Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/STADyUM

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo2 Summary

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Package: STADyUM

Version: 0.99.1

RVersion: 4.5

BiocVersion: 3.22

BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data STADyUM

BuildTime: 0 minutes 45.49 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: STADyUM_20250922192413

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: STADyUM. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 1. Build Package status: 1.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘STADyUM/DESCRIPTION’ ... OK
* preparing ‘STADyUM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘STADyUM’ ...
** this is package ‘STADyUM’ version ‘0.99.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c simPol.cpp -o simPol.o
simPol.cpp: In function ‘Rcpp::List simulate_polymerase_cpp(int, double, int, int, int, double, double, double, double, double, double, int, int, int, double, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >)’:
simPol.cpp:249:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<int> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  249 |     for (int step = 0; step < pos_matrices.size(); step++) {
      |                        ~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o STADyUM.so RcppExports.o simPol.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /tmp/RtmphozHoP/Rinst243f1453f8c43d/00LOCK-STADyUM/00new/STADyUM/libs
** R
** 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
Error: package or namespace load failed for ‘STADyUM’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘rtracklayer’
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmphozHoP/Rinst243f1453f8c43d/STADyUM’
      -----------------------------------
ERROR: package installation failed

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output

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