Yi Xiong
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/Aerith |
| git_branch: devel |
| git_last_commit: 4583495 |
| git_last_commit_date: 2025-11-12 04:06:43 -0500 (Wed, 12 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-04 11:34 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 22/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Aerith 0.99.11 (landing page) Yi Xiong
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 0.99.11 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Aerith.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Aerith_0.99.11.tar.gz |
| StartedAt: 2025-12-03 21:06:24 -0500 (Wed, 03 Dec 2025) |
| EndedAt: 2025-12-03 21:12:25 -0500 (Wed, 03 Dec 2025) |
| EllapsedTime: 361.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Aerith.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Aerith.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Aerith_0.99.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Aerith/DESCRIPTION’ ... OK
* this is package ‘Aerith’ version ‘0.99.11’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 20.1Mb
sub-directories of 1Mb or more:
extdata 4.1Mb
libs 14.1Mb
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 ... 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’
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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* 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
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/Aerith/libs/Aerith.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘exit’, possibly from ‘exit’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readMgf 10.478 0.511 10.992
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/Aerith.Rcheck/00check.log’
for details.
Aerith.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Aerith ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘Aerith’ ... ** this is package ‘Aerith’ version ‘0.99.11’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c extractPSMfeatures.cpp -o extractPSMfeatures.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c filterPSMs.cpp -o filterPSMs.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c filterPeptides.cpp -o filterPeptides.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c generateCFG.cpp -o generateCFG.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c getISOpeak.cpp -o getISOpeak.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c readScan.cpp -o readScan.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c readScans.cpp -o readScans.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c readSips.cpp -o readSips.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c readSpe2Peps.cpp -o readSpe2Peps.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c scorePSM.cpp -o scorePSM.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c writeScans.cpp -o writeScans.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/PSMfeatureExtractor.cpp -o lib/PSMfeatureExtractor.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/PSMpeakAnnotator.cpp -o lib/PSMpeakAnnotator.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/PSMsFiltrator.cpp -o lib/PSMsFiltrator.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/Spe2PepFileReader.cpp -o lib/Spe2PepFileReader.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/averagine.cpp -o lib/averagine.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/cfgParser.cpp -o lib/cfgParser.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/ftFileReader.cpp -o lib/ftFileReader.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/ftFileWriter.cpp -o lib/ftFileWriter.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/isotopologue.cpp -o lib/isotopologue.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/ms2scan.cpp -o lib/ms2scan.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/peptide.cpp -o lib/peptide.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/peptidesFiltrator.cpp -o lib/peptidesFiltrator.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/proNovoConfig.cpp -o lib/proNovoConfig.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/sipFileReader.cpp -o lib/sipFileReader.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/sipGenerator.cpp -o lib/sipGenerator.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c lib/sipPSM.cpp -o lib/sipPSM.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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Type 'license()' or 'licence()' for distribution details.
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> library(testthat)
> library(Aerith)
>
> test_check("Aerith")
[1] "/tmp/Rtmpi5bfLR/ft/Pan_052322_X13.FT1"
[2] "/tmp/Rtmpi5bfLR/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/tmp/Rtmpi5bfLR/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/tmp/Rtmpi5bfLR/ft/Pan_052322_X13.FT1"
[3] "/tmp/Rtmpi5bfLR/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[1] "/tmp/Rtmpi5bfLR/decoy/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
