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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 813/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.58.0  (landing page)
Wei Sun
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/genoCN
git_branch: RELEASE_3_20
git_last_commit: f53faf3
git_last_commit_date: 2024-10-29 09:33:31 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


INSTALL results for genoCN on palomino8

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: 1.58.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL genoCN
StartedAt: 2024-12-19 15:40:12 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 15:40:32 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 19.8 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL genoCN
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'genoCN' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-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"F:/biocbuild/bbs-3.20-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"F:/biocbuild/bbs-3.20-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 'baum_welch':
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,
      |          ^~
xCNV.c:1753:17: warning: 'pbf' may be used uninitialized [-Wmaybe-uninitialized]
 1753 |                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:769:18: note: 'pbf' was declared here
  769 |   double ws[10], pbf, baf;
      |                  ^~~
xCNV.c:1753:17: warning: 'nGtp' may be used uninitialized [-Wmaybe-uninitialized]
 1753 |                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:768:31: note: 'nGtp' was declared here
  768 |   int k1s[4], rid[4], cid[4], nGtp;
      |                               ^~~~
gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-genoCN/00new/genoCN/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)