===============================
R CMD BUILD
===============================
* checking for file ‘epimutacions/DESCRIPTION’ ... OK
* preparing ‘epimutacions’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epimutacions.Rmd’ using rmarkdown
Loading required package: epimutacionsData
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-11-24
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
require("minfi")
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
Selected epimutation detection method 'manova'
Selected method 'manova' required of 'bumphunter'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 1643 bumps.
66candidate regions were found for case sample 'GSM2562699'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 1928 bumps.
79candidate regions were found for case sample 'GSM2562700'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2039 bumps.
88candidate regions were found for case sample 'GSM2562701'
snapshotDate(): 2021-11-24
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
Quitting from lines 319-322 (epimutacions.Rmd)
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
BiocParallel errors
1 remote errors, element index: 1
10 unevaluated and other errors
first remote error:
Error in .SummarizedExperiment.charbound(j, colnames(x), fmt): <GenomicRatioSet>[,j] index out of bounds: GSM2808239
--- failed re-building ‘epimutacions.Rmd’
SUMMARY: processing the following file failed:
‘epimutacions.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
BiocCheckGitClone('epimutacions')
===============================
This is BiocCheckGitClone version 1.31.14. 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2294/ca1ef1b693aa449e90cfeec48c3e5b40fe88c7a3/epimutacions.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* 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 ‘0.99.12’
* 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 ‘epimutacions’ can be installed ... [56s/56s] 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 ... [53s/53s] OK
* checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [139s/156s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotate_epimutations 42.358 3.505 61.109
epi_preprocess 37.127 1.104 38.711
epimutations_one_leave_out 8.967 0.200 9.955
plot_epimutations 4.823 0.176 5.354
* 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: OK
===============================
BiocCheck('epimutacions_0.99.12.tar.gz')
===============================
This is BiocCheck version 1.31.14. 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 4.1.0 to 4.2.0.
* 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...
* 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 1:...; use seq_len() or seq_along()
Found in files:
epimutations.R (line 362, 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 251, column 17)
suppressWarnings() in R/epi_plot.R (line 273, column 14)
suppressWarnings() in R/epi_plot.R (line 291, column 14)
suppressMessages() in R/epi_plot.R (line 224, column 18)
suppressWarnings() in R/epimutations.R (line 192, column 7)
suppressWarnings() in R/epimutations.R (line 282, column 17)
* Checking function lengths * NOTE: Recommended function length <= 50 lines.
There are 14 functions > 50 lines.
The longest 5 functions are:
epimutations() (R/epimutations.R, line 74): 317 lines
plot_epimutations() (R/plot_epimutations.R, line 49): 223 lines
epi_quantile() (R/epi_quantile.R, line 26): 202 lines
mlmtst() (R/mlmtst.R, line 33): 127 lines
mlm() (R/mlm.R, line 53): 116 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* ERROR: Add a .R or .Rin file in tests/ directory or unit tests
will not be run by R CMD check. 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; 461 lines (9%) are > 80 characters
long.
First 6 lines:
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...
R/annotate_cpg.R:11 #' @param relat_col column name from where to extra...
R/annotate_cpg.R:13 #' @param omim a boolean, if TRUE will annotate OMI...
R/annotate_cpg.R:18 epi_col = 'cpg_ids', gene_col = 'GencodeBasicV12_...
* NOTE: Consider 4 spaces instead of tabs; 272 lines (5%) 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, 1350
lines(27%) 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/annotate_epimutations.R:39 function(epi_results,
R/annotate_epimutations.R:40 db = "IlluminaHumanMethylationE...
R/annotate_epimutations.R:41 build = "37", ...){
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: 1
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.