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This page was generated on 2024-03-29 11:36:04 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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

Package 1075/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.36.0  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/kebabs
git_branch: RELEASE_3_18
git_last_commit: 79c8b1b
git_last_commit_date: 2023-10-24 10:39:53 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for kebabs on nebbiolo2


To the developers/maintainers of the kebabs package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: kebabs
Version: 1.36.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL kebabs
StartedAt: 2024-03-27 15:12:25 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 15:14:14 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 108.4 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL kebabs
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp: In function ‘SEXPREC* gappyPairKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
GappyPairC.cpp:994:37: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  994 |                 annptr = annX.ptr[iX];
      |                          ~~~~~~~~~~~^
GappyPairC.cpp:3407:28: note: ‘annX.ByteStringVector::ptr’ was declared here
 3407 |     ByteStringVector x, y, annX, annY, annCharset;
      |                            ^~~~
GappyPairC.cpp:1160:41: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1160 |                     annptr = annY.ptr[iY];
      |                              ~~~~~~~~~~~^
GappyPairC.cpp:3407:34: note: ‘annY.ByteStringVector::ptr’ was declared here
 3407 |     ByteStringVector x, y, annX, annY, annCharset;
      |                                  ^~~~
GappyPairC.cpp:3472:34: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3472 |                 getKMPosDistGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY,
      |                 ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3473 |                                   k, m, normalized, symmetric, reverseComplement, posSpec,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3474 |                                   distWeight, maxSeqLength, &alphaInf);
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3472:34: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c MismatchC.cpp -o MismatchC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp: In function ‘SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
SpectrumC.cpp:679:37: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  679 |                 annptr = annX.ptr[iX];
      |                          ~~~~~~~~~~~^
SpectrumC.cpp:3156:28: note: ‘annX.ByteStringVector::ptr’ was declared here
 3156 |     ByteStringVector x, y, annX, annY, annCharset;
      |                            ^~~~
SpectrumC.cpp:835:41: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  835 |                     annptr = annY.ptr[iY];
      |                              ~~~~~~~~~~~^
SpectrumC.cpp:3156:34: note: ‘annY.ByteStringVector::ptr’ was declared here
 3156 |     ByteStringVector x, y, annX, annY, annCharset;
      |                                  ^~~~
SpectrumC.cpp:3220:33: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3220 |                 getKMPosDistSpec(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3221 |                                  k, normalized, symmetric, reverseComplement, posSpec, distWeight,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3222 |                                  maxSeqLength, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3220:33: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c svm.cpp -o svm.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-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)