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This page was generated on 2023-04-12 11:05:08 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

INSTALL results for kebabs on nebbiolo2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1022/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.32.0  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/kebabs
git_branch: RELEASE_3_16
git_last_commit: 559f77b
git_last_commit_date: 2022-11-01 11:10:39 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: kebabs
Version: 1.32.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL kebabs
StartedAt: 2023-04-10 15:57:31 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 15:59:30 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 118.9 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-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-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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)