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This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4349
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 806/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.59.0  (landing page)
Wei Sun
Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024)
git_url: https://git.bioconductor.org/packages/genoCN
git_branch: devel
git_last_commit: 32e05e9
git_last_commit_date: 2024-10-29 09:33:31 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped


BUILD results for genoCN on lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genoCN
StartedAt: 2024-11-24 16:56:52 -0500 (Sun, 24 Nov 2024)
EndedAt: 2024-11-24 16:56:55 -0500 (Sun, 24 Nov 2024)
EllapsedTime: 2.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tnorm_mle.c -o tnorm_mle.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utility.c -o utility.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c xCNV.c -o xCNV.o
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
  int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
               ^
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
  int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                        ^
xCNV.c:449:25: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    trans1 = (double**) Calloc(N, double*);
                        ^
xCNV.c:449:35: error: expected expression
    trans1 = (double**) Calloc(N, double*);
                                  ^
xCNV.c:450:39: error: expected expression
    trans1[0] = (double*) Calloc(N*N, double);
                                      ^
xCNV.c:455:33: error: expected expression
    v_old = (double *)Calloc(N, double);
                                ^
xCNV.c:456:33: error: expected expression
    v_new = (double *)Calloc(N, double);
                                ^
xCNV.c:458:32: error: expected expression
    path_m = (int**) Calloc(L, int*);
                               ^
xCNV.c:459:36: error: expected expression
    path_m[0] = (int*) Calloc(L*N, int);
                                   ^
xCNV.c:464:31: error: expected expression
    tmp = (double *)Calloc(N, double);
                              ^
xCNV.c:532:5: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    Free(v_old);
    ^
xCNV.c:532:5: note: did you mean 'free'?
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/malloc/_malloc.h:42:7: note: 'free' declared here
void     free(void *);
         ^
xCNV.c:579:19: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    v = (double *)Calloc(N, double);
                  ^
xCNV.c:579:29: error: expected expression
    v = (double *)Calloc(N, double);
                            ^
xCNV.c:581:35: error: expected expression
    trans1 = (double**) Calloc(N, double*);
                                  ^
xCNV.c:582:39: error: expected expression
    trans1[0] = (double*) Calloc(N*N, double);
                                      ^
xCNV.c:613:5: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    Free(v);
    ^
xCNV.c:652:19: error: implicit declaration of function 'Calloc' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    v = (double *)Calloc(N, double);
                  ^
xCNV.c:652:29: error: expected expression
    v = (double *)Calloc(N, double);
                            ^
xCNV.c:654:35: error: expected expression
    trans1 = (double**) Calloc(N, double*);
                                  ^
xCNV.c:655:39: error: expected expression
    trans1[0] = (double*) Calloc(N*N, double);
                                      ^
xCNV.c:683:3: error: implicit declaration of function 'Free' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  Free(v);
  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
make: *** [xCNV.o] Error 1
ERROR: compilation failed for package ‘genoCN’
* removing ‘/private/tmp/RtmpZCwc1K/Rinst1746d41f28c64/genoCN’
      -----------------------------------
ERROR: package installation failed