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BiocCheckGitClone('RegionPropertiesFeatures')
===============================
This is BiocCheckGitClone version 1.29.14. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
RegionPropertiesFeatures.Rproj
vignettes/.Rhistory
.DS_Store
inst/.DS_Store
inst/doc/.DS_Store
inst/figures/.DS_Store
man/.DS_Store
R/.DS_Store
vignettes/.DS_Store
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2183/4985692b1332265df4297e71454ea6c696652e49/RegionPropertiesFeatures.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RegionPropertiesFeatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegionPropertiesFeatures’ version ‘0.99.91’
* 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 ‘RegionPropertiesFeatures’ can be installed ... [28s/28s] 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] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'extractRegionProperty-methods.Rd':
\examples lines wider than 100 characters:
GSE63753_abcam <- readRDS(system.file("extdata", "GSE63753_abcam.rds", package = "RegionPropertiesFeatures"))
## The metadata column of the GRanges is a 0/1 vector, 1 for the positive m6A site, 0 is the negative DRACH:
GSE63753_abcam$exon_length <- extractRegionLength(GSE63753_abcam, exons(TxDb.Hsapiens.UCSC.hg19.knownGene))
geom_smooth(formula = y ~ splines::ns(x, 3), method = "glm", method.args = list(family = "binomial")) +
theme_classic() + labs(x = "log(length of exon)", y = "prob of m6A = 1", title = "LR fit with cubic splines")
Rd file 'genomeDerivedFeatures.Rd':
\examples lines wider than 100 characters:
clusteringY=X) #quantify clustering properties of x itself
Rd file 'topologyOnTranscripts.Rd':
\examples lines wider than 100 characters:
GSE63753_sysy <- readRDS(system.file("extdata", "GSE63753_sysy.rds", package = "RegionPropertiesFeatures"))
geom_smooth(formula = y ~ splines::ns(x, 8), method = "glm", method.args = list(family = "binomial")) +
scale_x_continuous(breaks = c(0, 0.33, 0.66, 0.9)) + scale_y_continuous(breaks = c(0, 0.25, 0.5, 0.75, 1)) +
theme_classic() + labs(x = "meta-tx topology", y = "prob of m6A = 1", title = "LR fit with cubic splines")
These lines will be truncated in the PDF manual.
* 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 ... [93s/93s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
genomeDerivedFeatures 60.163 0.728 60.893
topologyOnTranscripts 16.253 0.167 16.422
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘phastCons100way.UCSC.hg19’
* 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2183/4985692b1332265df4297e71454ea6c696652e49/RegionPropertiesFeatures.Rcheck/00check.log’
for details.
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BiocCheck('RegionPropertiesFeatures_0.99.91.tar.gz')
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This is BiocCheck version 1.29.14. 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 2 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)
RegionPropertiesFeaturesUsersGuide (shell.exec)
RPFUsersGuide (shell.exec)
* 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...
* 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...
* NOTE: License 'LGPL (>= 3)' unknown; licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/Vignette_V_1.0.0.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RegionPropertiesFeatures...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
suppressWarnings() in R/genomeDerivedFeatures.R (line 520,
column 16)
suppressWarnings() in R/genomeDerivedFeatures.R (line 550,
column 28)
suppressWarnings() in R/genomeDerivedFeatures.R (line 892,
column 36)
suppressMessages() in R/genomeDerivedFeatures.R (line 892,
column 19)
suppressWarnings() in R/sequenceDerivedFeatures.R (line 119,
column 16)
* Checking function lengths................
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
genomeDerivedFeatures() (R/genomeDerivedFeatures.R, line 125):
445 lines
EnumerateRegionFeatures() (R/genomeDerivedFeatures.R, line
571): 246 lines
sequenceDerivedFeatures() (R/sequenceDerivedFeatures.R, line
75): 84 lines
_anonymous_.511() (R/RegionPropertiesFunctions.R, line 511): 72
lines
_anonymous_.393() (R/RegionPropertiesFunctions.R, line 393): 71
lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
RegionPropertiesFeaturesUsersGuide.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
71% of man pages use one of these cases.
Found in the following files:
extractRegionProperty-methods.Rd
genomeDerivedFeatures.Rd
RegionPropertiesFeaturesUsersGuide.Rd
RPFUsersGuide.Rd
sampleSequence.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
extractRegionProperty-methods.Rd
genomeDerivedFeatures.Rd
RegionPropertiesFeaturesUsersGuide.Rd
RPFUsersGuide.Rd
sampleSequence.Rd
* Checking package NEWS...
* 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; 565 lines (16%) are > 80 characters
long.
First 6 lines:
R/AllGenerics.R:5 #' If not provided (\code{region=NULL}), the returned...
R/AllGenerics.R:6 #' @param property A vector specifying the properties...
R/AllGenerics.R:8 #' @param ambiguityMethod By default, for \code{logic...
R/AllGenerics.R:10 #' For other types of \code{property} input, the ret...
R/AllGenerics.R:11 #' If \code{ambiguityMethod} is \code{"mean"}, \code...
R/AllGenerics.R:12 #' then the mean, sum, minimum, and maximum values o...
* NOTE: Consider multiples of 4 spaces for line indents, 1295
lines(37%) are not.
First 6 lines:
R/AllGenerics.R:51 region,
R/AllGenerics.R:52 property,
R/AllGenerics.R:53 ambigui...
R/AllGenerics.R:54 maxgap=...
R/AllGenerics.R:55 minover...
R/AllGenerics.R:56 type=c(...
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