===============================
R CMD BUILD
===============================
* checking for file ‘AWAggregator/DESCRIPTION’ ... OK
* preparing ‘AWAggregator’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘AWAggregator_0.99.3.tar.gz’
===============================
BiocCheckGitClone('AWAggregator')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3774/8d0193132c75cb82374df64541c1e31e5547d668/AWAggregator
→ BiocVersion: 3.22
→ Package: AWAggregator
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3774/8d0193132c75cb82374df64541c1e31e5547d668/AWAggregator.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3774/8d0193132c75cb82374df64541c1e31e5547d668/AWAggregator
→ 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 v1.45.12 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/3774/8d0193132c75cb82374df64541c1e31e5547d668/AWAggregator.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 ‘AWAggregator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AWAggregator’ 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 ‘AWAggregator’ 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 ... [2s/2s] 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 ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [105s/92s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fitQuantInaccuracyModel 43.056 0.680 26.076
mergeTrainingSets 32.989 0.299 34.986
aggregateByAttributes 10.739 1.561 13.443
getPSMAttributes 4.536 0.025 5.023
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [26s/28s]
[26s/28s] 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: OK
===============================
BiocCheck('AWAggregator_0.99.3.tar.gz')
===============================
── Installing AWAggregator ─────────────────────────────────────────────────────
✔ Package installed successfully
── AWAggregator session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGexiXh/file256cf34e0b784/AWAggregator
→ BiocVersion: 3.22
→ Package: AWAggregator
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3774/8d0193132c75cb82374df64541c1e31e5547d668/AWAggregator.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmpGexiXh/file256cf34e0b784/AWAggregator
→ installDir: /tmp/RtmpGexiXh/file256cf38fa410a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AWAggregator ───────────────────────────────────────────
* 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...
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of AWAggregator...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/aggregateByAttributes.R (line 47, column 13)
• R/aggregateByAttributes.R (line 53, column 13)
• R/aggregateByAttributes.R (line 59, 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 4
functions greater than 50 lines.
The longest 5 functions are:
• getPSMAttributes() (R/getPSMAttributes.R): 84 lines
• ...
• getAvgScaledErrorOfLog2FC() (R/getAvgScaledErrorOfLog2FC.R): 67 lines
* Checking man page documentation...
* 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; 1 lines (0%) are > 80 characters long.
First few lines:
• R/mergeTrainingSets.R#L90 # https://stackoverflow.com/ ...
i NOTE: Consider multiples of 4 spaces for line indents; 18 lines (1%) are not.
First few lines:
• R/aggregateByAttributes.R#L43 predEr ...
• ...
• R/getPSMAttributes.R#L41 groupsExclu ...
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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 5 NOTES
i See the AWAggregator.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.