===============================
BiocCheckGitClone('JASPAR2022')
===============================
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/2427/b86c253756ec49552f12cf86570d78e9cb86d7dc/JASPAR2022.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 ‘JASPAR2022/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘JASPAR2022’ version ‘0.99.4’
* 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 ‘JASPAR2022’ can be installed ... [1s/15s] OK
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
extdata 7.3Mb
* 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 ...Loading required package: methods
Error: package or namespace load failed for ‘JASPAR2022’:
.onLoad failed in loadNamespace() for 'JASPAR2022', details:
call: read.csv(paste0(path, "/metadata.csv"))
error: could not find function "read.csv"
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 ... WARNING
Error: package or namespace load failed for ‘JASPAR2022’:
.onLoad failed in loadNamespace() for 'JASPAR2022', details:
call: read.csv(paste0(path, "/metadata.csv"))
error: could not find function "read.csv"
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error: .onLoad failed in loadNamespace() for 'JASPAR2022', details:
call: read.csv(paste0(path, "/metadata.csv"))
error: could not find function "read.csv"
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 ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘JASPAR2022’:
.onLoad failed in loadNamespace() for 'JASPAR2022', details:
call: read.csv(paste0(path, "/metadata.csv"))
error: could not find function "read.csv"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return && !quietly)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: lib
Execution halted
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/15s] NOTE
Error: .onLoad failed in loadNamespace() for 'JASPAR2022', details:
call: read.csv(paste0(path, "/metadata.csv"))
error: could not find function "read.csv"
Execution halted
* 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 ... [11s/23s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
JASPAR2022-class 9.123 0.331 9.453
* 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: 2 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2427/b86c253756ec49552f12cf86570d78e9cb86d7dc/JASPAR2022.Rcheck/00check.log’
for details.
===============================
BiocCheck('JASPAR2022_0.99.4.tar.gz')
===============================
This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
trying URL 'https://jaspar.genereg.net/download/database/JASPAR2022.sqlite'
Content type 'application/octet-stream' length 7688192 bytes (7.3 MB)
==================================================
downloaded 7.3 MB
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.14-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.14-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/tmp/RtmpITtqI1/file3ce46729daab14/lib/JASPAR2022" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 3.6.0 to 4.1.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
AnnotationData
* 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:
PackageType
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...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of JASPAR2022...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths....
* 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; 20 lines (10%) are > 80 characters
long.
First 6 lines:
R/AllClasses.R:3 #' @description The JASPAR2022 object class is a thin ...
man/JASPAR2022-class.Rd:15 \item{\code{db}}{Object of class \code{"char...
vignettes/JASPAR2022.Rmd:6 affiliation: Imperial College London, Fa...
vignettes/JASPAR2022.Rmd:30 JASPAR (http://jaspar.genereg.net) is an op...
vignettes/JASPAR2022.Rmd:31 transcription factor (TF)-binding profiles ...
vignettes/JASPAR2022.Rmd:32 across multiple species in six taxonomic gr...
* NOTE: Consider multiples of 4 spaces for line indents, 16
lines(8%) are not.
First 6 lines:
R/AllClasses.R:25 )
R/zzz.R:2 ns <- asNamespace(pkgname)
R/zzz.R:3 path <- system.file("extdata", package=pkgname, lib.loc=lib...
R/zzz.R:4 metaData <- read.csv(paste0(path, "/metadata.csv"))
R/zzz.R:5 download.file(metaData$SourceUrl, destfile =
R/zzz.R:6 paste0(path, "/", basename(metaData$SourceU...
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: 1
NOTE count: 6
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