===============================
R CMD BUILD
===============================
* checking for file ‘dmGsea/DESCRIPTION’ ... OK
* preparing ‘dmGsea’:
* 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 ‘dmGsea_0.99.0.tar.gz’
===============================
BiocCheckGitClone('dmGsea')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3711/31fd947f9a8cd6cca3a6c778dadba84cf2fe1dcd/dmGsea
→ BiocVersion: 3.22
→ Package: dmGsea
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3711/31fd947f9a8cd6cca3a6c778dadba84cf2fe1dcd/dmGsea.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3711/31fd947f9a8cd6cca3a6c778dadba84cf2fe1dcd/dmGsea
→ 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 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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3711/31fd947f9a8cd6cca3a6c778dadba84cf2fe1dcd/dmGsea.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dmGsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dmGsea’ version ‘0.99.0’
* 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 serialization versions ... OK
* checking whether package ‘dmGsea’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [24s/24s] 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 files in ‘vignettes’ ... OK
* checking examples ... [147s/179s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getIlluminaAnnotation 47.726 4.922 52.777
getMSigDB 37.716 1.117 61.017
getGO 13.120 1.073 14.286
getReactome 6.035 0.361 9.447
getKEGG 0.299 0.036 6.631
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [65s/59s]
[65s/59s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
> test_check("dmGsea")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gsPG.R:16:5'): gsPG runs without error and returns numeric output ──
Error in `.check_ncores(cores)`: 5 simultaneous processes spawned
Backtrace:
▆
1. └─dmGsea::gsPG(...) at test-gsPG.R:16:5
2. └─parallel::mclapply(...)
3. └─parallel:::.check_ncores(cores)
── Error ('test-gsProbe.R:16:5'): gsProbe runs with probe-level p-values ───────
Error in `.check_ncores(cores)`: 5 simultaneous processes spawned
Backtrace:
▆
1. └─dmGsea::gsProbe(...) at test-gsProbe.R:16:5
2. └─parallel::mclapply(...)
3. └─parallel:::.check_ncores(cores)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
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: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3711/31fd947f9a8cd6cca3a6c778dadba84cf2fe1dcd/dmGsea.Rcheck/00check.log’
for details.
===============================
BiocCheck('dmGsea_0.99.0.tar.gz')
===============================
── Installing dmGsea ───────────────────────────────────────────────────────────
✔ Package installed successfully
── dmGsea session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuCN1H9/file14ed412aa431bd/dmGsea
→ BiocVersion: 3.22
→ Package: dmGsea
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3711/31fd947f9a8cd6cca3a6c778dadba84cf2fe1dcd/dmGsea.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpuCN1H9/file14ed412aa431bd/dmGsea
→ installDir: /tmp/RtmpuCN1H9/file14ed4150a6007a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dmGsea ─────────────────────────────────────────────────
* 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 (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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 dmGsea...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/gsPG.R (line 165, column 9)
• ...
• R/gsRank.R (line 195, column 33)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/gsGene.R (line 56, column 10)
• ...
• R/utils.R (line 122, column 22)
* 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 4
functions greater than 50 lines.
The longest 5 functions are:
• betaFitPermu() (R/gsRank.R): 143 lines
• ...
• gsProbe() (R/gsProbe.R): 69 lines
* Checking man page documentation...
* 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 multiples of 4 spaces for line indents; 74 lines (4%) are not.
First few lines:
• R/gsPG.R#L153 Sig.Gene <- vapply(geneSet,function(x) ...
• ...
• vignettes/dmGsea.Rmd#L92 by variable numbers of probes per gene ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 4 NOTES
i See the dmGsea.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.