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This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4349
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 977/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hummingbird 1.17.0  (landing page)
Eleni Adam
Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 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)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped

BUILD results for hummingbird on lconway

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.

raw results


Summary

Package: hummingbird
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data hummingbird
StartedAt: 2024-11-24 17:14:00 -0500 (Sun, 24 Nov 2024)
EndedAt: 2024-11-24 17:14:08 -0500 (Sun, 24 Nov 2024)
EllapsedTime: 8.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data hummingbird
###
##############################################################################
##############################################################################


* checking for file ‘hummingbird/DESCRIPTION’ ... OK
* preparing ‘hummingbird’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* 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 ‘/private/tmp/Rtmp84bIro/Rinst175957c8a55dd/hummingbird’
      -----------------------------------
ERROR: package installation failed