Multiple platform build/check report for BioC 3.19 - INSTALL results for cliqueMS on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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*

INSTALL results for cliqueMS on kjohnson1

To the developers/maintainers of the cliqueMS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cliqueMS.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: cliqueMS

Version: 1.18.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cliqueMS

StartedAt: 2024-10-16 17:39:46 -0400 (Wed, 16 Oct 2024)

EndedAt: 2024-10-16 17:40:10 -0400 (Wed, 16 Oct 2024)

EllapsedTime: 24.4 seconds

RetCode: 1

Status: ERROR

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cliqueMS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized]
    completeroundscore += *ritv;
    ^~~~~~~~~~~~~~~~~~
./annotationCliqueMSR.h:733:28: note: initialize the variable 'completeroundscore' to silence this warning
  double completeroundscore,remainderroundscore = 0;
                           ^
                            = 0.0
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c findCliquesR.cpp -o findCliquesR.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c findIsotopesR.cpp -o findIsotopesR.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-cliqueMS/00new/cliqueMS/libs
** R
Error in .install_package_code_files(".", instdir) : 
files in 'Collate' field missing from '/Users/biocbuild/bbs-3.19-bioc/meat/cliqueMS/R':
  zzz.R
ERROR: unable to collate and parse R files for package ‘cliqueMS’
* removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cliqueMS’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cliqueMS’