snapCGH 1.58.0
John Marioni
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/snapCGH |
| Branch: RELEASE_3_11 |
| Last Commit: 390c7f3 |
| Last Changed Date: 2020-04-27 14:12:43 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | NA | |
| 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/snapCGH_1.58.0.tar.gz && rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.58.0.zip && rm snapCGH_1.58.0.tar.gz snapCGH_1.58.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 619k 100 619k 0 0 8950k 0 --:--:-- --:--:-- --:--:-- 9836k
install for i386
* installing *source* package 'snapCGH' ...
** 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 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];
^~~~~~~~
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** 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
plotSegmentedGenome html
processCGH html
read.clonesinfo html
readPositionalInfo html
removeByWeights html
runBioHMM html
runDNAcopy html
runGLAD html
runHMM html
runTilingArray html
sim.structure html
zoomChromosome html
zoomGenome 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 'snapCGH' ...
** 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 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];
^~~~~~~~
C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.58.0.zip
* DONE (snapCGH)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'snapCGH' successfully unpacked and MD5 sums checked