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INSTALL report for genoCN on malbec2

This page was generated on 2020-10-17 11:54:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE genoCN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 700/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.40.0
Wei Sun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/genoCN
Branch: RELEASE_3_11
Last Commit: 22c4c2f
Last Changed Date: 2020-04-27 14:21:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoCN
Version: 1.40.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL genoCN
StartedAt: 2020-10-16 16:05:38 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 16:05:44 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 5.8 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL genoCN
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c tnorm_mle.c -o tnorm_mle.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utility.c -o utility.o
utility.c: In function ‘readfile’:
utility.c:155:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(file,"%s",temp);
             ^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c xCNV.c -o xCNV.o
xCNV.c: In function ‘emiss’:
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:317:16: warning: unused variable ‘K’ [-Wunused-variable]
   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]
   double mu_b_tmp, sd_b_tmp;
                    ^~~~~~~~
xCNV.c:787:10: warning: unused variable ‘mu_b_tmp’ [-Wunused-variable]
   double mu_b_tmp, sd_b_tmp;
          ^~~~~~~~
xCNV.c:762:10: warning: variable ‘LL’ set but not used [-Wunused-but-set-variable]
   int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
          ^~
xCNV.c:1839:17: warning: ‘nGtp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:1839:17: warning: ‘pbf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-genoCN/00new/genoCN/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)