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This page was generated on 2026-04-25 11:35 -0400 (Sat, 25 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4978
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4722
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 22/2415HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Aerith 0.99.13  (landing page)
Yi Xiong
Snapshot Date: 2026-04-24 13:40 -0400 (Fri, 24 Apr 2026)
git_url: https://git.bioconductor.org/packages/Aerith
git_branch: devel
git_last_commit: e0405e6
git_last_commit_date: 2026-04-23 11:43:23 -0400 (Thu, 23 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
See other builds for Aerith in R Universe.

BUILD BIN results for Aerith on kjohnson3

To the developers/maintainers of the Aerith package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Aerith.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: Aerith
Version: 0.99.13
Command: rm -rf Aerith.buildbin-libdir && mkdir Aerith.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Aerith_0.99.13.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Aerith.buildbin-libdir
StartedAt: 2026-04-24 23:09:18 -0400 (Fri, 24 Apr 2026)
EndedAt: 2026-04-24 23:10:00 -0400 (Fri, 24 Apr 2026)
EllapsedTime: 41.8 seconds
RetCode: 0
Status:   OK  
PackageFile: Aerith_0.99.13.tgz
PackageFileSize: 10.59 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Aerith.buildbin-libdir && mkdir Aerith.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Aerith_0.99.13.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Aerith.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Aerith.buildbin-libdir Aerith_0.99.13.tar.gz'
>>>>>>> 

* installing *source* package ‘Aerith’ ...
** this is package ‘Aerith’ version ‘0.99.13’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++17
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractPSMfeatures.cpp -o extractPSMfeatures.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c filterPSMs.cpp -o filterPSMs.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c filterPeptides.cpp -o filterPeptides.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c generateCFG.cpp -o generateCFG.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c getISOpeak.cpp -o getISOpeak.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c readScan.cpp -o readScan.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c readScans.cpp -o readScans.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c readSips.cpp -o readSips.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c readSpe2Peps.cpp -o readSpe2Peps.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c scorePSM.cpp -o scorePSM.o
scorePSM.cpp:431:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  431 |                      ibeginPos, dPeptideMass, cIdentifyPrefix,
      |                      ^~~~~~~~~
scorePSM.cpp:431:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  431 |                      ibeginPos, dPeptideMass, cIdentifyPrefix,
      |                                 ^~~~~~~~~~~~
scorePSM.cpp:431:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  431 |                      ibeginPos, dPeptideMass, cIdentifyPrefix,
      |                                               ^~~~~~~~~~~~~~~
scorePSM.cpp:432:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  432 |                      cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
      |                      ^~~~~~~~~~~~~~~
scorePSM.cpp:432:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  432 |                      cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
      |                                       ^~~~~~~~~~~~~~~
scorePSM.cpp:432:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  432 |                      cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
      |                                                        ^~~~~~~~~~~~~~~
scorePSM.cpp:655:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  655 |                      ibeginPos, dPeptideMass, cIdentifyPrefix,
      |                      ^~~~~~~~~
scorePSM.cpp:655:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  655 |                      ibeginPos, dPeptideMass, cIdentifyPrefix,
      |                                 ^~~~~~~~~~~~
scorePSM.cpp:655:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  655 |                      ibeginPos, dPeptideMass, cIdentifyPrefix,
      |                                               ^~~~~~~~~~~~~~~
scorePSM.cpp:656:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  656 |                      cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
      |                      ^~~~~~~~~~~~~~~
scorePSM.cpp:656:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  656 |                      cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
      |                                       ^~~~~~~~~~~~~~~
scorePSM.cpp:656:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
  656 |                      cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
      |                                                        ^~~~~~~~~~~~~~~
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c writeScans.cpp -o writeScans.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/PSMfeatureExtractor.cpp -o lib/PSMfeatureExtractor.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/PSMpeakAnnotator.cpp -o lib/PSMpeakAnnotator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/PSMsFiltrator.cpp -o lib/PSMsFiltrator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/Spe2PepFileReader.cpp -o lib/Spe2PepFileReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/averagine.cpp -o lib/averagine.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/cfgParser.cpp -o lib/cfgParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/ftFileReader.cpp -o lib/ftFileReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/ftFileWriter.cpp -o lib/ftFileWriter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/isotopologue.cpp -o lib/isotopologue.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/ms2scan.cpp -o lib/ms2scan.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/peptide.cpp -o lib/peptide.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/peptidesFiltrator.cpp -o lib/peptidesFiltrator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/proNovoConfig.cpp -o lib/proNovoConfig.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/sipFileReader.cpp -o lib/sipFileReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/sipGenerator.cpp -o lib/sipGenerator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lib/sipPSM.cpp -o lib/sipPSM.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Aerith.so RcppExports.o extractPSMfeatures.o filterPSMs.o filterPeptides.o generateCFG.o getISOpeak.o readScan.o readScans.o readSips.o readSpe2Peps.o scorePSM.o writeScans.o lib/PSMfeatureExtractor.o lib/PSMpeakAnnotator.o lib/PSMsFiltrator.o lib/Spe2PepFileReader.o lib/averagine.o lib/cfgParser.o lib/ftFileReader.o lib/ftFileWriter.o lib/isotopologue.o lib/ms2scan.o lib/peptide.o lib/peptidesFiltrator.o lib/proNovoConfig.o lib/sipFileReader.o lib/sipGenerator.o lib/sipPSM.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/Aerith.buildbin-libdir/00LOCK-Aerith/00new/Aerith/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Aerith)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Aerith.buildbin-libdir/Aerith/libs/Aerith.so
>>>>>>> 

>>>>>>> Paths before fix:
Aerith.buildbin-libdir/Aerith/libs/Aerith.so:
	Aerith.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgcc_s.1.1.dylib" "Aerith.buildbin-libdir/Aerith/libs/Aerith.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgfortran.5.dylib" "Aerith.buildbin-libdir/Aerith/libs/Aerith.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libquadmath.0.dylib" "Aerith.buildbin-libdir/Aerith/libs/Aerith.so"

>>>>>>> Paths after fix:
Aerith.buildbin-libdir/Aerith/libs/Aerith.so:
	Aerith.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)