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
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo2 Summary

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Package: stPipe

Version: 0.99.94

RVersion: 4.5

BiocVersion: 3.22

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

BuildTime: 0 minutes 5.56 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: stPipe_20250704065728

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: 0. Installing package status: 1. Build Package status: 1.

nebbiolo2 BUILD SRC output

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

 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 ‘0.99.94’
** 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'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I'/home/biocbuild/bbs-3.22-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 member function ‘void ReadStats::reportStats()’:
st_demul.cpp:89:5: error: ‘cout’ was not declared in this scope; did you mean ‘std::cout’?
   89 |     cout << "Total number of reads: " << total << endl;
      |     ^~~~
      |     std::cout
In file included from st_demul.cpp:17:
/usr/include/c++/13/iostream:63:18: note: ‘std::cout’ declared here
   63 |   extern ostream cout;          ///< Linked to standard output
      |                  ^~~~
st_demul.cpp: In function ‘void RunDemultiplex(const char*, const char*, const char*, const char*, int, int, int, int, int, int)’:
st_demul.cpp:150:9: warning: unused variable ‘ndims’ [-Wunused-variable]
  150 |     int ndims = dataspace.getSimpleExtentDims(dims_out, NULL);
      |         ^~~~~
make: *** [/home/biocbuild/bbs-3.22-bioc/R/etc/Makeconf:209: st_demul.o] Error 1
ERROR: compilation failed for package ‘stPipe’
* removing ‘/tmp/RtmpUjZPHa/Rinst19d7e23c38fe6/stPipe’
      -----------------------------------
ERROR: package installation failed

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output

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