Yi Xiong
| Snapshot Date: 2026-04-29 13:40 -0400 (Wed, 29 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/Aerith |
| git_branch: RELEASE_3_23 |
| git_last_commit: 676c6b9 |
| git_last_commit_date: 2026-04-28 09:06:02 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-30 11:35 -0400 (Thu, 30 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" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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 22/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Aerith 1.0.0 (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 | 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. |
| Package: Aerith |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2026-04-29 18:21:48 -0400 (Wed, 29 Apr 2026) |
| EndedAt: 2026-04-29 18:22:29 -0400 (Wed, 29 Apr 2026) |
| EllapsedTime: 41.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Aerith.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-04-29 22:21:48 UTC
* using option ‘--no-vignettes’
* checking for file ‘Aerith/DESCRIPTION’ ... OK
* this is package ‘Aerith’ version ‘1.0.0’
* 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: ‘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 ... 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 ... 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck/00check.log’
for details.
Aerith.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Aerith ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘Aerith’ ... ** this is package ‘Aerith’ version ‘1.0.0’ ** 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 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 Patched (2026-04-24 r89963) -- "Because it was There"
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.
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] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/ft/Pan_052322_X13.FT1"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/ft/Pan_052322_X13.FT1"
[3] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/ft/Pan_052322_X13.FT1"
[3] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
size isdir
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin 108722 FALSE
mode
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin 644
mtime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin 2026-04-29 18:22:24
ctime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin 2026-04-29 18:22:24
atime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin 2026-04-29 18:22:24
uid gid
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin 506 20
uname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/a.pin biocbuild
grname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/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//Rtmp2aTzKj/sip/top3.tsv 55027
isdir
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv FALSE
mode
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv 644
mtime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv 2026-04-29 18:22:24
ctime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv 2026-04-29 18:22:24
atime
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv 2026-04-29 18:22:24
uid
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv 506
gid
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv 20
uname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/sip/top3.tsv biocbuild
grname
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2aTzKj/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
0.933 0.115 1.055
Aerith.Rcheck/Aerith-Ex.timings
| name | user | system | elapsed | |
| AAspectra-class | 0.003 | 0.000 | 0.003 | |
| BYion_peak_calculator_DIY | 0.002 | 0.000 | 0.002 | |
| annotatePSM | 0.004 | 0.001 | 0.005 | |
| annotatePrecursor | 0.001 | 0.001 | 0.001 | |
| calBYAtomCountAndBaseMass | 0.001 | 0.000 | 0.002 | |
| calPepAtomCount | 0.001 | 0.000 | 0.001 | |
| calPepNeutronMass | 0.001 | 0.001 | 0.001 | |
