Ulrich Bodenhofer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/kebabs |
| Branch: RELEASE_3_10 |
| Last Commit: fe29819 |
| Last Changed Date: 2019-10-29 13:09:06 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:23:59 -0400 (Wed, 15 Apr 2020).
| Package 885/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| kebabs 1.20.0 Ulrich Bodenhofer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: kebabs |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:kebabs.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings kebabs_1.20.0.tar.gz |
| StartedAt: 2020-04-15 04:14:04 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:18:38 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 273.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:kebabs.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings kebabs_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/kebabs.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'kebabs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'kebabs' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'kebabs' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
R 1.5Mb
data 1.2Mb
libs 2.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
kebabsDemo: no visible binding for global variable 'enhancerFB'
kebabsDemo: no visible binding for global variable 'yFB'
kebabsDemo: no visible binding for global variable 'ccseq'
kebabsDemo: no visible binding for global variable 'yCC'
Undefined global functions or variables:
ccseq enhancerFB yCC yFB
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/kebabs/libs/i386/kebabs.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/kebabs/libs/x64/kebabs.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
performModelSelection 12.42 0.25 12.69
performGridSearch 5.90 0.28 6.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
performModelSelection 11.59 0.25 11.86
performGridSearch 5.97 0.09 6.06
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/kebabs.Rcheck/00check.log'
for details.
kebabs.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/kebabs_1.20.0.tar.gz && rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=kebabs.buildbin-libdir kebabs_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL kebabs_1.20.0.zip && rm kebabs_1.20.0.tar.gz kebabs_1.20.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'kebabs' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ByteStringVector.c -o ByteStringVector.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ExplicitRepC.cpp -o ExplicitRepC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c GappyPairC.cpp -o GappyPairC.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c KernelUtils.cpp -o KernelUtils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function 'SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)':
MismatchC.cpp:432:41: warning: 'currValSqrt' may be used uninitialized in this function [-Wmaybe-uninitialized]
km(i,j) = kernelVal / currValSqrt;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c MotifC.cpp -o MotifC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PredictionC.cpp -o PredictionC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PredictionProfileC.cpp -o PredictionProfileC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c R_init_kebabs.cpp -o R_init_kebabs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rsvm.c -o Rsvm.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SparseMatrixHash.cpp -o SparseMatrixHash.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SpectrumC.cpp -o SpectrumC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SymmetricPairC.cpp -o SymmetricPairC.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c Utils.cpp -o Utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c svm.cpp -o svm.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o kebabs.dll tmp.def Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.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/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'kebabs'
finding HTML links ... done
BioVector-class html
finding level-2 HTML links ... done
BioVector html
ControlInformation-class html
CrossValidationResult-class html
CrossValidationResultAccessors html
ExplicitRepresentation-class html
ExplicitRepresentationAccessors html
GappyPairKernel-class html
KBModel-class html
KBModelAccessors html
KernelMatrix-class html
KernelMatrixAccessors html
LinearKernel html
MismatchKernel-class html
ModelSelectionResult-class html
ModelSelectionResultAccessors html
MotifKernel-class html
PredictionProfile-class html
PredictionProfileAccessors html
ROCData-class html
ROCDataAccessors html
SVMAccess html
SVMInformation-class html
SequenceKernel-class html
SpectrumKernel-class html
SymmetricPairKernel-class html
annotationSpecificKernel html
computeROCandAUC html
evaluatePrediction html
explicitRepresentation html
featureWeights html
gappyPairKernel html
genRandBioSeqs html
getPredProfMixture-methods html
getPredictionProfile-methods html
heatmap-methods html
kbsvm-methods html
kebabsCollectInfo html
kebabsData html
kebabsOverview html
mismatchKernel html
motifKernel html
performCrossValidation-methods html
performGridSearch html
performModelSelection html
plot-methods html
positionDependentKernel html
predict-methods html
sequenceKernel html
show-methods html
spectrumKernel html
symmetricPairKernel 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 'kebabs' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ByteStringVector.c -o ByteStringVector.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ExplicitRepC.cpp -o ExplicitRepC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c GappyPairC.cpp -o GappyPairC.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c KernelUtils.cpp -o KernelUtils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function 'SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)':
MismatchC.cpp:432:41: warning: 'currValSqrt' may be used uninitialized in this function [-Wmaybe-uninitialized]
km(i,j) = kernelVal / currValSqrt;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c MotifC.cpp -o MotifC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PredictionC.cpp -o PredictionC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PredictionProfileC.cpp -o PredictionProfileC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c R_init_kebabs.cpp -o R_init_kebabs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Rsvm.c -o Rsvm.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SparseMatrixHash.cpp -o SparseMatrixHash.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SpectrumC.cpp -o SpectrumC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SymmetricPairC.cpp -o SymmetricPairC.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c Utils.cpp -o Utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c svm.cpp -o svm.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o kebabs.dll tmp.def Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.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/kebabs.buildbin-libdir/kebabs/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'kebabs' as kebabs_1.20.0.zip
* DONE (kebabs)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'kebabs' successfully unpacked and MD5 sums checked
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kebabs.Rcheck/examples_i386/kebabs-Ex.timings
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kebabs.Rcheck/examples_x64/kebabs-Ex.timings
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