cn.mops 1.34.0
Gundula Povysil
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_11 |
| Last Commit: cbdd1f2 |
| Last Changed Date: 2020-04-27 14:27:50 -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 | 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/cn.mops_1.34.0.tar.gz && rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL cn.mops_1.34.0.zip && rm cn.mops_1.34.0.tar.gz cn.mops_1.34.0.zip
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install for i386
* installing *source* package 'cn.mops' ...
** 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 R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
double globalMean,globalSd,diff,M2,globalVariance;
^~~~~~~~
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^~~~~~~~~~~~
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
^~~~~~~~~~~~
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^~~~~~
In file included from segment.cpp:10:
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
#define beta Rf_beta
^~~~~~~
segment.cpp:64:9: note: in expansion of macro 'beta'
double beta,nn;
^~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.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/cn.mops.buildbin-libdir/00LOCK-cn.mops/00new/cn.mops/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cn.mops'
finding HTML links ... done
CNVDetectionResult html
CNVRanges html
X html
XRanges html
calcFractionalCopyNumbers-CNVDetectionResult-method
html
calcFractionalCopyNumbers html
calcIntegerCopyNumbers-CNVDetectionResult-method
html
calcIntegerCopyNumbers html
cn.mops html
cnvr-CNVDetectionResult-method html
cnvr html
cnvs-CNVDetectionResult-method html
cnvs html
exomeCounts html
exomecn.mops html
getReadCountsFromBAM html
getSegmentReadCountsFromBAM html
gr-CNVDetectionResult-method html
gr html
haplocn.mops html
individualCall-CNVDetectionResult-method
html
individualCall html
iniCall-CNVDetectionResult-method html
iniCall html
integerCopyNumber-CNVDetectionResult-method
html
integerCopyNumber html
localAssessments-CNVDetectionResult-method
html
localAssessments html
makeRobustCNVR html
normalizeChromosomes html
normalizeGenome html
normalizedData-CNVDetectionResult-method
html
normalizedData html
params-CNVDetectionResult-method html
params html
plot html
posteriorProbs-CNVDetectionResult-method
html
posteriorProbs html
referencecn.mops html
sampleNames-CNVDetectionResult-method html
sampleNames html
segment html
segmentation-CNVDetectionResult-method
html
segmentation html
segplot-CNVDetectionResult-method html
segplot html
show html
singlecn.mops 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 'cn.mops' ...
** 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 R_init_cnmops.c -o R_init_cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cnmops.cpp -o cnmops.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
double globalMean,globalSd,diff,M2,globalVariance;
^~~~~~~~
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^~~~~~~~~~~~
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
^~~~~~~~~~~~
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^~~~~~
In file included from segment.cpp:10:
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
#define beta Rf_beta
^~~~~~~
segment.cpp:64:9: note: in expansion of macro 'beta'
double beta,nn;
^~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.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/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.34.0.zip
* DONE (cn.mops)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'cn.mops' successfully unpacked and MD5 sums checked