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) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-25 11:35 -0400 (Sat, 25 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4978 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 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 22/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Aerith 0.99.13 (landing page) Yi Xiong
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| See other builds for Aerith in R Universe. | ||||||||||||||
|
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. |
| Package: Aerith |
| Version: 0.99.13 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Aerith.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Aerith_0.99.13.tar.gz |
| StartedAt: 2026-04-24 18:19:15 -0400 (Fri, 24 Apr 2026) |
| EndedAt: 2026-04-24 18:19:58 -0400 (Fri, 24 Apr 2026) |
| EllapsedTime: 42.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Aerith.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Aerith.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Aerith_0.99.13.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-24 22:19:15 UTC
* using option ‘--no-vignettes’
* checking for file ‘Aerith/DESCRIPTION’ ... OK
* this is package ‘Aerith’ version ‘0.99.13’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Aerith’ can be installed ... WARNING
Found the following significant warnings:
scorePSM.cpp:431:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:431:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:431:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:432:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:432:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:432:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:655:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:655:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:655:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:656:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:656:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
scorePSM.cpp:656:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... INFO
specified C++17
* checking installed package size ... INFO
installed size is 8.3Mb
sub-directories of 1Mb or more:
extdata 5.2Mb
libs 1.2Mb
png 1.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Rcpp’ ‘ggnewscale’ ‘methods’ ‘tidyr’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cal_isotope_abundance_fft: no visible global function definition for
‘fft’
cal_isotope_numbers: no visible global function definition for
‘rmultinom’
getPrecursorSpectra: no visible global function definition for ‘new’
getRealScan: no visible global function definition for ‘head’
getRealScanFromList: no visible global function definition for ‘new’
getRealScanWithCharge: no visible global function definition for ‘new’
getSipBYionSpectra: no visible global function definition for ‘new’
getSipPrecursorSpectra: no visible global function definition for ‘new’
isotope_abundance_fft: no visible global function definition for ‘fft’
plotFilteredPCTIntensitySummary: no visible binding for global variable
‘log2_intensity’
plotFilteredPCTIntensitySummary: no visible binding for global variable
‘MS1IsotopicAbundances’
plotMolecularFFTisotopes: no visible binding for global variable ‘MZ’
plotMolecularFFTisotopes: no visible binding for global variable ‘Prob’
plotMolecularIsotopes: no visible binding for global variable ‘MZ’
plotMolecularIsotopes: no visible global function definition for ‘desc’
plotMolecularIsotopes: no visible binding for global variable ‘Prob’
plotMolecularIsotopes: no visible binding for global variable ‘Formula’
plotPSMannotation: no visible global function definition for ‘new’
plotPSMsipPCT: no visible global function definition for ‘read.table’
plotPSMsipPCT: no visible global function definition for ‘median’
plotPrecursorAnnotation: no visible global function definition for
‘new’
plotPrecursorMzFrequency: no visible binding for global variable ‘mz’
plotPrecursorMzFrequency: no visible binding for global variable ‘time’
plotPrecursorMzFrequency: no visible binding for global variable
‘Frequency’
plotPrecursorMzFrequency: no visible global function definition for
‘topo.colors’
plotProSipPct: no visible global function definition for ‘read.table’
plotProSipPct: no visible global function definition for ‘median’
plotProSipPct: no visible global function definition for ‘sd’
plotProSipPct: no visible binding for global variable ‘Abundance’
plotRealScan: no visible binding for global variable ‘MZ’
plotRealScan: no visible binding for global variable ‘Prob’
plotRealScan: no visible binding for global variable ‘Kind’
plotSIPfilteredPCTIntensityBySample: no visible binding for global
variable ‘log2_intensity’
plotSIPfilteredPCTIntensityBySample: no visible binding for global
variable ‘MS1IsotopicAbundances’
plotScanFrequency: no visible binding for global variable
‘RetentionTime’
plotScanFrequency: no visible binding for global variable ‘Kind’
plotScoreDistribution: no visible binding for global variable
‘MassError’
plotScoreDistribution: no visible binding for global variable ‘scores’
plotScoreDistribution: no visible binding for global variable ‘IsDecoy’
plotScoreDistribution: no visible binding for global variable
‘parentCharges’
plotSipBYionLabel: no visible binding for global variable ‘Label’
plotSipBYionLabel: no visible binding for global variable ‘MZ’
plotSipBYionLabel: no visible binding for global variable ‘x’
plotSipBYionLabel: no visible binding for global variable ‘y’
plotTIC: no visible binding for global variable ‘RetentionTime’
plotTIC: no visible binding for global variable ‘RelativeTic’
readPSMtsv: no visible global function definition for ‘read.table’
readPepXMLtable: no visible global function definition for ‘across’
readPepXMLtable: no visible global function definition for ‘all_of’
readPepXMLtable: no visible binding for global variable
‘DatabaseAccess’
readPepXMLtable: no visible binding for global variable
‘DatabaseDescription’
summaryPSMsipPCT: no visible global function definition for
‘read.table’
summaryPSMsipPCT: no visible global function definition for ‘median’
summaryPSMsipPCT: no visible global function definition for ‘mad’
summaryPSMsipPCT: no visible global function definition for ‘sd’
summary_isotopic_df: no visible global function definition for ‘desc’
summary_isotopic_df: no visible binding for global variable ‘Count’
plot,AAspectra-missing: no visible binding for global variable ‘MZ’
plot,AAspectra-missing: no visible binding for global variable ‘Prob’
plot,AAspectra-missing: no visible binding for global variable ‘Kind’
Undefined global functions or variables:
Abundance Count DatabaseAccess DatabaseDescription Formula Frequency
IsDecoy Kind Label MS1IsotopicAbundances MZ MassError Prob
RelativeTic RetentionTime across all_of desc fft head log2_intensity
mad median mz new parentCharges read.table rmultinom scores sd time
topo.colors x y
Consider adding
importFrom("grDevices", "topo.colors")
importFrom("methods", "new")
importFrom("stats", "fft", "mad", "median", "rmultinom", "sd", "time")
importFrom("utils", "head", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'plotRealScan.Rd':
‘linewidth’
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck/00check.log’
for details.