[2] "/tmp/Rtmpi5bfLR/ft/Pan_052322_X13.FT1"
[3] "/tmp/Rtmpi5bfLR/target/Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"
size isdir mode mtime ctime
/tmp/Rtmpi5bfLR/a.pin 108751 FALSE 664 2025-12-03 21:11:01 2025-12-03 21:11:01
atime uid gid uname grname
/tmp/Rtmpi5bfLR/a.pin 2025-12-03 21:11:01 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 mtime
/tmp/Rtmpi5bfLR/sip/top3.tsv 55027 FALSE 664 2025-12-03 21:11:01
ctime atime uid gid
/tmp/Rtmpi5bfLR/sip/top3.tsv 2025-12-03 21:11:01 2025-12-03 21:11:01 1001 1001
uname grname
/tmp/Rtmpi5bfLR/sip/top3.tsv biocbuild biocbuild
MVHscore XcorrScore WDPscore
212.464027 5.356034 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
2.188 0.137 2.202
Aerith.Rcheck/Aerith-Ex.timings
| name | user | system | elapsed | |
| AAspectra-class | 0.004 | 0.000 | 0.005 | |
| BYion_peak_calculator_DIY | 0.003 | 0.000 | 0.004 | |
| annotatePSM | 0.010 | 0.002 | 0.012 | |
| calBYAtomCountAndBaseMass | 0.002 | 0.000 | 0.003 | |
| calPepAtomCount | 0.002 | 0.000 | 0.002 | |
| calPepNeutronMass | 0.000 | 0.001 | 0.001 | |
| calPepPrecursorMass | 0.001 | 0.000 | 0.001 | |
| cal_isotope_numbers | 0.396 | 0.006 | 0.401 | |
| cal_isotope_numbers_SIP | 1.131 | 0.032 | 1.162 | |
| cal_isotope_peaks_fft | 0.003 | 0.000 | 0.005 | |
| denoiseOneMS2ScanHasCharge | 0.931 | 0.025 | 0.959 | |
| extractPSMfeatures | 0.110 | 0.007 | 0.108 | |
| extractPSMfeaturesTargetAndDecoy | 0.116 | 0.002 | 0.102 | |
| extractPSMfeaturesTargetAndDecoytoPercolatorPin | 0.117 | 0.005 | 0.102 | |
| generateCFGs | 0.005 | 0.004 | 0.007 | |
| generateOneCFG | 0.001 | 0.002 | 0.003 | |
| getFilterThreshold | 0.009 | 0.000 | 0.011 | |
| getFilterThresholdTopPSMs | 0.017 | 0.000 | 0.017 | |
| getFilterThresholdTopPSMsSpe2Pep | 0.015 | 0.002 | 0.010 | |
| getMZ | 0.004 | 0.000 | 0.002 | |
| getPrecursorSpectra | 0.008 | 0.001 | 0.005 | |
| getRealScan | 0.320 | 0.004 | 0.324 | |
| getRealScanFromList | 0.31 | 0.00 | 0.31 | |
| getRealScanWithCharge | 0.132 | 0.002 | 0.133 | |
| getRealScans | 0.006 | 0.000 | 0.006 | |
| getRealScansWithCharges | 0.005 | 0.000 | 0.005 | |
| getRetentionTimeAndPrecursorInfo | 0.331 | 0.015 | 0.347 | |
| getSipBYionSpectra | 0.009 | 0.002 | 0.011 | |
| getSipPrecursorSpectra | 0.002 | 0.003 | 0.005 | |
| getTIC | 0.139 | 0.000 | 0.139 | |
| getUnfilteredPSMs | 0.018 | 0.001 | 0.019 | |
| getUnfilteredPeptides | 0.008 | 0.000 | 0.008 | |
| plot-AAspectra | 0.260 | 0.001 | 0.261 | |
| plotMolecularFFTisotopes | 0.153 | 0.000 | 0.153 | |
| plotMolecularIsotopes | 1.011 | 0.050 | 1.061 | |
| plotPSMannotation | 0.939 | 0.004 | 0.943 | |
| plotPSMs | 3.495 | 0.037 | 3.535 | |
| plotPSMsipPCT | 0.306 | 0.003 | 0.309 | |
| plotPrecursorMzFrequency | 0.435 | 0.002 | 0.437 | |
| plotProSipPct | 0.184 | 0.003 | 0.189 | |
| plotRealScan | 1.558 | 0.010 | 1.568 | |
| plotScanFrequency | 0.757 | 0.042 | 0.801 | |
| plotScanFrequencyMS2 | 0.530 | 0.004 | 0.534 | |
| plotScoreDistribution | 0.422 | 0.000 | 0.423 | |
| plotSipBYionLabel | 0.920 | 0.003 | 0.923 | |
| plotTIC | 0.272 | 0.000 | 0.272 | |
| precursor_peak_calculator | 0.001 | 0.000 | 0.002 | |
| precursor_peak_calculator_DIY | 0.002 | 0.001 | 0.003 | |
| precursor_peak_calculator_DIY_averagine | 0.003 | 0.000 | 0.002 | |
| rankyfify | 0.001 | 0.000 | 0.000 | |
| readAllScanMS1 | 0.182 | 0.002 | 0.184 | |
| readAllScanMS2 | 0.124 | 0.001 | 0.125 | |
| readFTheader | 0.073 | 0.001 | 0.074 | |
| readFilesScansTopPSMs | 0.012 | 0.001 | 0.013 | |
| readFilesScansTopPSMsFromOneFT2 | 0.017 | 0.001 | 0.018 | |
| readMgf | 10.478 | 0.511 | 10.992 | |
| readMzmlMS1 | 0.024 | 0.007 | 0.032 | |
| readMzmlMS2 | 0.011 | 0.002 | 0.013 | |
| readOneScanMS1 | 0.125 | 0.005 | 0.130 | |
| readOneScanMS2 | 0.003 | 0.000 | 0.003 | |
| readPSMtsv | 0.017 | 0.003 | 0.020 | |
| readPepXMLtable | 0.054 | 0.002 | 0.056 | |
| readScansMS1 | 0.085 | 0.004 | 0.088 | |
| readScansMS1Vector | 0.074 | 0.004 | 0.078 | |
| readScansMS2 | 0.004 | 0.001 | 0.005 | |
| readScansMS2Vector | 0.003 | 0.001 | 0.004 | |
| readSip | 0.009 | 0.000 | 0.009 | |
| readSips | 0.007 | 0.001 | 0.008 | |
| readSpe2Pep | 0.004 | 0.001 | 0.005 | |
| readSpe2PepFilesScansTopPSMs | 0.005 | 0.003 | 0.008 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.012 | 0.001 | 0.008 | |
| readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel | 0.018 | 0.002 | 0.010 | |
| readSpe2PepFilesScansTopPSMsFromOneFT2 | 0.016 | 0.000 | 0.008 | |
| readSpe2Peps | 0.009 | 0.002 | 0.009 | |
| residue_peak_calculator_DIY | 0.001 | 0.000 | 0.002 | |
| scoreIntensity | 0.001 | 0.000 | 0.001 | |
| scoreIntensityByCE | 0 | 0 | 0 | |
| scorePSM | 0.011 | 0.000 | 0.012 | |
| scorePSMsimple | 0.012 | 0.000 | 0.012 | |
| summaryPSMsipPCT | 0.023 | 0.000 | 0.023 | |
| writeAllScanMS1 | 0.200 | 0.001 | 0.201 | |
| writeAllScanMS2 | 0.129 | 0.001 | 0.130 | |
| writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel | 0.017 | 0.000 | 0.010 | |