===============================
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/2294/8d874af33ca7b0da903921353d68c6389f2b09bc/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 ‘0.99.7’
* 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 ... [31s/31s] 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 ... [32s/32s] OK
* 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 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 ... [15s/15s] OK
* 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
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BiocCheck('epimutacions_0.99.7.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...
* WARNING: Import stats, utils in DESCRIPTION as well as NAMESPACE.
* 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 326, column 21)
mlmtst.R (line 111, column 40)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
epimutations.R (line 328, column 31)
mlm.R (line 227, column 39)
mlmtst.R (line 58, column 15)
mlmtst.R (line 111, column 25)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/RtmpYQsmog/file196e156af807ee/epimutacions/R/annotate_cpg.R
(line 36, column 17)
/tmp/RtmpYQsmog/file196e156af807ee/epimutacions/R/annotate_cpg.R
(line 48, column 17)
/tmp/RtmpYQsmog/file196e156af807ee/epimutacions/R/annotate_cpg.R
(line 53, column 17)
/tmp/RtmpYQsmog/file196e156af807ee/epimutacions/R/epimutations.R
(line 176, column 25)
/tmp/RtmpYQsmog/file196e156af807ee/epimutacions/R/epimutations.R
(line 200, column 31)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 2
times)
T in R/mlmtst.R (line 151, column 39)
T in R/mlmtst.R (line 151, column 56)
* 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 260, column 17)
* Checking function lengths...............................
* NOTE: Recommended function length <= 50 lines.
There are 13 functions > 50 lines.
The longest 5 functions are:
epimutations() (R/epimutations.R, line 74): 278 lines
epi_quantile() (R/epi_quantile.R, line 26): 193 lines
plot_epimutations() (R/plot_epimutations.R, line 47): 164 lines
mlmtst() (R/mlmtst.R, line 33): 125 lines
mlm() (R/mlm.R, line 53): 116 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/printCoefmat.mp.Rd
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
epi_preprocess.Rd, mlm.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; 603 lines (13%) 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; 261 lines (6%) 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, 1177
lines(25%) 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...
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: 3
NOTE count: 11
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.