Aerith.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Aerith
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/4.6/Resources/library/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)
Aerith.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Aerith)
>
> test_check("Aerith")
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/ft/Pan_052322_X13.FT1"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/ft/Pan_052322_X13.FT1"
[3] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/ft/Pan_052322_X13.FT1"
[3] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
size isdir
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin 108722 FALSE
mode
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin 644
mtime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin 2026-04-24 18:19:53
ctime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin 2026-04-24 18:19:53
atime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin 2026-04-24 18:19:53
uid gid
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin 506 20
uname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin biocbuild
grname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/a.pin staff
Mass Prob
1 591.2976 7.416425e-01
2 592.3003 2.074472e-01
3 593.3026 4.325137e-02
4 594.3049 6.688482e-03
5 595.3072 8.669610e-04
6 596.3094 9.518739e-05
7 597.3117 8.284068e-06
$`HK~FL`
C H O N P S Kind BaseMass
1 6 7 1 3 0 0 B1 137.0589
2 12 19 3 5 0 0 B2 281.1488
3 21 28 4 6 0 0 B3 428.2172
4 6 13 2 1 0 0 Y1 131.0946
5 15 22 3 2 0 0 Y2 278.1630
6 21 34 5 4 0 0 Y3 422.2529
Mass Prob
1 591.2976 7.416425e-01
2 592.3003 2.074472e-01
3 593.3026 4.325137e-02
4 594.3049 6.688482e-03
5 595.3072 8.669610e-04
6 596.3094 9.518739e-05
7 597.3117 8.284068e-06
size
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 55027
isdir
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv FALSE
mode
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 644
mtime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 2026-04-24 18:19:53
ctime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 2026-04-24 18:19:53
atime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 2026-04-24 18:19:53
uid
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 506
gid
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv 20
uname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv biocbuild
grname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXqc51h/sip/top3.tsv staff
MVHscore XcorrScore WDPscore
212.400813 5.613975 108.651828
WDPscore
120.7406
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 25 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 25 ]
>
> proc.time()
user system elapsed
0.975 0.107 1.089
Aerith.Rcheck/Aerith-Ex.timings
| name | user | system | elapsed | |
| AAspectra-class | 0.006 | 0.000 | 0.006 | |
| BYion_peak_calculator_DIY | 0.001 | 0.001 | 0.002 | |
| annotatePSM | 0.004 | 0.001 | 0.006 | |
| annotatePrecursor | 0.002 | 0.001 | 0.003 | |
| calBYAtomCountAndBaseMass | 0.001 | 0.000 | 0.002 | |
| calPepAtomCount | 0.001 | 0.001 | 0.001 | |
| calPepNeutronMass | 0.001 | 0.000 | 0.001 | |
| calPepPrecursorMass | 0.001 | 0.000 | 0.001 | |
| cal_isotope_numbers | 0.161 | 0.002 | 0.165 | |
| cal_isotope_numbers_SIP | 0.389 | 0.003 | 0.397 | |
| cal_isotope_peaks_fft | 0.001 | 0.000 | 0.001 | |
| denoiseOneMS2ScanHasCharge | 0.358 | 0.008 | 0.368 | |
| extractPSMfeatures | 0.045 | 0.005 | 0.051 | |
| extractPSMfeaturesTargetAndDecoy | 0.045 | 0.005 | 0.051 | |
