Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 807/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genoCN 1.59.0 (landing page) Wei Sun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: genoCN |
Version: 1.59.0 |
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data genoCN |
StartedAt: 2024-12-22 23:26:07 -0000 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 23:26:09 -0000 (Sun, 22 Dec 2024) |
EllapsedTime: 2.0 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data genoCN ### ############################################################################## ############################################################################## * checking for file ‘genoCN/DESCRIPTION’ ... OK * preparing ‘genoCN’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘genoCN’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c tnorm_mle.c -o tnorm_mle.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utility.c -o utility.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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: error: 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: error: 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: *** [/home/biocbuild/R/R/etc/Makeconf:195: xCNV.o] Error 1 ERROR: compilation failed for package ‘genoCN’ * removing ‘/home/biocbuild/tmp/Rtmp2MXniZ/Rinst2feaa371c852ed/genoCN’ ----------------------------------- ERROR: package installation failed