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R CMD BUILD
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* checking for file ‘benchmark.data.scRNAseq/DESCRIPTION’ ... OK
* preparing ‘benchmark.data.scRNAseq’:
* checking DESCRIPTION meta-information ... 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 ‘benchmark.data.scRNAseq_0.99.0.tar.gz’
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BiocCheckGitClone('benchmark.data.scRNAseq')
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This is BiocCheckGitClone version 1.29.14. 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...
* ERROR: Do not use Author/Maintainer fields. Use Authors@R.
* 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/2279/benchmark.data.scRNAseq_20210922163322/benchmark.data.scRNAseq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchmark.data.scRNAseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchmark.data.scRNAseq’ 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 serialization versions ... OK
* checking whether package ‘benchmark.data.scRNAseq’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 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 Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'cellmix'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'cellmix':
‘library’
Assignments in \usage in documentation object 'cellmix':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'darmanis'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'darmanis':
‘library’
Assignments in \usage in documentation object 'darmanis':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'hca_bm'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'hca_bm':
‘library’
Assignments in \usage in documentation object 'hca_bm':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'hca_cb'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'hca_cb':
‘library’
Assignments in \usage in documentation object 'hca_cb':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'hipsc'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'hipsc':
‘library’
Assignments in \usage in documentation object 'hipsc':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'kolodziejczyk'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'kolodziejczyk':
‘library’
Assignments in \usage in documentation object 'kolodziejczyk':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'pbmc'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'pbmc':
‘library’
Assignments in \usage in documentation object 'pbmc':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pbmc"))
pbmc = x[[1]]
Undocumented arguments in documentation object 'pollen'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'pollen':
‘library’
Assignments in \usage in documentation object 'pollen':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "pollen"))
pollen = x[[1]]
Undocumented arguments in documentation object 'zeisel'
‘ExperimentHub’
Objects in \usage without \alias in documentation object 'zeisel':
‘library’
Assignments in \usage in documentation object 'zeisel':
hub <- ExperimentHub()
x <- query(hub, c("benchmark.data.scRNAseq", "zeisel"))
zeisel = x[[1]]
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘benchmark.data.scRNAseq.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... [4s/5s] OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode character ∼ (U+223C)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
Status: 1 ERROR, 3 WARNINGs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2279/benchmark.data.scRNAseq_20210922163322/benchmark.data.scRNAseq.Rcheck/00check.log’
for details.
===============================
BiocCheck('benchmark.data.scRNAseq_0.99.0.tar.gz')
===============================
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...
* 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 2.10 to 4.1.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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:
SequencingData, RNASeqData
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...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import SingleCellExperiment, ExperimentHub in NAMESPACE
as well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking vignette directory...
* ERROR: VignetteEngine specified but not in DESCRIPTION. Add the
VignetteEngine from the following files to DESCRIPTION:
benchmark.data.scRNAseq.Rmd
* ERROR: No VignetteEngine specified in vignette or DESCRIPTION.
Add VignetteEngine to the following files or add a default
VignetteBuilder in DESCRIPTION:
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested. Add the following to Suggests in
DESCRIPTION:
knitr
* WARNING: Evaluate more vignette chunks.
# of code chunks: 3
# of eval=FALSE: 0
# of nonexecutable code chunks by syntax: 3
# total unevaluated 3 (100%)
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/benchmark.data.scRNAseq.Rmd
* Checking whether vignette is built with 'R CMD build'...
* ERROR: Vignette must be built by 'R CMD build'. Please see the
`Vignette Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of benchmark.data.scRNAseq...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths..
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
10% of man pages use one of these cases.
Found in the following files:
benchmark.data.scRNAseq.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
benchmark.data.scRNAseq.Rd
* 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; 4 lines (1%) are > 80 characters
long.
First 4 lines:
man/hca_bm.Rd:9 \url{https://data.humancellatlas.org/explore/projects/c...
man/hca_cb.Rd:9 \url{https://data.humancellatlas.org/explore/projects/c...
man/pbmc.Rd:9 \url{https://support.10xgenomics.com/single-cell-gene-exp...
vignettes/benchmark.data.scRNAseq.Rmd:15 This package provides access t...
* NOTE: Consider multiples of 4 spaces for line indents, 3
lines(1%) are not.
First 3 lines:
vignettes/benchmark.data.scRNAseq.Rmd:6 %\VignetteIndexEntry{Single-C...
vignettes/benchmark.data.scRNAseq.Rmd:7 %\VignetteEngine{knitr::rmark...
vignettes/benchmark.data.scRNAseq.Rmd:9 BiocStyle::html_document
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: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 6
WARNING count: 3
NOTE count: 10
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
BiocCheck FAILED.