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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/genoCN_1.40.0.tar.gz && rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoCN.buildbin-libdir genoCN_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL genoCN_1.40.0.zip && rm genoCN_1.40.0.tar.gz genoCN_1.40.0.zip
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install for i386
* installing *source* package 'genoCN' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tnorm_mle.c -o tnorm_mle.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utility.c -o utility.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/genoCN.buildbin-libdir/00LOCK-genoCN/00new/genoCN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'genoCN'
finding HTML links ... done
code.genotype html
genoCNA html
genoCNV html
init.Para.CNA html
init.Para.CNV html
plotCN html
snpData html
snpInfo html
** 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
install for x64
* installing *source* package 'genoCN' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tnorm_mle.c -o tnorm_mle.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utility.c -o utility.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/genoCN.buildbin-libdir/genoCN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoCN' as genoCN_1.40.0.zip
* DONE (genoCN)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'genoCN' successfully unpacked and MD5 sums checked