Yi Xiong
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/Aerith |
| git_branch: devel |
| git_last_commit: 562352c |
| git_last_commit_date: 2026-05-04 22:26:53 -0400 (Mon, 04 May 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 22/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Aerith 1.1.1 (landing page) Yi Xiong
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Aerith |
| Version: 1.1.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Aerith.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Aerith_1.1.1.tar.gz |
| StartedAt: 2026-05-05 07:07:47 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 07:10:06 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 139.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Aerith.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Aerith.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Aerith_1.1.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/Aerith.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Aerith/DESCRIPTION’ ... OK
* this is package ‘Aerith’ version ‘1.1.1’
* 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 ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 35.1Mb
sub-directories of 1Mb or more:
extdata 5.2Mb
libs 27.9Mb
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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 binding for global variable ‘Prob’
plotMolecularIsotopes: no visible binding for global variable ‘Formula’
plotPrecursorMzFrequency: no visible binding for global variable ‘mz’
plotPrecursorMzFrequency: no visible binding for global variable
‘Frequency’
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’
readPepXMLtable: no visible binding for global variable
‘DatabaseAccess’
readPepXMLtable: no visible binding for global variable
‘DatabaseDescription’
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 log2_intensity mz parentCharges scores x y
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readMgf 14.021 0.511 14.574
plotPSMs 4.963 0.060 5.036
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.24-bioc/meat/Aerith.Rcheck/00check.log’
for details.
Aerith.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Aerith ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘Aerith’ ... ** this is package ‘Aerith’ version ‘1.1.1’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++17 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c extractPSMfeatures.cpp -o extractPSMfeatures.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c filterPSMs.cpp -o filterPSMs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c filterPeptides.cpp -o filterPeptides.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c generateCFG.cpp -o generateCFG.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c getISOpeak.cpp -o getISOpeak.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c readScan.cpp -o readScan.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c readScans.cpp -o readScans.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c readSips.cpp -o readSips.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c readSpe2Peps.cpp -o readSpe2Peps.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c scorePSM.cpp -o scorePSM.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c writeScans.cpp -o writeScans.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/PSMfeatureExtractor.cpp -o lib/PSMfeatureExtractor.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/PSMpeakAnnotator.cpp -o lib/PSMpeakAnnotator.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/PSMsFiltrator.cpp -o lib/PSMsFiltrator.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/Spe2PepFileReader.cpp -o lib/Spe2PepFileReader.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/averagine.cpp -o lib/averagine.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/cfgParser.cpp -o lib/cfgParser.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/ftFileReader.cpp -o lib/ftFileReader.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/ftFileWriter.cpp -o lib/ftFileWriter.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/isotopologue.cpp -o lib/isotopologue.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/ms2scan.cpp -o lib/ms2scan.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/peptide.cpp -o lib/peptide.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/peptidesFiltrator.cpp -o lib/peptidesFiltrator.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/proNovoConfig.cpp -o lib/proNovoConfig.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/sipFileReader.cpp -o lib/sipFileReader.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/sipGenerator.cpp -o lib/sipGenerator.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I. -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c lib/sipPSM.cpp -o lib/sipPSM.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/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 -fopenmp -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
R is a collaborative project with many contributors.
