cn.farms 1.28.0
Andreas Mitterecker
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cn.farms |
| Branch: RELEASE_3_7 |
| Last Commit: 73314ef |
| Last Changed Date: 2018-04-30 10:35:17 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| merida2 | 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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cn.farms_1.28.0.tar.gz && rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cn.farms_1.28.0.zip && rm cn.farms_1.28.0.tar.gz cn.farms_1.28.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'cn.farms' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
int method=0;
^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
^
laplace.cpp:393:86: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
moment2 = (-0.5*a+0.25*(b-1/sigmaZ)*(b-1/sigmaZ)+(b*leftWeight)/(sigmaZ)+(leftWeight*I1left*sqrtMa)/(sqrt(2.0)*sigmaZ))/(a*a);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cn.farms'
finding HTML links ... done
callSummarize html
cn.farms html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/cn.farms.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
cnLibrary html
combineData html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/combineData.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/combineData.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/combineData.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
createAnnotation html
createMatrix html
distributionDistance html
dnaCopySf html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/dnaCopySf.Rd:22: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
doCnFarmsSingle html
flcSnp6Std html
flcStd html
fragLengCorr html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/fragLengCorr.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/fragLengCorr.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
getFragmentSet html
getSingleProbeSetSize html
mlSummarization html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/mlSummarization.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/mlSummarization.Rd:36: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normAdd html
normalizeAverage html
normalizeCels html
normalizeNone html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/normalizeNone.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normalizeNpData html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/normalizeNpData.Rd:25: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normalizeQuantiles html
normalizeSequenceEffect html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/normalizeSequenceEffect.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normalizeSor html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/normalizeSor.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotDendrogram html
plotDensity html
plotEvalIc html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/plotEvalIc.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotRegions html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/plotRegions.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/plotRegions.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotSmoothScatter html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/plotSmoothScatter.Rd:9: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotViolines html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/plotViolines.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
slSummarization html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/slSummarization.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGQZ4c8/R.INSTALL1538117d5a44/cn.farms/man/slSummarization.Rd:35: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
sparseFarmsC html
summarizeFarmsExact html
summarizeFarmsExact2 html
summarizeFarmsExact3 html
summarizeFarmsGaussian html
summarizeFarmsMethods html
summarizeFarmsStatistics html
summarizeFarmsVariational html
summarizeWindowBps html
summarizeWindowMethods html
summarizeWindowStd html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cn.farms' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
int method=0;
^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
^
laplace.cpp:367:52: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.28.0.zip
* DONE (cn.farms)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cn.farms' successfully unpacked and MD5 sums checked
In R CMD INSTALL