===============================
R CMD BUILD
===============================
* checking for file ‘epiSeeker/DESCRIPTION’ ... OK
* preparing ‘epiSeeker’:
* 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
* building ‘epiSeeker_0.99.2.tar.gz’
===============================
BiocCheckGitClone('epiSeeker')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/b886c9d6cc92b720d997d45f5366a4555f25dd63/epiSeeker
→ BiocVersion: 3.22
→ Package: epiSeeker
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/b886c9d6cc92b720d997d45f5366a4555f25dd63/epiSeeker.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/b886c9d6cc92b720d997d45f5366a4555f25dd63/epiSeeker
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3952/b886c9d6cc92b720d997d45f5366a4555f25dd63/epiSeeker.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epiSeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epiSeeker’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘epiSeeker’ can be installed ... OK
* checking installed package size ... INFO
installed size is 6.5Mb
sub-directories of 1Mb or more:
data 4.9Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘RSQLite’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [19s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the package can be unloaded cleanly ... [18s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/17s] OK
* checking loading without being on the library search path ... [19s/19s] OK
* checking whether startup messages can be suppressed ... [19s/19s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' calls not declared from:
‘GEOmetadb’ ‘GEOquery’
Namespace in Imports field not imported from: ‘DSS’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [61s/61s] 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 ... [16s/16s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/54s] ERROR
Running examples in ‘epiSeeker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bmData
> ### Title: Constructor for bmData objects
> ### Aliases: bmData
>
> ### ** Examples
>
> data(Human_BSobj)
> tmp <- Human_BSobj[1:10,1]
> tmp_gr <- as.data.frame(tmp@rowRanges)
> bmData(value1 = assay(tmp, "M"),
+ value2 = assay(tmp, "cov"),
+ pos = tmp_gr$start,
+ chr = tmp_gr$seqnames)
Error in assay(tmp, "M") : could not find function "assay"
Calls: bmData -> vapply
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotateSeq 19.568 0.555 20.124
as.GRanges 14.204 0.146 14.350
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [132s/132s]
[132s/132s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [5s/5s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3952/b886c9d6cc92b720d997d45f5366a4555f25dd63/epiSeeker.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('epiSeeker_0.99.2.tar.gz')
===============================
── Installing epiSeeker ────────────────────────────────────────────────────────
✔ Package installed successfully
── epiSeeker session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpMIJjnz/file129427f1004ec/epiSeeker
→ BiocVersion: 3.22
→ Package: epiSeeker
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/b886c9d6cc92b720d997d45f5366a4555f25dd63/epiSeeker.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpMIJjnz/file129427f1004ec/epiSeeker
→ installDir: /tmp/RtmpMIJjnz/file12942732ad0634
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on epiSeeker ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (35%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• epiSeeker.rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of epiSeeker...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/enrichOverlap.R (line 221, column 18)
• ...
• R/utilities.R (line 495, column 27)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• annotateSeq.R (line 175, column 38)
• ...
• utilities.R (line 1184, column 36)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/annotateSeq.R (line 116, column 9)
• ...
• cat() in R/utilities.R (line 648, column 21)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/dplyr-verb.R (line 5, column 16)
• ...
• R/utilities.R (line 543, column 18)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/bmData.Rd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressWarnings() in R/addGeneAnno.R (line 31, column 9)
• ...
• suppressMessages() in R/utilities.R (line 436, column 25)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 45
functions greater than 50 lines.
The longest 5 functions are:
• plotBmProf.internal() (R/plotBmProf.R): 394 lines
• ...
• getGenomicAnnotation() (R/getGenomicAnnotation.R): 185 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• getPromoters.Rd
• ...
• plotAnnoPie-methods.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 561 lines (6%) are > 80 characters long.
First few lines:
• R/addGeneAnno.R#L24 message("geneID type is not supp ...
• ...
• vignettes/epiSeeker.rmd#L781 Here is the output of `sessionInfo()` on ...
i NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
First few lines:
• R/epiSeeker-package.R#L40 #' \item{areaStat}{ The sum of the tes ...
• ...
• R/getGenomicAnnotation.R#L195 annotation[j] <- lbs ...
i NOTE: Consider multiples of 4 spaces for line indents; 1938 lines (21%) are
not.
First few lines:
• R/AllGenerics.R#L15 function(x, r = 0.2, cex = 1.2, ...) ...
• ...
• vignettes/epiSeeker.rmd#L689 verbose = FALSE) ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.22/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.22/data/annotation
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/experiment/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.22/data/experiment
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/workflows/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.22/workflows
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 15 NOTES
i See the epiSeeker.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.