===============================
R CMD BUILD
===============================
* checking for file ‘ProteinGymR/DESCRIPTION’ ... OK
* preparing ‘ProteinGymR’:
* 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
* building ‘ProteinGymR_0.99.5.tar.gz’
===============================
BiocCheckGitClone('ProteinGymR')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/40f8a366dda10beb38ce5a36d782109a67758c6f/ProteinGymR
→ BiocVersion: 3.20
→ Package: ProteinGymR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/40f8a366dda10beb38ce5a36d782109a67758c6f/ProteinGymR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/40f8a366dda10beb38ce5a36d782109a67758c6f/ProteinGymR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/40f8a366dda10beb38ce5a36d782109a67758c6f/ProteinGymR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteinGymR/DESCRIPTION’ ... OK
* this is package ‘ProteinGymR’ version ‘0.99.5’
* 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 ‘ProteinGymR’ 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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 ... [13s/13s] NOTE
benchmark_models: no visible global function definition for ‘all_of’
benchmark_models: no visible global function definition for
‘everything’
benchmark_models: no visible binding for global variable ‘model’
benchmark_models: no visible binding for global variable ‘score’
benchmark_models: no visible binding for global variable ‘model_mean’
dms_corr_plot: no visible binding for global variable ‘uID’
dms_corr_plot: no visible binding for global variable ‘.data’
pg_correlate: no visible global function definition for ‘cor.test’
pg_filter_am_table: no visible binding for global variable ‘Entry Name’
pg_filter_am_table: no visible binding for global variable ‘.data’
pg_match_id: no visible global function definition for ‘na.omit’
pg_match_id: no visible binding for global variable ‘UniProt_id’
pg_match_id: no visible binding for global variable ‘mutant’
pg_match_id: no visible binding for global variable ‘AlphaMissense’
pg_match_id: no visible binding for global variable ‘DMS_score’
Undefined global functions or variables:
.data AlphaMissense DMS_score Entry Name UniProt_id all_of cor.test
everything model model_mean mutant na.omit score uID
Consider adding
importFrom("stats", "cor.test", "na.omit")
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 ... [57s/61s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ProteinGym_DMS 23.728 0.997 25.424
dms_corr_plot 17.726 0.178 19.837
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘tibble’
* checking tests ...
Running ‘testthat.R’ [7s/9s]
[8s/9s] 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 ... [2s/2s] OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/40f8a366dda10beb38ce5a36d782109a67758c6f/ProteinGymR.Rcheck/00check.log’
for details.
===============================
BiocCheck('ProteinGymR_0.99.5.tar.gz')
===============================
── Installing ProteinGymR ──────────────────────────────────────────────────────
✔ Package installed successfully
── ProteinGymR session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvhowEv/file2e2bf913eaa164/ProteinGymR
→ BiocVersion: 3.20
→ Package: ProteinGymR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/40f8a366dda10beb38ce5a36d782109a67758c6f/ProteinGymR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpvhowEv/file2e2bf913eaa164/ProteinGymR
→ installDir: /tmp/RtmpvhowEv/file2e2bf94fb84683
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ProteinGymR ────────────────────────────────────────────
* 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...
→ ExperimentData
* 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: Proteome
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (10%).
* Checking for pinned package versions in DESCRIPTION...
* 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 ProteinGymR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/dms_corr_plot.R (line 298, column 5)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/benchmark_models.R (line 33, column 14)
• ...
• R/dms_corr_plot.R (line 89, column 17)
* 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 3
functions greater than 50 lines.
The longest 5 functions are:
• benchmark_models() (R/benchmark_models.R): 78 lines
• pg_filter_am_table() (R/dms_corr_plot.R): 64 lines
• dms_corr_plot() (R/dms_corr_plot.R): 59 lines
* Checking man page documentation...
* 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; 6 lines (1%) are > 80 characters long.
First few lines:
• R/am_scores.R#L9 #' substitutions matching those in the P ...
• ...
• vignettes/data_import_and_representation.Rmd#L221
[here](https://biology.stackexchange.com ...
i NOTE: Consider multiples of 4 spaces for line indents; 3 lines (0%) are not.
First few lines:
• R/benchmark_models.R#L150 names_to = "model", ...
• R/benchmark_models.R#L151 values_to = "score") ...
• R/dms_corr_plot.R#L45 ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 7 NOTES
i See the ProteinGymR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.