===============================
R CMD BUILD
===============================
* checking for file ‘gutenTAG/DESCRIPTION’ ... OK
* preparing ‘gutenTAG’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘gutenTAG/inst/extdata/Example_processed.Rdata’
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘preProcess.R’
* building ‘gutenTAG_0.99.2.tar.gz’
===============================
BiocCheckGitClone('gutenTAG')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4210/b0e4c5dfddc4c6718b5340f9324ccc6837cf877d/gutenTAG
→ BiocVersion: 3.23
→ Package: gutenTAG
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4210/b0e4c5dfddc4c6718b5340f9324ccc6837cf877d/gutenTAG.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4210/b0e4c5dfddc4c6718b5340f9324ccc6837cf877d/gutenTAG
→ 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 NAMESPACE...
* 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 v1.47.20 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/4210/b0e4c5dfddc4c6718b5340f9324ccc6837cf877d/gutenTAG.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-26 17:04:05 UTC
* using option ‘--no-vignettes’
* checking for file ‘gutenTAG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gutenTAG’ version ‘0.99.2’
* 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 ‘gutenTAG’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... [18s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the package can be unloaded cleanly ... [18s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/17s] OK
* checking loading without being on the library search path ... [18s/18s] OK
* checking use of S3 registration ... 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 ... [55s/55s] NOTE
.finaliseCorrespondence: no visible binding for global variable
‘expected_mz_location’
.knn_weight_matrix: no visible global function definition for ‘dist’
imageChannel: no visible binding for global variable ‘y’
Undefined global functions or variables:
dist expected_mz_location y
Consider adding
importFrom("stats", "dist")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [101s/95s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
asAnnData 7.939 0.912 8.341
assignMetapeaks 4.470 1.596 5.499
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [83s/76s]
[83s/76s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Expected `cur_test$CorrespondenceMatrix$snr` to equal `c(...)`.
Differences:
actual | expected
[5] 3.999200215 | 3.999200215 [5]
[6] 0.000000000 | 0.000000000 [6]
[7] 2.446228358 | 2.446228358 [7]
[8] 2.882010153 - 2.900728537 [8]
[9] 3.816154384 | 3.816154384 [9]
[10] 0.000000000 | 0.000000000 [10]
[11] 1.546261050 | 1.546261050 [11]
── Failure ('test-generateMetapeaks.R:32:3'): generateMetapeaks works ──────────
Expected `max(cur_test$propagation_selection)` to equal 225.
Differences:
`actual`: 229.0
`expected`: 225.0
[ FAIL 5 | WARN 9 | SKIP 0 | PASS 184 ]
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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4210/b0e4c5dfddc4c6718b5340f9324ccc6837cf877d/gutenTAG.Rcheck/00check.log’
for details.
===============================
BiocCheck('gutenTAG_0.99.2.tar.gz')
===============================
── Installing gutenTAG ─────────────────────────────────────────────────────────
✔ Package installed successfully
── gutenTAG session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpeazkQL/file289cb27bbcb8e/gutenTAG
→ BiocVersion: 3.23
→ Package: gutenTAG
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4210/b0e4c5dfddc4c6718b5340f9324ccc6837cf877d/gutenTAG.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpeazkQL/file289cb27bbcb8e/gutenTAG
→ installDir: /tmp/RtmpeazkQL/file289cb268325eb2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gutenTAG ───────────────────────────────────────────────
* 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 4.1.0 to 4.6.0
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
MassSpectrometry, Lipidomics, Normalization, QualityControl, Classification,
Clustering, Regression, MultiChannel, ImmunoOncology, PeakDetection
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (35%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• gutenTAG.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of gutenTAG...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/computeSNR.R (line 53, column 11)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• smoothPeakCounts.R (line 22, column 92)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/readPanel.R (line 29, column 21)
• ...
• R/utils.R (line 147, column 35)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/imageChannel.R (line 49, column 40)
• R/utils.R (line 199, column 17)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/computeSNR.R (line 115, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
The longest 5 functions are:
• plotMetapeaks() (R/plotQC.R): 128 lines
• ...
• plotQCOverview() (R/plotQC.R): 72 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• plotMeanVsSNR.Rd
• ...
• plotSpatialSNR.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 13% of man
pages use at least one of these tags.
Found in files:
• plotMeanVsSNR.Rd
• ...
• plotSpatialSNR.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 174 lines (6%) are > 80 characters long.
First few lines:
• R/asCytoImageList.R#L34 matrix_list <- lapply(colnames(datafra ...
• ...
• vignettes/gutenTAG.Rmd#L412 developing the initial architecture of t ...
i NOTE: Consider multiples of 4 spaces for line indents; 936 lines (30%) are
not.
First few lines:
• R/asAnnData.R#L24 # extract data from object ...
• ...
• vignettes/gutenTAG.Rmd#L369 interpolate = FALSE) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.47.20 results ──────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 17 NOTES
i See the gutenTAG.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.