===============================
R CMD BUILD
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* 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_0.99.4.tar.gz
===============================
BiocCheckGitClone('ProteinGymR')
===============================
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/6f52bfda624fd8fc9064a7d05811b4ea250a6c8c/ProteinGymR
BiocVersion: 3.20
Package: ProteinGymR
PackageVersion: 0.99.4
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/6f52bfda624fd8fc9064a7d05811b4ea250a6c8c/ProteinGymR.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/6f52bfda624fd8fc9064a7d05811b4ea250a6c8c/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/3575/6f52bfda624fd8fc9064a7d05811b4ea250a6c8c/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 0.99.4
* 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 ... WARNING
Dependence on R version 4.4.1 not with patchlevel 0
* 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 ... NOTE
Namespaces in Imports field not imported from:
AnnotationHub tibble
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 ... [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 23.083 0.995 24.751
dms_corr_plot 18.338 0.267 19.936
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [8s/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 ... [3s/2s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/6f52bfda624fd8fc9064a7d05811b4ea250a6c8c/ProteinGymR.Rcheck/00check.log
for details.
===============================
BiocCheck('ProteinGymR_0.99.4.tar.gz')
===============================
Installing ProteinGymR
Package installed successfully
ProteinGymR session metadata
sourceDir: /tmp/RtmpIJDOQX/filec79d45fca1630/ProteinGymR
BiocVersion: 3.20
Package: ProteinGymR
PackageVersion: 0.99.4
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3575/6f52bfda624fd8fc9064a7d05811b4ea250a6c8c/ProteinGymR.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /tmp/RtmpIJDOQX/filec79d45fca1630/ProteinGymR
installDir: /tmp/RtmpIJDOQX/filec79d4624778a6
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 (17%).
* 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; 5 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#L87
[2023](https://papers.nips.cc/paper_file ...
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.