Eleni Adam
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| 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 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
| 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 977/2272 | 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 | |||||||||
|
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: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hummingbird |
| StartedAt: 2024-11-27 15:12:02 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 15:12:07 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 4.4 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hummingbird
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘hummingbird’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c em.cpp -o em.o
em.cpp:30:14: error: use of undeclared identifier 'asReal'
bin_size = asReal(binSize);
^
em.cpp:36:24: error: use of undeclared identifier 'getAttrib'; did you mean 'Rf_getAttrib'?
SEXP S_dim_matrices = getAttrib(normM, R_DimSymbol);
^~~~~~~~~
Rf_getAttrib
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:538:6: note: 'Rf_getAttrib' declared here
SEXP Rf_getAttrib(SEXP, SEXP);
^
em.cpp:40:27: error: use of undeclared identifier 'getAttrib'; did you mean 'Rf_getAttrib'?
SEXP S_dim_matrices_ab = getAttrib(abnormM, R_DimSymbol);
^~~~~~~~~
Rf_getAttrib
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:538:6: note: 'Rf_getAttrib' declared here
SEXP Rf_getAttrib(SEXP, SEXP);
^
em.cpp:146:5: error: use of undeclared identifier 'error'
error("Error allocating memory.\n");
^
em.cpp:151:5: error: use of undeclared identifier 'error'
error("Error allocating memory.\n");
^
em.cpp:156:5: error: use of undeclared identifier 'error'
error("Error allocating memory.\n");
^
em.cpp:161:5: error: use of undeclared identifier 'error'
error("Error allocating memory.\n");
^
em.cpp:166:5: error: use of undeclared identifier 'error'
error("Error allocating memory.\n");
^
em.cpp:171:5: error: use of undeclared identifier 'error'
error("Error allocating memory.\n");
^
em.cpp:799:22: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
SEXP S_em = PROTECT(allocMatrix(INTSXP, full_bins, 4));
^~~~~~~~~~~
Rf_allocMatrix
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
SEXP Rf_allocMatrix(SEXPTYPE, int, int);
^
em.cpp:807:23: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
SEXP S_em2 = PROTECT(allocMatrix(REALSXP, full_bins, 2));
^~~~~~~~~~~
Rf_allocMatrix
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
SEXP Rf_allocMatrix(SEXPTYPE, int, int);
^
em.cpp:815:23: error: use of undeclared identifier 'mkNamed'
SEXP S_res = PROTECT(mkNamed(VECSXP, names));
^
12 errors generated.
make: *** [em.o] Error 1
ERROR: compilation failed for package ‘hummingbird’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/hummingbird’