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] "/home/biocbuild/tmp/RtmpY0YPrs/ft/Pan_052322_X13.FT1"
[2] "/home/biocbuild/tmp/RtmpY0YPrs/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/home/biocbuild/tmp/RtmpY0YPrs/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/home/biocbuild/tmp/RtmpY0YPrs/ft/Pan_052322_X13.FT1"
[3] "/home/biocbuild/tmp/RtmpY0YPrs/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/home/biocbuild/tmp/RtmpY0YPrs/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/home/biocbuild/tmp/RtmpY0YPrs/ft/Pan_052322_X13.FT1"
[3] "/home/biocbuild/tmp/RtmpY0YPrs/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
size isdir mode mtime
/home/biocbuild/tmp/RtmpY0YPrs/a.pin 108722 FALSE 644 2026-05-05 07:10:00
ctime atime
/home/biocbuild/tmp/RtmpY0YPrs/a.pin 2026-05-05 07:10:00 2026-05-05 07:10:00
uid gid uname grname
/home/biocbuild/tmp/RtmpY0YPrs/a.pin 1001 1001 biocbuild biocbuild
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 isdir mode
/home/biocbuild/tmp/RtmpY0YPrs/sip/top3.tsv 55014 FALSE 644
mtime
/home/biocbuild/tmp/RtmpY0YPrs/sip/top3.tsv 2026-05-05 07:10:00
ctime
/home/biocbuild/tmp/RtmpY0YPrs/sip/top3.tsv 2026-05-05 07:10:00
atime uid gid
/home/biocbuild/tmp/RtmpY0YPrs/sip/top3.tsv 2026-05-05 07:10:00 1001 1001
uname grname
/home/biocbuild/tmp/RtmpY0YPrs/sip/top3.tsv biocbuild biocbuild
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
2.668 0.250 2.909
Aerith.Rcheck/Aerith-Ex.timings
| name | user | system | elapsed | |
| AAspectra-class | 0.005 | 0.004 | 0.012 | |
| BYion_peak_calculator_DIY | 0.003 | 0.002 | 0.005 | |
| annotatePSM | 0.012 | 0.000 | 0.015 | |
| annotatePrecursor | 0.003 | 0.000 | 0.004 | |
| calBYAtomCountAndBaseMass | 0.004 | 0.000 | 0.004 | |
| calPepAtomCount | 0.003 | 0.000 | 0.002 | |
| calPepNeutronMass | 0.002 | 0.000 | 0.002 | |
| calPepPrecursorMass | 0.002 | 0.000 | 0.002 | |
| cal_isotope_numbers | 0.702 | 0.016 | 0.721 | |
| cal_isotope_numbers_SIP | 1.725 | 0.020 | 1.751 | |
| cal_isotope_peaks_fft | 0.006 | 0.000 | 0.006 | |
| denoiseOneMS2ScanHasCharge | 1.242 | 0.016 | 1.265 | |
| extractPSMfeatures | 0.104 | 0.004 | 0.110 | |
| extractPSMfeaturesTargetAndDecoy | 0.105 | 0.000 | 0.107 | |
| extractPSMfeaturesTargetAndDecoytoPercolatorPin | 0.104 | 0.004 | 0.108 | |
| generateCFGs | 0.003 | 0.004 | 0.007 | |
| generateOneCFG | 0.002 | 0.000 | 0.003 | |
| getFilterThreshold | 0.011 | 0.000 | 0.014 | |
| getFilterThresholdTopPSMs | 0.022 | 0.000 | 0.022 | |
| getFilterThresholdTopPSMsSpe2Pep | 0.013 | 0.000 | 0.012 | |
| getMZ | 0.002 | 0.000 | 0.002 | |
| getPrecursorSpectra | 0.006 | 0.000 | 0.006 | |
| getRealScan | 0.539 | 0.036 | 0.576 | |
| getRealScanFromList | 0.643 | 0.008 | 0.652 | |
| getRealScanWithCharge | 0.206 | 0.004 | 0.211 | |
| getRealScans | 0.007 | 0.000 | 0.010 | |
| getRealScansWithCharges | 0.007 | 0.000 | 0.007 | |
