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R CMD BUILD
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* checking for file ‘JASPAR2022/DESCRIPTION’ ... OK
* preparing ‘JASPAR2022’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘JASPAR2022_0.99.2.tar.gz’
===============================
BiocCheckGitClone('JASPAR2022')
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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
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2427/639a4842675e45beb065672414f8a90fe51b5dfc/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’ ... ERROR
Required fields missing or empty:
‘Author’ ‘Maintainer’
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2427/639a4842675e45beb065672414f8a90fe51b5dfc/JASPAR2022.Rcheck/00check.log’
for details.
===============================
BiocCheck('JASPAR2022_0.99.2.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/Rtmps9j6p1/file2eeb3e49277b22/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...
* ERROR: No Authors@R [cre] field in DESCRIPTION file.
* 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...
Error in getMaintainerEmail(pkgdir) : object 'email' not found
Calls: BiocCheck ... checkForBiocDevelSubscription -> getMaintainerEmail
Execution halted