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This page was generated on 2026-03-07 11:33 -0500 (Sat, 07 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4453 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" | 3376 |
| 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 962/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Harman 1.39.0 (landing page) Jason Ross
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for Harman in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Harman package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Harman.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. |
| Package: Harman |
| Version: 1.39.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Harman |
| StartedAt: 2026-03-06 16:20:40 -0500 (Fri, 06 Mar 2026) |
| EndedAt: 2026-03-06 16:20:44 -0500 (Fri, 06 Mar 2026) |
| EllapsedTime: 4.0 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Harman
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Harman’ ...
** this is package ‘Harman’ version ‘1.39.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include `/home/biocbuild/bbs-3.23-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -I. -fpic -g -O2 -Wall -Werror=format-security -c Harman.cpp -o Harman.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
In file included from Harman.cpp:181:
CMapSelectKFromN.h:52:24: error: expected ‘)’ before ‘maxN’
52 | CFactorials<T>(size_t maxN)
| ~ ^~~~~
| )
CMapSelectKFromN.h: In constructor ‘CMapSelectKFromN::CMapSelectKFromN(std::pair<long unsigned int, long unsigned int>, size_t)’:
CMapSelectKFromN.h:391:70: error: no matching function for call to ‘CFactorials<double>::CFactorials(int)’
391 | this->_factn = (CFactorials<double> *) new CFactorials<double>(20) ;
| ^
CMapSelectKFromN.h:45:26: note: candidate: ‘constexpr CFactorials<double>::CFactorials()’
45 | template <class T> class CFactorials
| ^~~~~~~~~~~
CMapSelectKFromN.h:45:26: note: candidate expects 0 arguments, 1 provided
CMapSelectKFromN.h:45:26: note: candidate: ‘constexpr CFactorials<double>::CFactorials(const CFactorials<double>&)’
CMapSelectKFromN.h:45:26: note: no known conversion for argument 1 from ‘int’ to ‘const CFactorials<double>&’
CMapSelectKFromN.h:45:26: note: candidate: ‘constexpr CFactorials<double>::CFactorials(CFactorials<double>&&)’
CMapSelectKFromN.h:45:26: note: no known conversion for argument 1 from ‘int’ to ‘CFactorials<double>&&’
Harman.cpp: In constructor ‘CSimulateBatchDistribution::CSimulateBatchDistribution(size_t, CExperimentWithPCAData*, size_t)’:
Harman.cpp:1466:70: error: no matching function for call to ‘CFactorials<double>::CFactorials(int)’
1466 | this->_factn = (CFactorials<double> *) new CFactorials<double>(20) ;
| ^
CMapSelectKFromN.h:45:26: note: candidate: ‘constexpr CFactorials<double>::CFactorials()’
45 | template <class T> class CFactorials
| ^~~~~~~~~~~
CMapSelectKFromN.h:45:26: note: candidate expects 0 arguments, 1 provided
CMapSelectKFromN.h:45:26: note: candidate: ‘constexpr CFactorials<double>::CFactorials(const CFactorials<double>&)’
CMapSelectKFromN.h:45:26: note: no known conversion for argument 1 from ‘int’ to ‘const CFactorials<double>&’
CMapSelectKFromN.h:45:26: note: candidate: ‘constexpr CFactorials<double>::CFactorials(CFactorials<double>&&)’
CMapSelectKFromN.h:45:26: note: no known conversion for argument 1 from ‘int’ to ‘CFactorials<double>&&’
Harman.cpp: In function ‘SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Harman.cpp:3008:3: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
3008 | else
| ^~~~
Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
3022 | std::vector<unsigned int> tr_std_tmp = Rcpp::as<std::vector<unsigned int> >(tr) ;
| ^~~
In file included from Harman.cpp:182:
CSelectRandom.h: In instantiation of ‘std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(size_t, size_t, size_t, size_t) [with T = double; size_t = long unsigned int]’:
Harman.cpp:1764:79: required from here
CSelectRandom.h:943:48: warning: comparison of integer expressions of different signedness: ‘long long int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
943 | while (currval < howManyIN)
| ~~~~~~~~^~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:197: Harman.o] Error 1
ERROR: compilation failed for package ‘Harman’
* removing ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/Harman’