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R CMD BUILD
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* checking for file chevreul/DESCRIPTION ... OK
* preparing chevreul:
* 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 chevreul_0.99.49.tar.gz
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BiocCheckGitClone('chevreul')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/35a31e85826752fc39620fab443b4a45dd1a40a3/chevreul
BiocVersion: 3.20
Package: chevreul
PackageVersion: 0.99.49
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/35a31e85826752fc39620fab443b4a45dd1a40a3/chevreul.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/35a31e85826752fc39620fab443b4a45dd1a40a3/chevreul
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 N: (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 v1.41.16 results
0 ERRORS | 0 WARNINGS | 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3332/35a31e85826752fc39620fab443b4a45dd1a40a3/chevreul.Rcheck
* using R version 4.4.1 (2024-06-14)
* 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 chevreul/DESCRIPTION ... OK
* checking extension type ... Package
* this is package chevreul version 0.99.49
* 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 chevreul 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 ... [20s/20s] OK
* checking whether the package can be loaded with stated dependencies ... [21s/21s] OK
* checking whether the package can be unloaded cleanly ... [20s/20s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [20s/20s] OK
* checking loading without being on the library search path ... [18s/18s] OK
* checking whether startup messages can be suppressed ... [18s/18s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
Namespaces in Imports field not imported from:
'ExperimentHub' 'httr'
All declared Imports should be used.
Missing or unexported object: 'chevreul::cc.genes.cyclone'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [65s/65s] OK
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [9s/9s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [72s/72s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [31s/31s]
[31s/31s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
`annotate_cell_cycle(small_example_dataset)` threw an unexpected error.
Message: 'cc.genes.cyclone' is not an exported object from 'namespace:chevreul'
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...) at test-annotate_cell_cycle.R:3:5
2. testthat:::expect_condition_matching(...)
3. testthat:::quasi_capture(...)
4. testthat (local) .capture(...)
5. base::withCallingHandlers(...)
6. rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. chevreul:::annotate_cell_cycle(small_example_dataset)
8. scran::cyclone(object, chevreul::cc.genes.cyclone, gene.names = rownames(object))
9. scran::cyclone(object, chevreul::cc.genes.cyclone, gene.names = rownames(object))
10. scran (local) .local(x, ...)
11. scran::cyclone(assay(x, i = assay.type), ...)
12. scran::cyclone(assay(x, i = assay.type), ...)
13. scran (local) .local(x, ...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 1 WARNING
See
/home/pkgbuild/packagebuilder/workers/jobs/3332/35a31e85826752fc39620fab443b4a45dd1a40a3/chevreul.Rcheck/00check.log
for details.
===============================
BiocCheck('chevreul_0.99.49.tar.gz')
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Installing chevreul
Package installed successfully
chevreul session metadata
sourceDir: /tmp/RtmpvBL32t/file1deb3b1f419f0b/chevreul
BiocVersion: 3.20
Package: chevreul
PackageVersion: 0.99.49
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3332/35a31e85826752fc39620fab443b4a45dd1a40a3/chevreul.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /tmp/RtmpvBL32t/file1deb3b1f419f0b/chevreul
installDir: /tmp/RtmpvBL32t/file1deb3b4f96722e
isTarBall: TRUE
platform: unix
Running BiocCheck on chevreul
* 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...
! W: Package files exceed the 5MB size limit.
Files over the limit:
/tmp/RtmpvBL32t/file1deb3b1f419f0b/chevreul//inst/doc/visualization.html
/tmp/RtmpvBL32t/file1deb3b1f419f0b/chevreul/inst/doc/visualization.html
/tmp/RtmpvBL32t/file1deb3b1f419f0b/chevreul/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...
* 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 (25%).
* 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 chevreul...
* Checking coding practice...
i N: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/chevreul_app.R (line 711, column 13)
...
print in R/shiny_modules.R (line 1172, column 26)
i N: Avoid the use of 'paste' in condition signals
Found in files:
R/wiggleplotr.R (line 50, column 13)
i N: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils.R (line 153, column 25)
R/utils.R (line 153, column 71)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
The longest 5 functions are:
chevreulApp() (R/chevreul_app.R): 602 lines
...
server() (R/minimal_chevreul_app.R): 212 lines
* Checking man page documentation...
i N: Consider adding runnable examples to man pages that document exported
objects.
build_bigwig_db.Rd
...
minimalChevreulApp.Rd
i N: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
Found in files:
chevreulApp.Rd
dockerChevreulApp.Rd
minimalChevreulApp.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 N: Consider shorter lines; 311 lines (4%) are > 80 characters long.
First few lines:
R/docker_app.R#L7 #' @param db_name path to sqlite databa ...
...
vignettes/visualization.Rmd#L31 crop = NULL, ## Related to https://s ...
i N: Consider multiples of 4 spaces for line indents; 93 lines (1%) are not.
First few lines:
R/chevreul_app.R#L16 diffex_scheme ...
...
vignettes/visualization.Rmd#L140 ...
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 v1.41.16 results
0 ERRORS | 1 WARNINGS | 8 NOTES
i See the chevreul.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.