Ulrich Bodenhofer
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: RELEASE_3_13 |
| git_last_commit: 6abd0f9 |
| git_last_commit_date: 2021-06-18 09:06:41 -0400 (Fri, 18 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:43 -0400 (Fri, 15 Oct 2021).
|
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 966/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.26.1 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 20.04.2 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 | | ||||||||
| Package: kebabs |
| Version: 1.26.1 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL kebabs |
| StartedAt: 2021-10-14 06:34:31 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 06:36:21 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 110.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL kebabs
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -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]
432 | km(i,j) = kernelVal / currValSqrt;
| ~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -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]
3677 | pKeypool = keyPool;
| ~~~~~~~~~^~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rsvm.c -o Rsvm.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SpectrumC.cpp -o SpectrumC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c svm.cpp -o svm.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o kebabs.so 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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-kebabs/00new/kebabs/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (kebabs)