| getRetentionTimeAndPrecursorInfo | 0.446 | 0.004 | 0.453 | |
| getSipBYionSpectra | 0.015 | 0.000 | 0.014 | |
| getSipPrecursorSpectra | 0.005 | 0.000 | 0.005 | |
| getTIC | 0.214 | 0.000 | 0.215 | |
| getUnfilteredPSMs | 0.025 | 0.000 | 0.025 | |
| getUnfilteredPeptides | 0.012 | 0.000 | 0.012 | |
| plot-AAspectra | 0.442 | 0.000 | 0.443 | |
| plotMolecularFFTisotopes | 0.271 | 0.012 | 0.283 | |
| plotMolecularIsotopes | 1.623 | 0.004 | 1.632 | |
| plotPSMannotation | 1.396 | 0.004 | 1.403 | |
| plotPSMs | 4.963 | 0.060 | 5.036 | |
| plotPSMsipPCT | 0.354 | 0.016 | 0.371 | |
| plotPrecursorAnnotation | 0.612 | 0.004 | 0.618 | |
| plotPrecursorMzFrequency | 0.651 | 0.000 | 0.652 | |
| plotProSipPct | 0.326 | 0.000 | 0.329 | |
| plotRealScan | 2.219 | 0.000 | 2.224 | |
| plotScanFrequency | 1.305 | 0.004 | 1.312 | |
| plotScanFrequencyMS2 | 0.960 | 0.016 | 0.979 | |
| plotScoreDistribution | 0.803 | 0.003 | 0.809 | |
| plotSipBYionLabel | 1.423 | 0.000 | 1.426 | |
| plotTIC | 0.533 | 0.001 | 0.536 | |
| precursor_peak_calculator | 0.002 | 0.000 | 0.003 | |
| precursor_peak_calculator_DIY | 0.004 | 0.000 | 0.004 | |
| precursor_peak_calculator_DIY_averagine | 0.003 | 0.000 | 0.003 | |
| rankyfify | 0 | 0 | 0 | |
| readAllScanMS1 | 0.241 | 0.007 | 0.250 | |
| readAllScanMS2 | 0.267 | 0.000 | 0.268 | |
| readFTheader | 0.086 | 0.004 | 0.090 | |
| readFilesScansTopPSMs | 0.012 | 0.004 | 0.016 | |
| readFilesScansTopPSMsFromOneFT2 | 0.017 | 0.000 | 0.018 | |
| readMgf | 14.021 | 0.511 | 14.574 | |
| readMzmlMS1 | 0.034 | 0.004 | 0.039 | |
| readMzmlMS2 | 0.018 | 0.000 | 0.018 | |
| readOneScanMS1 | 0.094 | 0.004 | 0.098 | |
| readOneScanMS2 | 0.001 | 0.002 | 0.003 | |
| readPSMtsv | 0.028 | 0.001 | 0.028 | |
| readPepXMLtable | 0.076 | 0.004 | 0.083 | |
| readScansMS1 | 0.096 | 0.004 | 0.100 | |
| readScansMS1Vector | 0.082 | 0.004 | 0.086 | |
| readScansMS2 | 0.007 | 0.000 | 0.008 | |
| readScansMS2Vector | 0.005 | 0.000 | 0.005 | |
| readSip | 0.011 | 0.000 | 0.010 | |
| readSips | 0.01 | 0.00 | 0.01 | |
| readSpe2Pep | 0.006 | 0.000 | 0.006 | |
| readSpe2PepFilesScansTopPSMs | 0.009 | 0.000 | 0.010 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.010 | 0.000 | 0.011 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel | 0.011 | 0.000 | 0.012 | |
| readSpe2PepFilesScansTopPSMsFromOneFT2 | 0.01 | 0.00 | 0.01 | |
| readSpe2Peps | 0.013 | 0.000 | 0.013 | |
| residue_peak_calculator_DIY | 0.002 | 0.000 | 0.003 | |
| scoreIntensity | 0.002 | 0.000 | 0.002 | |
| scoreIntensityByCE | 0 | 0 | 0 | |
| scorePSM | 0.016 | 0.000 | 0.016 | |
| scorePSMsimple | 0.016 | 0.000 | 0.016 | |
| summaryPSMsipPCT | 0.034 | 0.000 | 0.034 | |
| writeAllScanMS1 | 0.242 | 0.008 | 0.250 | |
| writeAllScanMS2 | 0.213 | 0.008 | 0.222 | |
| writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.012 | 0.000 | 0.011 | |