Ulrich Bodenhofer
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: master |
| git_last_commit: a228803 |
| git_last_commit_date: 2022-01-14 08:59:22 -0400 (Fri, 14 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:51 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the kebabs package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/kebabs.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 981/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.29.1 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: kebabs |
| Version: 1.29.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:kebabs.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings kebabs_1.29.1.tar.gz |
| StartedAt: 2022-03-17 19:25:03 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:27:59 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 176.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:kebabs.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings kebabs_1.29.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/kebabs.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.1'
* 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 5.5Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 1.2Mb
libs 1.6Mb
* 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
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
performModelSelection 10.57 0.04 10.61
performGridSearch 5.25 0.12 5.38
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/kebabs.Rcheck/00check.log'
for details.
kebabs.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL kebabs
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'kebabs' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ByteStringVector.c -o ByteStringVector.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ExplicitRepC.cpp -o ExplicitRepC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GappyPairC.cpp -o GappyPairC.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c KernelUtils.cpp -o KernelUtils.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c MotifC.cpp -o MotifC.o
MotifC.cpp: In function 'void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)':
MotifC.cpp:3677:18: warning: 'keyPool' may be used uninitialized in this function [-Wmaybe-uninitialized]
pKeypool = keyPool;
~~~~~~~~~^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c PredictionC.cpp -o PredictionC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c PredictionProfileC.cpp -o PredictionProfileC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_kebabs.cpp -o R_init_kebabs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Rsvm.c -o Rsvm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SparseMatrixHash.cpp -o SparseMatrixHash.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SpectrumC.cpp -o SpectrumC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SymmetricPairC.cpp -o SymmetricPairC.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Utils.cpp -o Utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c svm.cpp -o svm.o
C:/rtools40/mingw64/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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-kebabs/00new/kebabs/libs/x64
** 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
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-kebabs/00new/kebabs/help/annotationSpecificKernel.html
computeROCandAUC html
evaluatePrediction html
explicitRepresentation html
featureWeights html
gappyPairKernel html
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genRandBioSeqs html
getPredProfMixture-methods html
getPredictionProfile-methods html
heatmap-methods html
kbsvm-methods html
kebabsCollectInfo html
kebabsData html
kebabsOverview html
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mismatchKernel html
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motifKernel html
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performCrossValidation-methods html
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performGridSearch html
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performModelSelection html
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plot-methods html
positionDependentKernel html
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predict-methods html
sequenceKernel html
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** 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
* DONE (kebabs)
Making 'packages.html' ... done
kebabs.Rcheck/kebabs-Ex.timings
| name | user | system | elapsed | |
| BioVector | 0.03 | 0.00 | 0.03 | |
| CrossValidationResultAccessors | 0 | 0 | 0 | |
| KBModelAccessors | 0 | 0 | 0 | |
| KernelMatrixAccessors | 0 | 0 | 0 | |
| LinearKernel | 3.70 | 0.03 | 3.73 | |
| ModelSelectionResultAccessors | 0 | 0 | 0 | |
| PredictionProfileAccessors | 0.02 | 0.00 | 0.02 | |
| ROCDataAccessors | 0 | 0 | 0 | |
| SVMAccess | 0.09 | 0.00 | 0.09 | |
| annotationSpecificKernel | 0.13 | 0.00 | 0.13 | |
| computeROCandAUC | 2.84 | 1.08 | 3.92 | |
| evaluatePrediction | 0.61 | 0.03 | 0.64 | |
| explicitRepresentation | 0.12 | 0.00 | 0.13 | |
| featureWeights | 0.24 | 0.00 | 0.23 | |
| gappyPairKernel | 0.01 | 0.00 | 0.02 | |
| genRandBioSeqs | 0.04 | 0.00 | 0.03 | |
| getPredProfMixture-methods | 2.17 | 0.24 | 2.40 | |
| getPredictionProfile-methods | 0.83 | 0.11 | 0.94 | |
| heatmap-methods | 0.37 | 0.03 | 0.41 | |
| kbsvm-methods | 0.22 | 0.01 | 0.23 | |
| kebabsCollectInfo | 0.03 | 0.02 | 0.05 | |
| kebabsOverview | 0.28 | 0.05 | 0.33 | |
| mismatchKernel | 0.02 | 0.00 | 0.01 | |
| motifKernel | 0 | 0 | 0 | |
| performCrossValidation-methods | 0.18 | 0.03 | 0.22 | |
| performGridSearch | 5.25 | 0.12 | 5.38 | |
| performModelSelection | 10.57 | 0.04 | 10.61 | |
| plot-methods | 0.40 | 0.05 | 0.45 | |
| positionDependentKernel | 0 | 0 | 0 | |
| predict-methods | 0.22 | 0.02 | 0.24 | |
| sequenceKernel | 0.03 | 0.00 | 0.03 | |
| show-methods | 0.02 | 0.01 | 0.03 | |
| spectrumKernel | 0 | 0 | 0 | |
| symmetricPairKernel | 0.08 | 0.02 | 0.09 | |