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R CMD BUILD
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* checking for file gINTomics/DESCRIPTION ... OK
* preparing gINTomics:
* 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 gINTomics_0.99.2.tar.gz
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BiocCheckGitClone('gINTomics')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: gINTomics
PackageVersion: 0.99.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3352/e0f2b556abf0699093e70accd68e8e26ee778024/gINTomics
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* 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 results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3352/e0f2b556abf0699093e70accd68e8e26ee778024/gINTomics.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file gINTomics/DESCRIPTION ... OK
* this is package gINTomics 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 gINTomics 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 ... [17s/17s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the package can be unloaded cleanly ... [17s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/17s] OK
* checking loading without being on the library search path ... [17s/17s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
.def_enrich
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [60s/60s] NOTE
.build_histo: no visible binding for global variable chr_cov
.build_histo: no visible binding for global variable significance
.build_ridge: no visible binding for global variable coef
.build_ridge: no visible binding for global variable significance
.circos_preprocess: no visible binding for global variable cnv_met
.prepare_cnv_heatmap: no visible binding for global variable cnv
.prepare_gen_heatmap: no visible binding for global variable met
.prepare_gen_heatmap: no visible binding for global variable cnv
.prepare_met_heatmap: no visible binding for global variable met
.prepare_mirna_heatmap: no visible binding for global variable
mirna_cnv
.prepare_network: no visible binding for global variable omics
.prepare_reactive_histo_tf: no visible binding for global variable
Freq
.prepare_reactive_venn: no visible binding for global variable
cnv_met
.prepare_reactive_venn: no visible binding for global variable pval
.shiny_preprocess: no visible binding for global variable cov
plot_tf_distribution: no visible binding for global variable Freq
Undefined global functions or variables:
Freq chr_cov cnv cnv_met coef cov met mirna_cnv omics pval
significance
Consider adding
importFrom("stats", "coef", "cov")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'dot_plotly.Rd':
\examples lines wider than 100 characters:
#gen_enr <- run_genomic_enrich(multiomics_integration, qvalueCutoff = 1, pvalueCutoff = 0.05, pAdjustMethod = "none")
These lines will be truncated in the PDF manual.
* 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [155s/162s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
extract_model_res 13.167 1.663 15.789
run_shiny 12.821 1.128 14.630
plot_ridge 10.610 0.875 12.166
plot_heatmap 10.213 1.032 11.995
plot_venn 9.739 1.008 11.431
plot_network 9.458 0.912 11.051
plot_volcano 9.575 0.795 11.062
plot_chr_distribution 9.446 0.756 11.083
plot_tf_distribution 9.016 0.653 10.643
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [88s/89s]
[88s/89s] 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: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3352/e0f2b556abf0699093e70accd68e8e26ee778024/gINTomics.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('gINTomics_0.99.2.tar.gz')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: gINTomics
PackageVersion: 0.99.2
sourceDir: /tmp/RtmpHzxRyn/file35342f2e8d6f6e/gINTomics
installDir: /tmp/RtmpHzxRyn/file35342f2db80aa5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3352/e0f2b556abf0699093e70accd68e8e26ee778024/gINTomics.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
* NOTE: Update R version dependency from 4.3.0 to 4.4.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (38%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 gINTomics...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/dot_plotly.Rd
Found @ in man/extract_model_res.Rd
Found @ in man/plot_chr_distribution.Rd
Found @ in man/plot_heatmap.Rd
Found @ in man/plot_network.Rd
Found @ in man/plot_ridge.Rd
Found @ in man/plot_tf_distribution.Rd
Found @ in man/plot_venn.Rd
Found @ in man/plot_volcano.Rd
Found @ in man/run_cnv_integration.Rd
Found @ in man/run_genomic_enrich.Rd
Found @ in man/run_genomic_integration.Rd
Found @ in man/run_met_integration.Rd
Found @ in man/run_multiomics.Rd
Found @ in man/run_shiny.Rd
Found @ in man/run_tf_enrich.Rd
Found @ in man/run_tf_integration.Rd
Found @ in vignettes/gINTomics.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 49 functions greater than 50 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...
* NOTE: Consider shorter lines; 44 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 379 lines
(5%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 5 NOTES
See the gINTomics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.