| calPepPrecursorMass | 0.000 | 0.000 | 0.001 | |
| cal_isotope_numbers | 0.165 | 0.002 | 0.166 | |
| cal_isotope_numbers_SIP | 0.415 | 0.005 | 0.421 | |
| cal_isotope_peaks_fft | 0.001 | 0.000 | 0.002 | |
| denoiseOneMS2ScanHasCharge | 0.288 | 0.005 | 0.294 | |
| extractPSMfeatures | 0.046 | 0.005 | 0.051 | |
| extractPSMfeaturesTargetAndDecoy | 0.044 | 0.005 | 0.050 | |
| extractPSMfeaturesTargetAndDecoytoPercolatorPin | 0.045 | 0.004 | 0.051 | |
| generateCFGs | 0.002 | 0.012 | 0.015 | |
| generateOneCFG | 0.001 | 0.001 | 0.002 | |
| getFilterThreshold | 0.003 | 0.001 | 0.005 | |
| getFilterThresholdTopPSMs | 0.007 | 0.001 | 0.007 | |
| getFilterThresholdTopPSMsSpe2Pep | 0.003 | 0.001 | 0.004 | |
| getMZ | 0.000 | 0.000 | 0.001 | |
| getPrecursorSpectra | 0.001 | 0.000 | 0.002 | |
| getRealScan | 0.120 | 0.001 | 0.121 | |
| getRealScanFromList | 0.110 | 0.001 | 0.112 | |
| getRealScanWithCharge | 0.051 | 0.001 | 0.052 | |
| getRealScans | 0.003 | 0.000 | 0.002 | |
| getRealScansWithCharges | 0.002 | 0.000 | 0.002 | |
| getRetentionTimeAndPrecursorInfo | 0.149 | 0.010 | 0.166 | |
| getSipBYionSpectra | 0.004 | 0.001 | 0.005 | |
| getSipPrecursorSpectra | 0.001 | 0.001 | 0.002 | |
| getTIC | 0.060 | 0.000 | 0.072 | |
| getUnfilteredPSMs | 0.007 | 0.001 | 0.008 | |
| getUnfilteredPeptides | 0.003 | 0.000 | 0.004 | |
| plot-AAspectra | 0.099 | 0.000 | 0.100 | |
| plotMolecularFFTisotopes | 0.064 | 0.000 | 0.064 | |
| plotMolecularIsotopes | 0.401 | 0.002 | 0.403 | |
| plotPSMannotation | 0.263 | 0.001 | 0.265 | |
| plotPSMs | 1.509 | 0.008 | 1.519 | |
| plotPSMsipPCT | 0.086 | 0.001 | 0.087 | |
| plotPrecursorAnnotation | 0.134 | 0.001 | 0.135 | |
| plotPrecursorMzFrequency | 0.170 | 0.002 | 0.171 | |
| plotProSipPct | 0.080 | 0.001 | 0.084 | |
| plotRealScan | 0.899 | 0.002 | 0.903 | |
| plotScanFrequency | 0.381 | 0.008 | 0.391 | |
| plotScanFrequencyMS2 | 0.265 | 0.007 | 0.279 | |
| plotScoreDistribution | 0.201 | 0.002 | 0.205 | |
| plotSipBYionLabel | 0.363 | 0.003 | 0.370 | |
| plotTIC | 0.095 | 0.001 | 0.096 | |
| precursor_peak_calculator | 0.001 | 0.000 | 0.001 | |
| precursor_peak_calculator_DIY | 0.001 | 0.001 | 0.001 | |
| precursor_peak_calculator_DIY_averagine | 0.001 | 0.000 | 0.002 | |
| rankyfify | 0 | 0 | 0 | |
| readAllScanMS1 | 0.076 | 0.005 | 0.082 | |
| readAllScanMS2 | 0.052 | 0.001 | 0.052 | |
| readFTheader | 0.036 | 0.004 | 0.040 | |
| readFilesScansTopPSMs | 0.004 | 0.001 | 0.005 | |
| readFilesScansTopPSMsFromOneFT2 | 0.004 | 0.000 | 0.005 | |
| readMgf | 4.772 | 0.117 | 4.896 | |
| readMzmlMS1 | 0.011 | 0.002 | 0.013 | |
| readMzmlMS2 | 0.006 | 0.001 | 0.007 | |
| readOneScanMS1 | 0.053 | 0.006 | 0.060 | |
| readOneScanMS2 | 0.003 | 0.001 | 0.004 | |
| readPSMtsv | 0.012 | 0.001 | 0.012 | |
| readPepXMLtable | 0.024 | 0.002 | 0.026 | |
| readScansMS1 | 0.043 | 0.006 | 0.049 | |
| readScansMS1Vector | 0.041 | 0.005 | 0.045 | |
| readScansMS2 | 0.002 | 0.001 | 0.002 | |
| readScansMS2Vector | 0.001 | 0.000 | 0.002 | |
| readSip | 0.028 | 0.001 | 0.030 | |
| readSips | 0.004 | 0.001 | 0.004 | |
| readSpe2Pep | 0.002 | 0.000 | 0.002 | |
| readSpe2PepFilesScansTopPSMs | 0.002 | 0.000 | 0.003 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.003 | 0.000 | 0.003 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel | 0.002 | 0.001 | 0.004 | |
| readSpe2PepFilesScansTopPSMsFromOneFT2 | 0.002 | 0.000 | 0.002 | |
| readSpe2Peps | 0.004 | 0.000 | 0.005 | |
| residue_peak_calculator_DIY | 0.000 | 0.001 | 0.002 | |
| scoreIntensity | 0.000 | 0.000 | 0.001 | |
| scoreIntensityByCE | 0 | 0 | 0 | |
| scorePSM | 0.005 | 0.001 | 0.006 | |
| scorePSMsimple | 0.006 | 0.000 | 0.006 | |
| summaryPSMsipPCT | 0.010 | 0.001 | 0.011 | |
| writeAllScanMS1 | 0.090 | 0.007 | 0.097 | |
| writeAllScanMS2 | 0.049 | 0.002 | 0.050 | |
| writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.003 | 0.001 | 0.004 | |