Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/superintervalsr
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: superintervalsr
Version: 0.99.3
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data superintervalsr
BuildTime: 0 minutes 45.32 seconds
CheckCommand: BiocCheckGitClone('superintervalsr') && /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3870/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr.install-out.txt superintervalsr_0.99.3.tar.gz && BiocCheck('superintervalsr_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 0 minutes 28.92 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 50.18 KiB
BuildID:: superintervalsr_20250807105420
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: superintervalsr. 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 superintervalsr/DESCRIPTION ... OK
* preparing superintervalsr:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted LazyData from DESCRIPTION
* building superintervalsr_0.99.3.tar.gz


nebbiolo2 CHECK output

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

 BiocCheckGitClone('superintervalsr')

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

 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr
 BiocVersion: 3.22
 Package: superintervalsr
 PackageVersion: 0.99.3
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr.BiocCheck
 BiocCheckVersion: 1.45.12
 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr
 installDir: NULL
 isTarBall: FALSE
 platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
  incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr/.gitignore'
* 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 v1.45.12 results 
 0 ERRORS |  0 WARNINGS | i 1 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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

* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr.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 superintervalsr/DESCRIPTION ... OK
* checking extension type ... Package
* this is package superintervalsr version 0.99.3
* 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 superintervalsr can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* checking C++ specification ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
  -Werror=format-security
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R [1s/1s]
 [1s/1s] 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 ... [4s/4s] OK
* DONE

Status: 2 NOTEs
See
  /home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr.Rcheck/00check.log
for details.





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 BiocCheck('superintervalsr_0.99.3.tar.gz')

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

 Installing superintervalsr 
 Package installed successfully
 superintervalsr session metadata 
 sourceDir: /tmp/RtmpLrG8XJ/file3add9a75107bc4/superintervalsr
 BiocVersion: 3.22
 Package: superintervalsr
 PackageVersion: 0.99.3
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3870/37609f582a616a74d235940b1a0da0d3add069ef/superintervalsr.BiocCheck
 BiocCheckVersion: 1.45.12
 sourceDir: /tmp/RtmpLrG8XJ/file3add9a75107bc4/superintervalsr
 installDir: /tmp/RtmpLrG8XJ/file3add9a30cbd910
 isTarBall: TRUE
 platform: unix
 Running BiocCheck on superintervalsr 
* 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 4.3.0 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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 superintervalsr...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
 superintervalsr.R (line 116, column 22)
 ...
 superintervalsr.R (line 243, column 15)
* 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...
i NOTE: Consider shorter lines; 35 lines (3%) are > 80 characters long.
First few lines:
 R/RcppExports.R#L9 .Call(`_superintervalsr_create_inter ...
 ...
 vignettes/workflows.Rmd#L353 cat("SuperIntervals count.batch:", round ...
i NOTE: Consider multiples of 4 spaces for line indents; 166 lines (14%) are
not.
First few lines:
 R/superintervalsr.R#L30 if (missing(x)) { ...
 ...
 vignettes/workflows.Rmd#L304 search_idxs(gene_imap, start(test_quer ...
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 v1.45.12 results 
 1 ERRORS |  0 WARNINGS | i 6 NOTES
i See the superintervalsr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo2 BUILD BIN output

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