===============================
R CMD BUILD
===============================
* checking for file ‘MotifPeeker/DESCRIPTION’ ... OK
* preparing ‘MotifPeeker’:
* 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 ‘MotifPeeker_0.99.5.tar.gz’
===============================
BiocCheckGitClone('MotifPeeker')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/32bfd3fccf4dd4babce8e6e074102a5d3c2386f7/MotifPeeker
→ BiocVersion: 3.20
→ Package: MotifPeeker
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/32bfd3fccf4dd4babce8e6e074102a5d3c2386f7/MotifPeeker.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/32bfd3fccf4dd4babce8e6e074102a5d3c2386f7/MotifPeeker
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/32bfd3fccf4dd4babce8e6e074102a5d3c2386f7/MotifPeeker.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotifPeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotifPeeker’ version ‘0.99.5’
* 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 ‘MotifPeeker’ can be installed ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [34s/34s] 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/28s] ERROR
Running examples in ‘MotifPeeker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: denovo_motifs
> ### Title: Find de-novo motifs in sequences
> ### Aliases: denovo_motifs
>
> ### ** Examples
>
> data("CTCF_TIP_peaks", package = "MotifPeeker")
> if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
+ genome_build <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
+
+ res <- denovo_motifs(list(CTCF_TIP_peaks),
+ trim_seq_width = 100,
+ genome_build = genome_build,
+ denovo_motifs = 2,
+ filter_n = 6,
+ out_dir = tempdir())
+ print(res[[1]]$consensus)
+ }
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in .check_valid_command_path(validPathHierarchy[[1]]): Command: /home/pkgbuild/meme/bin, does not exist.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [28s/29s]
[28s/29s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Error in `.check_valid_command_path(validPathHierarchy[[1]])`: Command: /home/pkgbuild/meme/bin, does not exist.
Backtrace:
▆
1. └─MotifPeeker::motif_enrichment(...) at test-motif_enrichment.R:8:5
2. ├─memes::runAme(...)
3. └─memes:::runAme.default(...)
4. └─memes:::search_meme_path(path = meme_path, util = "ame")
5. └─cmdfun (local) f(path, util)
6. └─cmdfun::.check_valid_command_path(validPathHierarchy[[1]])
── Error ('test-summit_to_motif.R:7:5'): list outputted by summit_to_motif function ──
Error in `.check_valid_command_path(validPathHierarchy[[1]])`: Command: /home/pkgbuild/meme/bin, does not exist.
Backtrace:
▆
1. └─MotifPeeker::summit_to_motif(...) at test-summit_to_motif.R:7:5
2. └─memes::runFimo(...)
3. └─memes:::search_meme_path(path = meme_path, util = "fimo")
4. └─cmdfun (local) f(path, util)
5. └─cmdfun::.check_valid_command_path(validPathHierarchy[[1]])
[ FAIL 6 | WARN 2 | SKIP 2 | PASS 125 ]
Error: Test failures
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/32bfd3fccf4dd4babce8e6e074102a5d3c2386f7/MotifPeeker.Rcheck/00check.log’
for details.
===============================
BiocCheck('MotifPeeker_0.99.5.tar.gz')
===============================
── Installing MotifPeeker ──────────────────────────────────────────────────────
✔ Package installed successfully
── MotifPeeker session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpT3Zk2Y/file10f22b2fda5f79/MotifPeeker
→ BiocVersion: 3.20
→ Package: MotifPeeker
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3483/32bfd3fccf4dd4babce8e6e074102a5d3c2386f7/MotifPeeker.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpT3Zk2Y/file10f22b2fda5f79/MotifPeeker
→ installDir: /tmp/RtmpT3Zk2Y/file10f22b345bf824
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MotifPeeker ────────────────────────────────────────────
* 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 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 (50%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MotifPeeker...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/plot_motif_comparison.R (line 52, column 46)
• ...
• cat() in R/print_labels.R (line 42, column 9)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• MotifPeeker() (R/MotifPeeker.R): 138 lines
• ...
• plot_motif_comparison() (R/plot_motif_comparison.R): 53 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
Found in files:
• find_motifs.Rd
• ...
• plot_enrichment_overall.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; 23 lines (1%) are > 80 characters long.
First few lines:
• R/calc_frip.R#L7 #' \deqn{\text{FRiP} = \frac{(\text{numb ...
• ...
• vignettes/troubleshooting.Rmd#L42 Additionally, follow the [runtime gu ...
i NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
First few lines:
• R/utilities.R#L148 "unique experiment ...
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...
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 5 NOTES
i See the MotifPeeker.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.