===============================
BiocCheckGitClone('Aerith')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250718114207/Aerith
BiocVersion: 3.22
Package: Aerith
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250718114207/Aerith.BiocCheck
BiocCheckVersion: 1.45.8
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250718114207/Aerith
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* 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 v1.45.8 results
0 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_20250718114207/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 0.99.3
* 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 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 ... OK
* 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 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 ... [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 ... NOTE
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 '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 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 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 ... [43s/43s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readMgf 9.959 0.444 10.405
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [1s/1s]
[1s/1s] 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 ... [4s/4s] OK
* DONE
Status: 1 WARNING, 9 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250718114207/Aerith.Rcheck/00check.log
for details.
===============================
BiocCheck('Aerith_0.99.3.tar.gz')
===============================
Installing Aerith
Package installed successfully
Aerith session metadata
sourceDir: /tmp/RtmpvpLZak/file27a7953ab6f121/Aerith
BiocVersion: 3.22
Package: Aerith
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20250718114207/Aerith.BiocCheck
BiocCheckVersion: 1.45.8
sourceDir: /tmp/RtmpvpLZak/file27a7953ab6f121/Aerith
installDir: /tmp/RtmpvpLZak/file27a795476f5b16
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...
* 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/Aerith-package.Rd
...
man/readSips.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; 253 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.8 results
0 ERRORS | 2 WARNINGS | i 9 NOTES
i See the Aerith.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.