cn.farms 1.34.0
Andreas Mitterecker
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/cn.farms |
| Branch: RELEASE_3_10 |
| Last Commit: 47595d2 |
| Last Changed Date: 2019-10-29 13:08:19 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ 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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### rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.34.0.tar.gz
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install for i386
* installing *source* package 'cn.farms' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/cn.farms.buildbin-libdir/00LOCK-cn.farms/00new/cn.farms/libs/i386
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** 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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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-3.10-bioc/tmpdir/RtmpuWZtlQ/R.INSTALL2dd828295873/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 from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'cn.farms' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.34.0.zip
* DONE (cn.farms)