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R CMD BUILD
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* checking for file ‘epimutacions/DESCRIPTION’ ... OK
* preparing ‘epimutacions’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘epimutacions_0.99.2.tar.gz’
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BiocCheckGitClone('epimutacions')
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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...
* 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/2294/cf2de6e4644a65f9b3519e7276baa630d63e0558/epimutacions.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 ‘epimutacions/DESCRIPTION’ ... OK
* this is package ‘epimutacions’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Packages suggested but not available: 'mlm', 'epimutacionsData'
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2294/cf2de6e4644a65f9b3519e7276baa630d63e0558/epimutacions.Rcheck/00check.log’
for details.
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BiocCheck('epimutacions_0.99.2.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...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
function (object)
epi_quantile (chr)
* 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...
* 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...
* 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...
* 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 epimutacions...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
annotate_cpg.R (line 62, column 30)
epimutations.R (line 327, column 21)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
epimutations.R (line 329, column 31)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/RtmpvJNk43/file378a583e80d81c/epimutacions/R/annotate_cpg.R
(line 36, column 17)
/tmp/RtmpvJNk43/file378a583e80d81c/epimutacions/R/annotate_cpg.R
(line 48, column 17)
/tmp/RtmpvJNk43/file378a583e80d81c/epimutacions/R/annotate_cpg.R
(line 53, column 17)
/tmp/RtmpvJNk43/file378a583e80d81c/epimutacions/R/epimutations.R
(line 176, column 25)
/tmp/RtmpvJNk43/file378a583e80d81c/epimutacions/R/epimutations.R
(line 200, column 31)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
times)
suppressWarnings() in R/epi_plot.R (line 210, column 17)
suppressWarnings() in R/epi_plot.R (line 226, column 14)
suppressWarnings() in R/epi_plot.R (line 242, column 14)
suppressMessages() in R/epi_plot.R (line 183, column 18)
suppressWarnings() in R/epimutations.R (line 190, column 7)
suppressWarnings() in R/epimutations.R (line 261, column 17)
* Checking function lengths.............................
* NOTE: Recommended function length <= 50 lines.
There are 10 functions > 50 lines.
The longest 5 functions are:
epimutations() (R/epimutations.R, line 74): 279 lines
epi_quantile() (R/epi_quantile.R, line 26): 193 lines
plot_epimutations() (R/plot_epimutations.R, line 49): 164 lines
annotate_cpg() (R/annotate_cpg.R, line 16): 95 lines
get_regions() (R/epi_quantile.R, line 76): 78 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
epi_preprocess.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
3% of man pages use one of these cases.
Found in the following files:
epi_preprocess.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
epi_preprocess.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; 559 lines (15%) are > 80 characters
long.
First 6 lines:
R/add_ensemble_regulatory.R:87 out <- data.frame(ensembl_reg_id = past...
R/add_ensemble_regulatory.R:88 ensembl_reg_coordinates = paste(r...
R/add_ensemble_regulatory.R:90 ensembl_reg_tissues = paste(reg_v...
R/annotate_cpg.R:7 #' @param split a character string containing the se...
R/annotate_cpg.R:9 #' @param gene_col column name from where to extract...
R/annotate_cpg.R:10 #' @param feat_col column name from where to extrac...
* NOTE: Consider 4 spaces instead of tabs; 262 lines (7%) contain
tabs.
First 6 lines:
R/add_ensemble_regulatory.R:33
R/add_ensemble_regulatory.R:34 ## Create connection to ENSEMBL
R/add_ensemble_regulatory.R:35 mart <- biomaRt::useEnsembl(biomart = "...
R/add_ensemble_regulatory.R:36 ensembl <- biomaRt::useDataset(dataset ...
R/add_ensemble_regulatory.R:37 mart = mart)
R/add_ensemble_regulatory.R:39 reg_res <- lapply(seq_len(nrow(epimutat...
* NOTE: Consider multiples of 4 spaces for line indents, 884
lines(23%) are not.
First 6 lines:
R/add_ensemble_regulatory.R:30
R/add_ensemble_regulatory.R:31 ## Remove chr from chromosome
R/add_ensemble_regulatory.R:32 epimutations$chromosome <- gsub("chr",...
R/epi_beta.R:24 diff_threshold, min_cpgs = 3, max...
R/epi_beta.R:25
R/epi_beta.R:26
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...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 14
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.