===============================
BiocCheckGitClone('OGRE')
===============================
This is BiocCheckGitClone version 1.30.0. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2431/36b9c1ae7df7ab073a0499832583bfe99acdeb7c/OGRE.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OGRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OGRE’ version ‘0.99.3’
* 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 ‘OGRE’ can be installed ... [29s/29s] 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [28s/28s] NOTE
gvizPlot : <anonymous>: warning in AnnotationTrack(start =
tmp$subjStart, end = tmp$subjEnd, chr = tmp$subjChr, name = x, id =
regionLabels, fontsize.title = 24, featureAnnotation = "id",
fontcolor.title = "black", fontcolor = "black", fontcolor.group =
"black", fontcolor.item = "black", rotation.item = 20): partial
argument match of 'chr' to 'chromosome'
gvizPlot: no visible global function definition for 'setNames'
gvizPlot : <anonymous>: no visible binding for global variable
'subjType'
gvizPlot : <anonymous>: no visible binding for global variable
'queryID'
gvizPlot: no visible global function definition for 'pdf'
gvizPlot: no visible global function definition for 'dev.off'
sumPlot: no visible binding for global variable 'query'
sumPlot: no visible binding for global variable 'xtext'
sumPlot: no visible binding for global variable 'lab'
Undefined global functions or variables:
dev.off lab pdf query queryID setNames subjType xtext
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/26s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gvizPlot 4.879 0.827 10.656
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2431/36b9c1ae7df7ab073a0499832583bfe99acdeb7c/OGRE.Rcheck/00check.log’
for details.
===============================
BiocCheck('OGRE_0.99.3.tar.gz')
===============================
This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 8 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
gvizPlot (setNames)
gvizPlot (subjType)
gvizPlot (queryID)
gvizPlot (pdf)
gvizPlot (dev.off)
sumPlot (query)
sumPlot (xtext)
sumPlot (lab)
* 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 4.0 to 4.1.0.
* 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
See http://bioconductor.org/developers/how-to/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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/OGRE.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of OGRE...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/methods.R (line 158, column 9)
R/methods.R (line 165, column 23)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
methods.R (line 221, column 42)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.........
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
sumPlot() (R/methods.R, line 136): 55 lines
gvizPlot() (R/methods.R, line 213): 49 lines
fOverlaps() (R/methods.R, line 88): 35 lines
OGREDataSetFromDir() (R/main.R, line 17): 25 lines
readQuery() (R/methods.R, line 28): 20 lines
* Checking man page documentation...
* 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
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 93 lines (15%) are > 80 characters
long.
First 6 lines:
R/main.R:3 #' Builds a `OGREDataset` from user specified directories co...
R/main.R:4 #' A `OGREDataset` is a `GenomicRangesList` with stores data...
R/main.R:5 #' @param queryFolder A \code{character} path pointing to th...
R/main.R:6 #' @param subjectFolder A \code{character} path pointing to ...
R/main.R:13 #' mySubjectFolder <- file.path(system.file('extdata', pack...
R/main.R:14 #' myOGRE <- OGREDataSetFromDir(queryFolder=myQueryFolder,s...
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
First 1 lines:
vignettes/OGRE.Rmd:38 ```
* NOTE: Consider multiples of 4 spaces for line indents, 153
lines(24%) are not.
First 6 lines:
R/main.R:18 assertthat::assert_that(!is.null(queryFolder),msg="Please...
R/main.R:19 assertthat::assert_that(!is.null(subjectFolder),msg="Plea...
R/main.R:20 assertthat::assert_that(is(queryFolder,"character"),msg="...
R/main.R:21 assertthat::assert_that(is(subjectFolder,"character"),msg...
R/main.R:24 message("Initializing OGREDataSet... ")
R/main.R:25 OGREDataSet <- GRangesList()
See http://bioconductor.org/developers/how-to/coding-style/
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 name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output