===============================
BiocCheckGitClone('Aerith')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith
→ BiocVersion: 3.22
→ Package: Aerith
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• Aerith.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Aerith/DESCRIPTION’ ... OK
* this is package ‘Aerith’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... NOTE
Found export directives that require package ‘methods’:
‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* 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 ... NOTE
Found the following hidden files and directories:
src/.clang-format
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 33.8Mb
sub-directories of 1Mb or more:
extdata 7.2Mb
libs 26.3Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
GPL-3.0
Standardizable: FALSE
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘Rcpp’ ‘ggnewscale’ ‘tidyr’
All declared Imports should be used.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] 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’
plot.AAspectra: no visible binding for global variable ‘MZ’
plot.AAspectra: no visible binding for global variable ‘Prob’
plot.AAspectra: no visible binding for global variable ‘Kind’
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’
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: no visible binding for global variable ‘MZ’
plot,AAspectra: no visible binding for global variable ‘Prob’
plot,AAspectra: no visible binding for global variable ‘Kind’
Undefined global functions or variables:
Abundance Count DatabaseAccess DatabaseDescription Formula Frequency
IsDecoy Kind Label MZ MassError Prob RelativeTic RetentionTime across
all_of desc fft head 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 ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'extractPSMfeaturesTargetAndDecoytoPercolatorPin.Rd':
\examples lines wider than 100 characters:
extractPSMfeaturesTargetAndDecoytoPercolatorPin(target_dir, decoy_dir, 3, ft_dir, 3, FALSE, pin_path)
Rd file 'plotScanFrequencyMS2.Rd':
\examples lines wider than 100 characters:
plotScanFrequency(a, binwidth = 0.1, breaks = seq(9, 10, by = 0.2)) + plotScanFrequencyMS2(b, binwidth = 0.1)
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'calBYAtomCountAndBaseMass.Rd'
‘AAstrs’
Documented arguments not in \usage in Rd file 'calBYAtomCountAndBaseMass.Rd':
‘AAstr’
Undocumented arguments in Rd file 'calPepAtomCount.Rd'
‘AAstrs’
Documented arguments not in \usage in Rd file 'calPepAtomCount.Rd':
‘AAstr’
Undocumented arguments in Rd file 'calPepNeutronMass.Rd'
‘AAstrs’
Documented arguments not in \usage in Rd file 'calPepNeutronMass.Rd':
‘AAstr’
Undocumented arguments in Rd file 'calPepPrecursorMass.Rd'
‘AAstrs’
Documented arguments not in \usage in Rd file 'calPepPrecursorMass.Rd':
‘AAstr’
Documented arguments not in \usage in Rd file 'generateCFGs.Rd':
‘pct’ ‘center’ ‘width’
Undocumented arguments in Rd file 'plot-AAspectra-method.Rd'
‘x’ ‘linewidth’
Undocumented arguments in Rd file 'plotPSMannotation.Rd'
‘observedSpect’
Documented arguments not in \usage in Rd file 'plotPSMannotation.Rd':
‘obaservedSpect’
Undocumented arguments in Rd file 'precursor_peak_calculator_DIY_averagine.Rd'
‘AAstrs’
Documented arguments not in \usage in Rd file 'precursor_peak_calculator_DIY_averagine.Rd':
‘AAstr’
Undocumented arguments in Rd file 'readPSMtsv.Rd'
‘tsv’
Documented arguments not in \usage in Rd file 'readPSMtsv.Rd':
‘file_path’
Undocumented arguments in Rd file 'readPepXMLtable.Rd'
‘pepXML’
Documented arguments not in \usage in Rd file 'readPepXMLtable.Rd':
‘ms’
Undocumented arguments in Rd file 'readScansMS1Vector.Rd'
‘scanNumbersVector’
Documented arguments not in \usage in Rd file 'readScansMS1Vector.Rd':
‘startScanNumber’ ‘endScanNumber’
Undocumented arguments in Rd file 'scorePSMold.Rd'
‘realCharge’
Undocumented arguments in Rd file 'writeAllScanMS1.Rd'
‘scansList’
Documented arguments not in \usage in Rd file 'writeAllScanMS1.Rd':
‘scans’
Undocumented arguments in Rd file 'writeAllScanMS2.Rd'
‘scansList’
Documented arguments not in \usage in Rd file 'writeAllScanMS2.Rd':
‘scans’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'plot.AAspectra.Rd':
‘plot.AAspectra’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'plot-AAspectra-method.Rd':
‘AAspectra’
Argument items with no description in Rd file 'plot.AAspectra.Rd':
‘linewidth’
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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
-fopenmp