| extractPSMfeaturesTargetAndDecoytoPercolatorPin | 0.045 | 0.006 | 0.051 | |
| generateCFGs | 0.002 | 0.013 | 0.015 | |
| generateOneCFG | 0.001 | 0.001 | 0.003 | |
| getFilterThreshold | 0.006 | 0.001 | 0.007 | |
| getFilterThresholdTopPSMs | 0.007 | 0.000 | 0.008 | |
| getFilterThresholdTopPSMsSpe2Pep | 0.002 | 0.002 | 0.004 | |
| getMZ | 0.001 | 0.000 | 0.001 | |
| getPrecursorSpectra | 0.002 | 0.001 | 0.002 | |
| getRealScan | 0.115 | 0.001 | 0.117 | |
| getRealScanFromList | 0.111 | 0.002 | 0.112 | |
| getRealScanWithCharge | 0.051 | 0.001 | 0.052 | |
| getRealScans | 0.002 | 0.001 | 0.004 | |
| getRealScansWithCharges | 0.002 | 0.000 | 0.002 | |
| getRetentionTimeAndPrecursorInfo | 0.146 | 0.008 | 0.157 | |
| getSipBYionSpectra | 0.005 | 0.001 | 0.005 | |
| getSipPrecursorSpectra | 0.001 | 0.001 | 0.002 | |
| getTIC | 0.046 | 0.000 | 0.047 | |
| getUnfilteredPSMs | 0.008 | 0.000 | 0.008 | |
| getUnfilteredPeptides | 0.003 | 0.000 | 0.004 | |
| plot-AAspectra | 0.099 | 0.001 | 0.102 | |
| plotMolecularFFTisotopes | 0.054 | 0.000 | 0.055 | |
| plotMolecularIsotopes | 0.357 | 0.003 | 0.363 | |
| plotPSMannotation | 0.309 | 0.003 | 0.313 | |
| plotPSMs | 1.431 | 0.014 | 1.453 | |
| plotPSMsipPCT | 0.081 | 0.002 | 0.084 | |
| plotPrecursorAnnotation | 0.128 | 0.001 | 0.129 | |
| plotPrecursorMzFrequency | 0.172 | 0.002 | 0.174 | |
| plotProSipPct | 0.072 | 0.002 | 0.084 | |
| plotRealScan | 0.938 | 0.004 | 0.950 | |
| plotScanFrequency | 0.282 | 0.006 | 0.287 | |
| plotScanFrequencyMS2 | 0.222 | 0.007 | 0.233 | |
| plotScoreDistribution | 0.157 | 0.004 | 0.163 | |
| plotSipBYionLabel | 0.272 | 0.002 | 0.273 | |
| plotTIC | 0.105 | 0.002 | 0.109 | |
| precursor_peak_calculator | 0.001 | 0.000 | 0.001 | |
| precursor_peak_calculator_DIY | 0.001 | 0.000 | 0.001 | |
| precursor_peak_calculator_DIY_averagine | 0.000 | 0.001 | 0.001 | |
| rankyfify | 0 | 0 | 0 | |
| readAllScanMS1 | 0.073 | 0.005 | 0.082 | |
| readAllScanMS2 | 0.050 | 0.001 | 0.050 | |
| readFTheader | 0.035 | 0.004 | 0.040 | |
| readFilesScansTopPSMs | 0.004 | 0.000 | 0.005 | |
| readFilesScansTopPSMsFromOneFT2 | 0.005 | 0.001 | 0.005 | |
| readMgf | 4.820 | 0.132 | 4.997 | |
| readMzmlMS1 | 0.011 | 0.001 | 0.013 | |
| readMzmlMS2 | 0.005 | 0.001 | 0.006 | |
| readOneScanMS1 | 0.056 | 0.006 | 0.065 | |
| readOneScanMS2 | 0.005 | 0.001 | 0.006 | |
| readPSMtsv | 0.012 | 0.001 | 0.014 | |
| readPepXMLtable | 0.044 | 0.001 | 0.046 | |
| readScansMS1 | 0.046 | 0.004 | 0.051 | |
| readScansMS1Vector | 0.039 | 0.004 | 0.044 | |
| readScansMS2 | 0.002 | 0.001 | 0.002 | |
| readScansMS2Vector | 0.001 | 0.000 | 0.002 | |
| readSip | 0.004 | 0.001 | 0.005 | |
| readSips | 0.004 | 0.001 | 0.005 | |
| readSpe2Pep | 0.002 | 0.000 | 0.002 | |
| readSpe2PepFilesScansTopPSMs | 0.003 | 0.001 | 0.004 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.002 | 0.001 | 0.003 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel | 0.002 | 0.000 | 0.004 | |
| readSpe2PepFilesScansTopPSMsFromOneFT2 | 0.003 | 0.000 | 0.003 | |
| readSpe2Peps | 0.005 | 0.001 | 0.006 | |
| residue_peak_calculator_DIY | 0.001 | 0.000 | 0.002 | |
| scoreIntensity | 0.001 | 0.000 | 0.001 | |
| scoreIntensityByCE | 0.000 | 0.000 | 0.001 | |
| scorePSM | 0.005 | 0.000 | 0.005 | |
| scorePSMsimple | 0.006 | 0.000 | 0.006 | |
| summaryPSMsipPCT | 0.011 | 0.001 | 0.012 | |
| writeAllScanMS1 | 0.085 | 0.006 | 0.092 | |
| writeAllScanMS2 | 0.049 | 0.001 | 0.050 | |
| writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.003 | 0.001 | 0.004 | |