snapCGH 1.52.0
John Marioni
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/snapCGH |
| Branch: RELEASE_3_8 |
| Last Commit: 7f9020f |
| Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/snapCGH_1.52.0.tar.gz && rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.52.0.zip && rm snapCGH_1.52.0.tar.gz snapCGH_1.52.0.zip
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install for i386
* installing *source* package 'snapCGH' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
^
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
^
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
^
optimizer.c: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
alpha[k][t] = alpha[k][t] + alpha[d][t-1]*gammaC[d][k];
^
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: more than one default provided in switch() call
** help
*** installing help indices
converting help for package 'snapCGH'
finding HTML links ... done
IDProbes html
LargeDataObject html
SegList html
Viterbi.five html
Viterbi.four html
Viterbi.three html
Viterbi.two html
cbind html
chrominfo.Mb html
compareSegmentations html
convert.output html
dim html
dimnames html
filter html
find.param.five html
find.param.four html
find.param.one html
find.param.three html
find.param.two html
findBreakPoints html
fit.model html
genomePlot html
heatmapGenome html
imputeMissingValues html
log2ratios html
mergeStates html
non.zero.length.distr.non.tiled html
non.zero.length.distr.tiled html
plotSegmentedGenome html
processCGH html
read.clonesinfo html
readPositionalInfo html
removeByWeights html
runBioHMM html
runDNAcopy html
runGLAD html
runHMM html
runTilingArray html
sim.structure html
zero.length.distr.non.tiled html
zero.length.distr.tiled html
zoomChromosome html
zoomGenome html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'snapCGH' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
^
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
^
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
^
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for(t = 1; t < nrow1; t++){
^
optimizer.c: In function 'fr_four':
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for(t = 1; t < nrow1; t++){
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.52.0.zip
* DONE (snapCGH)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'snapCGH' successfully unpacked and MD5 sums checked
In R CMD INSTALL