===============================
BiocCheckGitClone('chevreulPlot')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/7d93cd559b4f5e9e5ad780774f2893bbdabae46e/chevreulPlot
→ BiocVersion: 3.21
→ Package: chevreulPlot
→ PackageVersion: 0.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/7d93cd559b4f5e9e5ad780774f2893bbdabae46e/chevreulPlot.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/7d93cd559b4f5e9e5ad780774f2893bbdabae46e/chevreulPlot
→ 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/3332/7d93cd559b4f5e9e5ad780774f2893bbdabae46e/chevreulPlot.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 ‘chevreulPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chevreulPlot’ version ‘0.99.14’
* 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'
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 ‘chevreulPlot’ can be installed ... OK
* checking installed package size ... INFO
installed size is 12.5Mb
sub-directories of 1Mb or more:
data 4.6Mb
extdata 7.7Mb
* 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 ... [14s/14s] WARNING
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: methods
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Attaching package: ‘graphics’
The following object is masked from ‘package:stats4’:
plot
Loading required package: stats
Attaching package: ‘stats’
The following objects are masked from ‘package:stats4’:
AIC, BIC, coef, confint, logLik, nobs, profile, update, vcov
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Loading required package: chevreulProcess
Loading required package: scater
Loading required package: scuttle
Loading required package: ggplot2
Error: package or namespace load failed for 'chevreulPlot' in loadNamespace(package, lib.loc):
there is no package called 'chevreulPlot'
Execution halted
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... [0s/0s] WARNING
Error in library(chevreulPlot) :
there is no package called ‘chevreulPlot’
Calls: suppressMessages -> withCallingHandlers -> library
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] WARNING
Error in loadNamespace("chevreulPlot") :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
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("chevreulPlot") :
there is no package called ‘chevreulPlot’
Calls: suppressMessages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking loading without being on the library search path ... [0s/0s] WARNING
Error in library(chevreulPlot, lib.loc = "/home/pkgbuild/packagebuilder/workers/jobs/3332/R-libs") :
there is no package called ‘chevreulPlot’
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 ‘chevreulPlot’
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘chevreulPlot’
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 ‘chevreulPlot’
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 ‘chevreulPlot’
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 ‘chevreulPlot’
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) : there is no package called ‘chevreulPlot’
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 ‘chevreulPlot’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘chevreulPlot’
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 ‘chevreulPlot’
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 ‘chevreulPlot’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘chevreulPlot’
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 ‘chevreulPlot’
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 ‘chevreulPlot’
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 ‘chevreulPlot’
Execution halted
* checking contents of ‘data’ directory ... WARNING
Output for data("cc.genes.cyclone", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("ensembl_version", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("grch38", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("grch38_tx2gene", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("human_to_mouse_homologs", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("small_example_dataset", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("tiny_sce", package = "chevreulPlot"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘chevreulPlot’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
* checking data for non-ASCII characters ... [8s/8s] 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(chevreulPlot)
Error in library(chevreulPlot) :
there is no package called 'chevreulPlot'
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) :
there is no package called ‘chevreulPlot’
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, 13 WARNINGs, 7 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3332/7d93cd559b4f5e9e5ad780774f2893bbdabae46e/chevreulPlot.Rcheck/00check.log’
for details.
===============================
BiocCheck('chevreulPlot_0.99.14.tar.gz')
===============================
── Installing chevreulPlot ─────────────────────────────────────────────────────
✔ Package installed successfully
── chevreulPlot session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpgs9Z4w/file7a5344d22dcdf/chevreulPlot
→ BiocVersion: 3.21
→ Package: chevreulPlot
→ PackageVersion: 0.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/7d93cd559b4f5e9e5ad780774f2893bbdabae46e/chevreulPlot.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmpgs9Z4w/file7a5344d22dcdf/chevreulPlot
→ installDir: /tmp/Rtmpgs9Z4w/file7a53479bb58b2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on chevreulPlot ───────────────────────────────────────────
* 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...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/Rtmpgs9Z4w/file7a5344d22dcdf/chevreulPlot//inst/doc/visualization.html
• /tmp/Rtmpgs9Z4w/file7a5344d22dcdf/chevreulPlot/inst/doc/visualization.html
• /tmp/Rtmpgs9Z4w/file7a5344d22dcdf/chevreulPlot/inst/doc/visualization.html
* 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 (27%).
* 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 chevreulPlot...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/plotting.R (line 97, column 5)
* 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 4
functions greater than 50 lines.
The longest 5 functions are:
• plot_gene_coverage_by_var() (R/wiggleplotr.R): 108 lines
• ...
• plot_transcript_composition() (R/plotting.R): 60 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...
i NOTE: Consider shorter lines; 9 lines (1%) are > 80 characters long.
First few lines:
• R/globals.R#L1 utils::globalVariables(c(".", "Cluster", ...
• ...
• vignettes/visualization.Rmd#L119 plotted using `plot_marker_features`. Th ...
i NOTE: Consider multiples of 4 spaces for line indents; 57 lines (5%) are not.
First few lines:
• R/plotting.R#L25 embedding = "UMAP", ...
• ...
• vignettes/visualization.Rmd#L139 ...
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 | ⚠ 1 WARNINGS | i 6 NOTES
i See the chevreulPlot.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.