===============================
R CMD BUILD
===============================
* checking for file broadSeq/DESCRIPTION ... OK
* preparing broadSeq:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
broadSeq/inst/extdata/rat_vole_mouseSE_salmon.rds
* building broadSeq_0.99.0.tar.gz
===============================
BiocCheckGitClone('broadSeq')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: broadSeq
PackageVersion: 0.99.0
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3381/broadSeq_20240404151900/broadSeq
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/3381/broadSeq_20240404151900/broadSeq.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 broadSeq/DESCRIPTION ... OK
* this is package broadSeq version 0.99.0
* 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 broadSeq 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [35s/35s] NOTE
genes_plot: warning in facet(facet.by, scale = "free"): partial
argument match of 'scale' to 'scales'
volcanoPlot: warning in ggscatter(x = lFCName, y = "padj", color =
"Significant", palette = palette, title = "Volcano plot", label =
labelName, repel = TRUE, label.rectangle = TRUE, show.legend = FALSE,
label.select = selectedLabel): partial argument match of
'show.legend' to 'show.legend.text'
assay_plot: no visible global function definition for ggarrange
assay_plot: no visible global function definition for text_grob
biplotAnyPC: no visible binding for global variable PC
biplotAnyPC: no visible binding for global variable var_pct
biplotAnyPC: no visible global function definition for pull
biplotAnyPC: no visible binding for global variable gene
biplotAnyPC: no visible global function definition for aes
biplotAnyPC: no visible global function definition for arrow
biplotAnyPC: no visible global function definition for unit
combinedEnrichment: no visible global function definition for
keytypes
extract_topGeneLoadings: no visible global function definition for
desc
extract_topGeneLoadings: no visible global function definition for
all_of
genes_plot: no visible global function definition for rowData
normalizeEdgerCPM: no visible global function definition for is
plotAnyPC: no visible binding for global variable PC
plotAnyPC: no visible binding for global variable var_pct
plotHeatmapCluster: no visible global function definition for is
plotHeatmapCluster: no visible global function definition for colData
plotHeatmapCluster: no visible global function definition for rowData
plotHeatmapCluster: no visible global function definition for all_of
plot_MDS: no visible global function definition for is
plot_MDS: no visible global function definition for dist
plot_MDS: no visible global function definition for cmdscale
plot_MDS: no visible global function definition for colData
prcompTidy: no visible global function definition for is
prcompTidy: no visible global function definition for prcomp
prcompTidy: no visible binding for global variable stdev
prcompTidy: no visible binding for global variable var
prcompTidy: no visible binding for global variable var_pct
prcompTidy: no visible binding for global variable PC
prcompTidy: no visible binding for global variable .
prcompTidy: no visible binding for global variable gene
transformDESeq2: no visible global function definition for is
transformDESeq2: no visible global function definition for assays<-
transformDESeq2: no visible global function definition for assay
use_DELocal: no visible global function definition for desc
use_DELocal: no visible binding for global variable relative.logFC
use_EBSeq: no visible global function definition for desc
use_EBSeq: no visible binding for global variable PPDE
use_NOIseq: no visible global function definition for desc
use_NOIseq: no visible binding for global variable prob
use_SAMseq: no visible binding for global variable q-value(%)
use_deseq2: no visible binding for global variable padj
use_edgeR: no visible binding for global variable logFC
use_edgeR: no visible binding for global variable FDR
use_edgeR: no visible global function definition for :=
use_limma: no visible global function definition for par
use_limma: no visible binding for global variable logFC
use_limma: no visible binding for global variable B
use_limma: no visible global function definition for :=
volcanoPlot: no visible global function definition for labs
volcanoPlot: no visible global function definition for geom_abline
Undefined global functions or variables:
. := B FDR PC PPDE aes all_of arrow assay assays<- cmdscale colData
desc dist gene geom_abline ggarrange is keytypes labs logFC padj par
prcomp prob pull q-value(%) relative.logFC rowData stdev text_grob
unit var var_pct
Consider adding
importFrom("graphics", "par")
importFrom("methods", "is")
importFrom("stats", "cmdscale", "dist", "prcomp", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in vignettes ... OK
* checking examples ... [58s/58s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sampleAssay_plot 7.804 0.200 8.005
use_multDE 7.368 0.088 7.457
* 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 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3381/broadSeq_20240404151900/broadSeq.Rcheck/00check.log
for details.
===============================
BiocCheck('broadSeq_0.99.0.tar.gz')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: broadSeq
PackageVersion: 0.99.0
sourceDir: /tmp/RtmpTu3N9z/file37436b549bcf8e/broadSeq
installDir: /tmp/RtmpTu3N9z/file37436b4912673c
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3381/broadSeq_20240404151900/broadSeq.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 3.5.0 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...
* NOTE: Consider adding these automatically suggested biocViews:
Sequencing, Coverage, GeneSetEnrichment, GO
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (50%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of broadSeq...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 2 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 195 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 171 lines
(8%) 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 | 14 NOTES
See the broadSeq.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.