Bioconductor Single Package Builder - Build History

Snapshot Date:

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

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

[top]

Package: stPipe

Version: 0.99.1

RVersion: 4.5

BiocVersion: 3.21

BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data stPipe

BuildTime: 0 minutes 41.87 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: stPipe_20250328013008

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

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

nebbiolo1 BUILD SRC output

[top]

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

 R CMD BUILD

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

* checking for file ‘stPipe/DESCRIPTION’ ... OK
* preparing ‘stPipe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘stPipe’ ...
** this is package ‘stPipe’ 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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c st_demul.cpp -o st_demul.o
st_demul.cpp: In function ‘void RunDemultiplex(const char*, const char*, const char*, const char*, int, int, int, int, int, int)’:
st_demul.cpp:151:9: warning: unused variable ‘ndims’ [-Wunused-variable]
  151 |     int ndims = dataspace.getSimpleExtentDims(dims_out, NULL);
      |         ^~~~~
st_demul.cpp:217:9: warning: variable ‘l_r2’ set but not used [-Wunused-but-set-variable]
  217 |     int l_r2 = 0;
      |         ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-example.cpp -o test-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o stPipe.so RcppExports.o st_demul.o test-example.o test-runner.o -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /tmp/RtmpfvOdaz/Rinst3fa3e417ff361a/00LOCK-stPipe/00new/stPipe/libs
** R
** data
*** moving datasets to lazyload DB
** 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
Error: package or namespace load failed for ‘stPipe’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/tmp/RtmpfvOdaz/Rinst3fa3e417ff361a/00LOCK-stPipe/00new/stPipe/libs/stPipe.so':
  /tmp/RtmpfvOdaz/Rinst3fa3e417ff361a/00LOCK-stPipe/00new/stPipe/libs/stPipe.so: undefined symbol: _ZN2H515FileAccPropList7DEFAULTE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpfvOdaz/Rinst3fa3e417ff361a/stPipe’
      -----------------------------------
ERROR: package installation failed

nebbiolo1 CHECK output

[top]

nebbiolo1 BUILD BIN output

[top]