* 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/pkgbuild/packagebuilder/workers/jobs/3828/R-libs/Aerith/libs/Aerith.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] ERROR
Running examples in ‘Aerith-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotPSMs
> ### Title: plot PSMs from FT2 files and PSM results
> ### Aliases: plotPSMs
>
> ### ** Examples
>
> element <- "C13"
> demo_file <- system.file("extdata", "demo.psm.txt", package = "Aerith")
> psm <- readPSMtsv(demo_file)
> psm <- psm[psm$Filename=="Pan_052322_X13.FT2", ]
> psm <- psm[psm$ScanNumber %in% c("4068","2596","8182"), ]
> demo_file <- system.file("extdata", "X13_4068_2596_8182.ft2", package = "Aerith")
> ft2 <- readAllScanMS2(demo_file)
> ftFileNames <- psm$Filename
> scanNumbers <- psm$ScanNumber
> proNames <- psm$ProteinNames
> charges <- psm$ParentCharge
> pep <- psm$OriginalPeptide
> pep <- stringr::str_sub(pep, 2, -2)
> pct <- psm$SearchName
> pct <- as.numeric(stringr::str_sub(
+ stringr::str_split(pct, "_", simplify = T)[, 2], 1, -4)) / 100 / 1000
Error in is_logical(x, n = 1) : T used instead of TRUE
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> check_bool -> is_bool -> is_logical
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
6 596.3094 9.518739e-05
7 597.3117 8.284068e-06
[1] "/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith.Rcheck/tests/testthat"
[ FAIL 1 | WARN 1 | SKIP 4 | PASS 3 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test-extractPSMfeatures.R:3:1',
'test-precursor_BY_mass_peak_calculator.R:15:1',
'test-precursor_peak_calculator_DIY.R:3:1', 'test-readSpe2Peps.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scorePSM.R:5:5'): annotatePSM ──────────────────────────────────
Error in `file(file, "rt")`: cannot open the connection
Backtrace:
▆
1. └─Aerith::readPSMtsv("../../rmd/input data format/pct1.psm.txt") at test_scorePSM.R:5:5
2. └─utils::read.table(tsv, sep = "\t", quote = "", header = TRUE)
3. └─base::file(file, "rt")
[ FAIL 1 | WARN 1 | SKIP 4 | PASS 3 ]
Error: Test failures
Execution halted
* 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 ... [4s/4s] OK
* DONE
Status: 2 ERRORs, 4 WARNINGs, 10 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith.Rcheck/00check.log’
for details.
===============================
BiocCheck('Aerith_0.99.1.tar.gz')
===============================
── Installing Aerith ───────────────────────────────────────────────────────────
✔ Package installed successfully
── Aerith session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpvtxl3c/file1300c14e73b843/Aerith
→ BiocVersion: 3.22
→ Package: Aerith
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250630184209/Aerith.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/Rtmpvtxl3c/file1300c14e73b843/Aerith
→ installDir: /tmp/Rtmpvtxl3c/file1300c14ab6a5e3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Aerith ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
i NOTE: License 'GPL-3.0' unknown; refer to $R_HOME/share/licenses/license.db
i and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• Aerith.Rmd
• ...
• Visualization-of-SIP-proteomic-result.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/Aerith.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Aerith...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/getRealScanWithCharge.Rd
i Found @ in man/getSipBYionSpectra.Rd
i Found @ in vignettes/Score-function-test-of-PSM.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
The longest 5 functions are:
• plotPSMannotation() (R/plotAAspectra.R): 73 lines
• plotPSMsipPCT() (R/plotProteinSipPct.R): 58 lines
• plotMolecularIsotopes() (R/SIPmontecarlo.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/extractPSMfeatures.Rd
• ...
• man/readScansMS2Vector.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• generateCFGs.Rd
• ...
• scorePSMold.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 251 lines (7%) are > 80 characters long.
First few lines:
• R/Aerith-package.R#L4 #' @description Visualisation of peptide ...
• ...
• vignettes/Visualization-of-SIP-proteomic-result.Rmd#L27
rmarkdown::render("Visualization-of-SIP- ...
i NOTE: Consider multiples of 4 spaces for line indents; 560 lines (15%) are
not.
First few lines:
• R/plotAAspectra.R#L34 nMass <- nrow(spectra) ...
• ...
• vignettes/Theoretic-spectra-generation-of-SIP-labeled-peptide.Rmd#L18
fig.width = 10 ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | i 10 NOTES
i See the Aerith.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.