===============================
BiocCheckGitClone('chevreulProcess')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/cf36c17c27ff50391da5f992349e73b7eff038e9/chevreulProcess
BiocVersion: 3.21
Package: chevreulProcess
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/cf36c17c27ff50391da5f992349e73b7eff038e9/chevreulProcess.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/cf36c17c27ff50391da5f992349e73b7eff038e9/chevreulProcess
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 v1.43.2 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/3332/cf36c17c27ff50391da5f992349e73b7eff038e9/chevreulProcess.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* 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 chevreulProcess/DESCRIPTION ... OK
* checking extension type ... Package
* this is package chevreulProcess version 0.99.8
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 chevreulProcess 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the package can be unloaded cleanly ... [17s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/17s] OK
* checking loading without being on the library search path ... [20s/20s] OK
* checking whether startup messages can be suppressed ... [17s/17s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Error: undefined exports: add_percent_mito, find_all_markers, genes_to_transcripts, get_colData, get_feature_types, get_features, get_sce_metadata, get_variable_features, integration_workflow, load_bigwigs, propagate_spreadsheet_changes, query_experiment, record_experiment_data, regress_cell_cycle, reintegrate_sce, rename_sce, retrieve_experiment, sce_calcn, sce_cluster, sce_de, sce_integrate, sce_preprocess, sce_process, set_colData, set_feature_type, splitByCol, stash_marker_features, transcripts_to_genes
Call sequence:
3: stop(gettextf("undefined exports: %s", undef), domain = NA)
2: namespaceExport(ns, exports)
1: loadNamespace(package, lib.loc)
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 chevreulProcess
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 ... [2s/2s] NOTE
Error in find.package(package, lib.loc) :
there is no package called chevreulProcess
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) :
there is no package called chevreulProcess
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 chevreulProcess
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) :
there is no package called chevreulProcess
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 chevreulProcess
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 chevreulProcess
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called chevreulProcess
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called chevreulProcess
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) :
there is no package called chevreulProcess
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 chevreulProcess
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 chevreulProcess
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 chevreulProcess
Execution halted
* checking contents of data directory ... WARNING
Output for data("cc.genes.cyclone", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("ensembl_version", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("grch38", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("grch38_tx2gene", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("human_to_mouse_homologs", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("small_example_dataset", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("tiny_sce", package = "chevreulProcess"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called chevreulProcess
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
* checking data for non-ASCII characters ... [9s/9s] OK
* checking data for ASCII and uncompressed saves ... 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:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(chevreulProcess)
Error in library(chevreulProcess) :
there is no package called 'chevreulProcess'
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) :
there is no package called chevreulProcess
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 ... [7s/7s] OK
* DONE
Status: 1 ERROR, 7 WARNINGs, 6 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/cf36c17c27ff50391da5f992349e73b7eff038e9/chevreulProcess.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreulProcess_0.99.8.tar.gz')
===============================
Installing chevreulProcess
Package installed successfully
chevreulProcess session metadata
sourceDir: /tmp/RtmpFoTIMI/filef6ea433c37e47/chevreulProcess
BiocVersion: 3.21
Package: chevreulProcess
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/cf36c17c27ff50391da5f992349e73b7eff038e9/chevreulProcess.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpFoTIMI/filef6ea433c37e47/chevreulProcess
installDir: /tmp/RtmpFoTIMI/filef6ea462285b86
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreulProcess
* 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...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0.
* 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...
i NOTE: Consider adding these automatically suggested biocViews: ImmunoOncology
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 (38%).
* 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 chevreulProcess...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/wiggleplotr.R (line 54, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils.R (line 169, column 25)
R/utils.R (line 170, column 28)
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
sce_de() (R/cluster.R): 68 lines
record_experiment_data() (R/utils.R): 51 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
integration_workflow.Rd
...
reintegrate_sce.Rd
* 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; 9 lines (0%) are > 80 characters long.
First few lines:
R/pipeline.R#L27 sce_integrate <- function(sce_list, reso ...
...
R/utils.R#L45 metadata(object)[["experiment"]] ...
i NOTE: Consider multiples of 4 spaces for line indents; 76 lines (4%) are not.
First few lines:
R/cluster.R#L22 diffex_scheme ...
...
R/workflow.R#L43 ...
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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 8 NOTES
i See the chevreulProcess.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.