Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/SpiecEasi
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 24.04.3 LTS)/x86_64   OK     WARNINGS     skipped     OK  

nebbiolo2 Summary

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Package: SpiecEasi
Version: 1.99.2
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpiecEasi
BuildTime: 1 minutes 0.63 seconds
CheckCommand: BiocCheckGitClone('SpiecEasi') && /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3961/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3961/SpiecEasi_20251017075518/SpiecEasi.install-out.txt SpiecEasi_1.99.2.tar.gz && BiocCheck('SpiecEasi_1.99.2.tar.gz', `new-package`=TRUE)
CheckTime: 3 minutes 31.37 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 3105.83 KiB
BuildID:: SpiecEasi_20251017075518
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SpiecEasi. 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: 0.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘SpiecEasi/DESCRIPTION’ ... OK
* preparing ‘SpiecEasi’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘SpiecEasi_1.99.2.tar.gz’


nebbiolo2 CHECK output

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

 BiocCheckGitClone('SpiecEasi')

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

→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3961/SpiecEasi_20251017075518/SpiecEasi
→ BiocVersion: 3.22
→ Package: SpiecEasi
→ PackageVersion: 1.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3961/SpiecEasi_20251017075518/SpiecEasi.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3961/SpiecEasi_20251017075518/SpiecEasi
→ 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 NAMESPACE...
* 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 v1.45.20 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/3961/SpiecEasi_20251017075518/SpiecEasi.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpiecEasi/DESCRIPTION’ ... OK
* this is package ‘SpiecEasi’ version ‘1.99.2’
* 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 ‘SpiecEasi’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
    libs      5.9Mb
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘phyloseq’
  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 ... [9s/9s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [5s/5s] OK
* checking data for ASCII and uncompressed saves ... 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 ... [72s/72s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
pval.sparccboot  20.294  0.208  20.502
sparccboot       20.001  0.086  20.088
multi.spiec.easi 11.536  0.105  11.642
spiec.easi       10.884  0.053  10.937
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [38s/38s]
 [39s/39s] 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: 5 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3961/SpiecEasi_20251017075518/SpiecEasi.Rcheck/00check.log’
for details.





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

 BiocCheck('SpiecEasi_1.99.2.tar.gz')

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

── Installing SpiecEasi ────────────────────────────────────────────────────────
✔ Package installed successfully
── SpiecEasi session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi
→ BiocVersion: 3.22
→ Package: SpiecEasi
→ PackageVersion: 1.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3961/SpiecEasi_20251017075518/SpiecEasi.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi
→ installDir: /tmp/RtmpjgPILF/file365a2229f6dfb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpiecEasi ──────────────────────────────────────────────
* 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...
! WARNING: New package x version starting with non-zero value (e.g., 1.y.z,
2.y.z); got ‘1.99.2’.
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (9%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• cross-domain-interactions.Rmd
• ...
• troubleshooting.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi/vignettes/cross-domain-interactions.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi/vignettes/latent-variable-models.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi/vignettes/phyloseq-integration.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi/vignettes/pulsar-parallel.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi/vignettes/SpiecEasi.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpjgPILF/file365a2245388d60/SpiecEasi/vignettes/troubleshooting.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SpiecEasi...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/fitdistr.R (line 265, column 22)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
• suppressWarnings() in R/SparseICov.R (line 118, column 9)
• suppressWarnings() in R/spiec-easi.R (line 298, column 3)
• suppressMessages() in R/utilities.R (line 146, column 5)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• robustPCA() (R/SparseLowRankICov.R): 192 lines
• ...
• coat() (R/coat.R): 65 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/pval.sparccboot.Rd
• ...
• man/sparseLowRankiCov.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• getOptInd.Rd
• ...
• triu.Rd
* 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; 283 lines (6%) are > 80 characters long.
First few lines:
• R/coat.R#L3 #' Compositional-adjusted thresholding b ...
• ...
• vignettes/troubleshooting.Rmd#L255 message("Saved trimmed cache file: " ...
i NOTE: Consider multiples of 4 spaces for line indents; 454 lines (10%) are
not.
First few lines:
• R/coat.R#L44 theta <- switch(adapt, ...
• ...
• vignettes/troubleshooting.Rmd#L258 }) ...
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 v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | i 9 NOTES
i See the SpiecEasi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo2 BUILD BIN output

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