mu_b_tmp, sd_b_tmp;
      |                    ^~~~~~~~
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
  787 |   double mu_b_tmp, sd_b_tmp;
      |          ^~~~~~~~
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
  762 |   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
      |          ^~
make: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:289: xCNV.o] Error 1
ERROR: compilation failed for package 'genoCN'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/genoCN'