===============================
R CMD BUILD
===============================
* checking for file ‘MSstatsResponse/DESCRIPTION’ ... OK
* preparing ‘MSstatsResponse’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘MSstatsResponse_0.99.0.tar.gz’
===============================
BiocCheckGitClone('MSstatsResponse')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3958/MSstatsResponse_20250926191956/MSstatsResponse
→ BiocVersion: 3.22
→ Package: MSstatsResponse
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3958/MSstatsResponse_20250926191956/MSstatsResponse.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3958/MSstatsResponse_20250926191956/MSstatsResponse
→ 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 v1.45.18 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/3958/MSstatsResponse_20250926191956/MSstatsResponse.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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
* using option ‘--no-vignettes’
* checking for file ‘MSstatsResponse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsResponse’ version ‘0.99.0’
* 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 ‘MSstatsResponse’ 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 ... 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 ... [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:
‘MSstats’ ‘MSstatsTMT’ ‘purrr’ ‘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 ... [6s/6s] OK
* 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 ... [8s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [9s/11s]
[9s/11s] 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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3958/MSstatsResponse_20250926191956/MSstatsResponse.Rcheck/00check.log’
for details.
===============================
BiocCheck('MSstatsResponse_0.99.0.tar.gz')
===============================
── Installing MSstatsResponse ──────────────────────────────────────────────────
✔ Package installed successfully
── MSstatsResponse session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpILNAOj/file13aa253d403507/MSstatsResponse
→ BiocVersion: 3.22
→ Package: MSstatsResponse
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3958/MSstatsResponse_20250926191956/MSstatsResponse.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpILNAOj/file13aa253d403507/MSstatsResponse
→ installDir: /tmp/RtmpILNAOj/file13aa2555d33032
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MSstatsResponse ────────────────────────────────────────
* 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...
* 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...
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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (22%).
* 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:
• MSstatsResponse.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MSstatsResponse...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/Fit_Isotonic_Regression.R (line 258, column 20)
• R/Utils.R (line 27, column 3)
• R/Visualize_Isotonic_Fit.R (line 212, column 22)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/ExperimentalDesignSimulation.R (line 83, column 28)
• ...
• R/Visualize_Isotonic_Fit.R (line 237, column 22)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/ExperimentalDesignSimulation.R (line 104, column 15)
• ...
• R/IC50_prediction.R (line 124, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/ExperimentalDesignSimulation.R (line 376, column 10)
• R/Fit_Isotonic_Regression.R (line 135, column 23)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
• suppressWarnings() in R/Fit_Isotonic_Regression.R (line 97, column 9)
• suppressWarnings() in R/Visualize_Isotonic_Fit.R (line 94, column 5)
• suppressWarnings() in R/Visualize_Isotonic_Fit.R (line 217, column 7)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
• .extractTemplatesFromData() (R/ExperimentalDesignSimulation.R): 132 lines
• ...
• plotIsotonic() (R/Visualize_Isotonic_Fit.R): 111 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
Found in files:
• DoseResponseFit.Rd
• ...
• PredictIC50.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• DoseResponseFit.Rd
• ...
• PredictIC50.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; 129 lines (5%) are > 80 characters long.
First few lines:
• R/ExperimentalDesignSimulation.R#L1 #' Test future experimental design using
...
• ...
• vignettes/MSstatsResponse.Rmd#L410 2. Choi, M., et al. (2014). MSstats: an
...
i NOTE: Consider multiples of 4 spaces for line indents; 785 lines (33%) are
not.
First few lines:
• R/ExperimentalDesignSimulation.R#L84 N_ ...
• ...
• vignettes/MSstatsResponse.Rmd#L404 ...
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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 13 NOTES
i See the MSstatsResponse.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.