===============================
BiocCheckGitClone('asuri')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/asuri_20250630182910/asuri
→ BiocVersion: 3.22
→ Package: asuri
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/asuri_20250630182910/asuri.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/asuri_20250630182910/asuri
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.7 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/3793/asuri_20250630182910/asuri.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘asuri/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘asuri’ 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 whether package ‘asuri’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... NOTE
Namespace in Imports field not imported from: ‘lubridate’
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 ... [25s/25s] OK
* checking Rd files ... [7s/7s] 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 ... [57s/57s] ERROR
Running examples in ‘asuri-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genePheno
> ### Title: Identify Predictive Genes for a Phenotype
> ### Aliases: genePheno
>
> ### ** Examples
>
> data(seBRCA)
>
> # prefilterSAM ---
> groupsVector <- SummarizedExperiment::colData(seBRCA)$ER.IHC
> set.seed(5)
> DE_list_genes <- prefilterSAM(seBRCA, groupsVector)
2025-06-30 14:38:09.591725
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|==================================================| 99%
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2025-06-30 14:38:59.134842
>
> # genePheno ---
> vectorSampleID <- rownames(SummarizedExperiment::colData(seBRCA))
> vectorGroups <- SummarizedExperiment::colData(seBRCA)$ER.IHC
>
> Pred_ER.IHC <- genePheno(seBRCA, DE_list_genes, vectorGroups, vectorSampleID)
Error in genePheno(seBRCA, DE_list_genes, vectorGroups, vectorSampleID) :
'vectorGroups' must be a numeric vector.
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, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3793/asuri_20250630182910/asuri.Rcheck/00check.log’
for details.
===============================
BiocCheck('asuri_0.99.0.tar.gz')
===============================
── Installing asuri ────────────────────────────────────────────────────────────
✔ Package installed successfully
── asuri session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri
→ BiocVersion: 3.22
→ Package: asuri
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/asuri_20250630182910/asuri.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri
→ installDir: /tmp/RtmpyOEMg9/file12ef4d6307e96d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on asuri ──────────────────────────────────────────────────
* 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 (27%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• asuri.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:103: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:104: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:122: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:170: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:171: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:96: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:97: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:137: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:66: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:67: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
* Checking for library/require of asuri...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/plotFunctions.R (line 262, column 14)
• R/plotFunctions.R (line 263, column 15)
* 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 12
functions greater than 50 lines.
The longest 5 functions are:
• patientRisk() (R/patientRisk.R): 550 lines
• ...
• plotKmCustomGroups() (R/plotFunctions.R): 125 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:103: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:104: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:122: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:170: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:171: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:96: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:97: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:137: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:66: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:67: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:103: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:104: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:122: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:170: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:171: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:96: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:97: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:137: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:66: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:67: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:103: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/genePheno.Rd:104: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:122: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:170: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/patientRisk.Rd:171: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:96: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_PatientRisk.Rd:97: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:137: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:66: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:67: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpyOEMg9/file12ef4d79f0a42b/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 143 lines (4%) are > 80 characters long.
First few lines:
• vignettes/asuri.Rmd#L2 title: "ASURI: An R Package for Survival ...
• ...
• vignettes/asuri.Rmd#L504 ```{r predSurv, fig.cap="Survival curve ...
i NOTE: Consider multiples of 4 spaces for line indents; 738 lines (19%) are
not.
First few lines:
• R/genePheno.R#L92 stop("SEdata must be a 'Summarized ...
• ...
• vignettes/asuri.Rmd#L421 nrow = length( ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.45.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the asuri.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.