===============================
BiocCheckGitClone('gINTomics')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: gINTomics
PackageVersion: 0.99.5
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3352/f0548672e0a577c772ef60557521d1a721f963df/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
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3352/f0548672e0a577c772ef60557521d1a721f963df/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 0.99.5
* 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 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 ... [18s/18s] 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 ... [18s/18s] WARNING
Warning: S3 method residuals.DGEGLM was declared in NAMESPACE but not found
Error in namespaceExport(ns, exports) :
undefined exports: create_multiassay, dot_plotly, extract_model_res, plot_chr_distribution, plot_heatmap, plot_network, plot_ridge, plot_tf_distribution, plot_venn, plot_volcano, run_cnv_integration, run_genomic_enrich, run_genomic_integration, run_met_integration, run_multiomics, run_shiny, run_tf_enrich, run_tf_integration
Calls: <Anonymous> ... withCallingHandlers -> eval -> eval -> loadNamespace -> namespaceExport
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [0s/0s] WARNING
Error in loadNamespace("gINTomics") :
there is no package called gINTomics
Calls: suppressMessages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking loading without being on the library search path ... [0s/0s] WARNING
Error in library(gINTomics, lib.loc = "/home/pkgbuild/packagebuilder/workers/jobs/3352/R-libs") :
there is no package called gINTomics
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
See section Generic functions and methods in the Writing R
Extensions manual.
* checking replacement functions ... WARNING
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named value.
* checking foreign function calls ... NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
See chapter System and foreign language interfaces in the Writing R
Extensions manual.
* checking R code for possible problems ... [3s/3s] NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) : there is no package called gINTomics
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: suppressPackageStartupMessages ... withCallingHandlers -> <Anonymous> -> Rd_db -> find.package
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Warning in gzfile(file, "rb") :
cannot open compressed file '', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> readRDS -> gzfile
Execution halted
* checking for missing documentation entries ... WARNING
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> dirname -> find.package
Execution halted
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking for code/documentation mismatches ... WARNING
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter Writing R documentation files in the Writing R
Extensions manual.
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking Rd contents ... NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Execution halted
* checking contents of data directory ... WARNING
Output for data("miRBase_conversion", package = "gINTomics"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called gINTomics
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("ov_test_tcga_omics", package = "gINTomics"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called gINTomics
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
* 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 ... SKIPPED
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [0s/0s]
[1s/1s] ERROR
Running the tests in tests/testthat.R failed.
Complete output:
> library(testthat)
> library(gINTomics)
Error in library(gINTomics) : there is no package called 'gINTomics'
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) :
there is no package called gINTomics
Execution halted
* 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 ERROR, 11 WARNINGs, 7 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3352/f0548672e0a577c772ef60557521d1a721f963df/gINTomics.Rcheck/00check.log
for details.
===============================
BiocCheck('gINTomics_0.99.5.tar.gz')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: gINTomics
PackageVersion: 0.99.5
sourceDir: /tmp/RtmprVfrAK/file3fa6484cdd36d5/gINTomics
installDir: /tmp/RtmprVfrAK/file3fa648341940f7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3352/f0548672e0a577c772ef60557521d1a721f963df/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...
* 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 (40%).
* 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; 47 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 386 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 | 4 NOTES
See the gINTomics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.