===============================
R CMD BUILD
===============================
* checking for file ‘SigFun/DESCRIPTION’ ... OK
* preparing ‘SigFun’:
* 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 ‘SigFun_0.99.0.tar.gz’
===============================
BiocCheckGitClone('SigFun')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3734/SigFun_20250224152636/SigFun
→ BiocVersion: 3.21
→ Package: SigFun
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3734/SigFun_20250224152636/SigFun.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3734/SigFun_20250224152636/SigFun
→ 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 v1.43.12 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/3734/SigFun_20250224152636/SigFun.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 ‘SigFun/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigFun’ 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 ... ERROR
Found the following files with duplicate lower-cased file names:
data/sig2GSEA_input.RData
File names must not differ just by case to be usable on all R
platforms.
Please rename the files and try again.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SigFun’ 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 ... [7s/7s] 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 ... [22s/22s] NOTE
plot_bar: no visible global function definition for ‘metadata’
plot_heat: no visible global function definition for ‘metadata’
sig2Fun: no visible global function definition for ‘metadata’
sig2Fun: no visible global function definition for ‘metadata<-’
sig2GSEA: no visible global function definition for ‘metadata’
sig2GSEA: no visible global function definition for ‘metadata<-’
sigCor: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
metadata metadata<-
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] ERROR
Running examples in ‘SigFun-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_bar
> ### Title: plot_bar
> ### Aliases: plot_bar
>
> ### ** Examples
>
> data("demo")
> output_path <- tempdir()
> res_plot <- plot_bar(
+ SE_data.fgsea=SE_data,
+ output_path=output_path,
+ topN=10,
+ significat_type="pval",
+ strings=c("KEGG"))
Error in metadata(SE_data.fgsea) : could not find function "metadata"
Calls: plot_bar -> %>% -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [137s/89s]
[137s/90s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-sig2Fun.R:28:3'): sig2Fun processes data correctly and creates expected outputs ──
!is.null(result@metadata$fgseaRes) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-sig2Fun.R:29:3'): sig2Fun processes data correctly and creates expected outputs ──
!is.null(result@metadata$cor.df) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-sig2Fun.R:119:3'): sig2Fun handles parameter variations correctly ──
... != 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 120 ]
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: 3 ERRORs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3734/SigFun_20250224152636/SigFun.Rcheck/00check.log’
for details.
===============================
BiocCheck('SigFun_0.99.0.tar.gz')
===============================
── Installing SigFun ───────────────────────────────────────────────────────────
✔ Package installed successfully
── SigFun session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwitnOf/file33730f5a3e4af1/SigFun
→ BiocVersion: 3.21
→ Package: SigFun
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3734/SigFun_20250224152636/SigFun.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/RtmpwitnOf/file33730f5a3e4af1/SigFun
→ installDir: /tmp/RtmpwitnOf/file33730f10cc263b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SigFun ─────────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.4.0 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...
* 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 (24%).
* 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 .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 SigFun...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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...
* 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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.43.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 2 NOTES
i See the SigFun.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.