Eleni Adam
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/hummingbird |
| git_branch: devel |
| git_last_commit: 8a0488f |
| git_last_commit_date: 2024-10-29 10:49:11 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:40 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 979/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hummingbird 1.17.0 (landing page) Eleni Adam
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the hummingbird package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hummingbird.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: hummingbird |
| Version: 1.17.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL hummingbird |
| StartedAt: 2025-01-03 15:07:56 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 15:07:59 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 3.0 seconds |
| RetCode: 1 |
| Status: ERROR |
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL hummingbird
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘hummingbird’ ...
** 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/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c em.cpp -o em.o
em.cpp: In function ‘SEXPREC* hummingbirdEMinternal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
em.cpp:30:28: error: ‘asReal’ was not declared in this scope
30 | bin_size = asReal(binSize);
| ^~~~~~
em.cpp:36:31: error: ‘getAttrib’ was not declared in this scope; did you mean ‘Rf_getAttrib’?
36 | SEXP S_dim_matrices = getAttrib(normM, R_DimSymbol);
| ^~~~~~~~~
| Rf_getAttrib
em.cpp:146:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
146 | error("Error allocating memory.\n");
| ^~~~~
| perror
em.cpp:151:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
151 | error("Error allocating memory.\n");
| ^~~~~
| perror
em.cpp:156:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
156 | error("Error allocating memory.\n");
| ^~~~~
| perror
em.cpp:161:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
161 | error("Error allocating memory.\n");
| ^~~~~
| perror
em.cpp:166:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
166 | error("Error allocating memory.\n");
| ^~~~~
| perror
em.cpp:171:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
171 | error("Error allocating memory.\n");
| ^~~~~
| perror
In file included from utils.h:2,
from em.cpp:1:
em.cpp:799:29: error: ‘allocMatrix’ was not declared in this scope; did you mean ‘Rf_allocMatrix’?
799 | SEXP S_em = PROTECT(allocMatrix(INTSXP, full_bins, 4));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
em.cpp:815:30: error: ‘mkNamed’ was not declared in this scope; did you mean ‘Rf_mkNamed’?
815 | SEXP S_res = PROTECT(mkNamed(VECSXP, names));
| ^~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: em.o] Error 1
ERROR: compilation failed for package ‘hummingbird’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/hummingbird’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/hummingbird’