Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/asuri

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)/x86_64	OK	ERROR	skipped	OK

nebbiolo2 Summary

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Package: asuri

Version: 0.99.2

RVersion: 4.5

BiocVersion: 3.22

BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data asuri

BuildTime: 0 minutes 42.84 seconds

CheckCommand: BiocCheckGitClone('asuri') && /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3793/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/asuri.install-out.txt asuri_0.99.2.tar.gz && BiocCheck('asuri_0.99.2.tar.gz', `new-package`=TRUE)

CheckTime: 3 minutes 48.87 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 3142.83 KiB

BuildID:: asuri_20250709095657

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: asuri. Starting Build package. Starting Check package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘asuri/DESCRIPTION’ ... OK
* preparing ‘asuri’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: asuri
* saving partial Rd database
* 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 ‘asuri_0.99.2.tar.gz’

nebbiolo2 CHECK output

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===============================

 BiocCheckGitClone('asuri')

===============================

→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/asuri
→ BiocVersion: 3.22
→ Package: asuri
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/asuri.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/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/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/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 ‘0.99.2’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [26s/26s] 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 ... [10s/10s] 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 ... [3s/3s] OK
* DONE

Status: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/asuri.Rcheck/00check.log’
for details.





===============================

 BiocCheck('asuri_0.99.2.tar.gz')

===============================

── Installing asuri ────────────────────────────────────────────────────────────
✔ Package installed successfully
── asuri session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri
→ BiocVersion: 3.22
→ Package: asuri
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3793/903c6c9d157c855d23a28ac972c5504b3eba6c69/asuri.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri
→ installDir: /tmp/Rtmpc9OdVN/file7599b59b8efe3
→ 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/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:106: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:124: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:172: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:173: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:98: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:99: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:139: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:70: unknown macro '\insertRef'
* Checking for library/require of asuri...
* Checking coding practice...
* 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/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:106: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:124: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:172: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:173: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:98: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:99: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:139: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:70: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:106: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:124: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:172: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:173: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:98: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:99: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:139: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:70: unknown macro '\insertRef'
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• genePheno.Rd
• ...
• prefilterSAM.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:105: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/genePheno.Rd:106: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:123: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/geneSurv.Rd:124: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:172: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/patientRisk.Rd:173: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:98: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_PatientRisk.Rd:99: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:138: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/predict_SurvCurve.Rd:139: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:68: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmpc9OdVN/file7599b52a74ad7/asuri/man/prefilterSAM.Rd:70: unknown macro '\insertRef'
i NOTE: Usage of dontrun / donttest tags found in man page examples. 86% of man
pages use at least one of these tags.
Found in files:
• genePheno.Rd
• ...
• prefilterSAM.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• genePheno.Rd
• ...
• prefilterSAM.Rd
* 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; 147 lines (4%) are > 80 characters long.
First few lines:
• vignettes/asuri.Rmd#L2 title: "ASURI: An R Package for Survival ...
• ...
• vignettes/asuri.Rmd#L513 Finally, two Bioconductor packages that ...
i NOTE: Consider multiples of 4 spaces for line indents; 738 lines (19%) are
not.
First few lines:
• R/genePheno.R#L94 stop("SEdata must be a 'Summarized ...
• ...
• vignettes/asuri.Rmd#L418 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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the asuri.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo2 BUILD BIN output

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