Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 20.04.4 LTS)/x86_64   OK     OK     skipped     OK  

nebbiolo2 Summary

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Package: omada
Version: 0.99.15
RVersion: 4.2
BiocVersion: 3.16
BuildCommand: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data omada
BuildTime: 1 minutes 15.75 seconds
CheckCommand: BiocCheckGitClone('omada') && /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2668/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2668/c1ad01731d9d66a843fdab0132bdc8dd9093859f/omada.install-out.txt omada_0.99.15.tar.gz && BiocCheck('omada_0.99.15.tar.gz', `new-package`=TRUE)
CheckTime: 7 minutes 0.42 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 199.04 KiB
BuildID:: omada_20220624062350
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: omada. 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. Checking Package status: 0.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘omada/DESCRIPTION’ ... OK
* preparing ‘omada’:
* 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
* building ‘omada_0.99.15.tar.gz’


nebbiolo2 CHECK output

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

 BiocCheckGitClone('omada')

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

─ BiocCheckVersion: 1.33.10
─ BiocVersion: 3.16
─ Package: omada
─ PackageVersion: 0.99.15
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2668/c1ad01731d9d66a843fdab0132bdc8dd9093859f/omada
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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

 R CMD CHECK

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

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2668/c1ad01731d9d66a843fdab0132bdc8dd9093859f/omada.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘0.99.15’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'pdfCluster', 'kernlab', 'fpc', 'Rcpp', 'diceR', 'ggplot2',
  'reshape', 'clusterCrit', 'clValid', 'glmnet', 'dplyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘omada’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rcpp’ ‘clusterCrit’ ‘glmnet’ ‘kernlab’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] NOTE
clusterVoting: no visible binding for global variable ‘k’
clusterVoting: no visible binding for global variable ‘Frequency’
clusteringMethodSelection: no visible binding for global variable
  ‘value’
clusteringMethodSelection: no visible binding for global variable
  ‘methods’
featureSelection: no visible binding for global variable ‘featureSet’
featureSelection: no visible binding for global variable ‘means’
geneSignatures: no visible global function definition for ‘where’
geneSignatures: no visible binding for global variable ‘features’
geneSignatures: no visible binding for global variable ‘value’
geneSignatures: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  Frequency featureSet features k means methods value variable where
Consider adding
  importFrom("utils", "methods")
to your NAMESPACE file.
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [324s/324s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                                   user system elapsed
get_feature_selection_optimal_number_of_features 28.450  0.071  28.522
get_feature_selection_scores                     25.929  0.108  26.037
get_cluster_voting_metric_votes                  18.958  0.084  19.042
plot_feature_selection                           18.603  0.028  18.631
get_partition_agreement_scores                   18.355  0.056  18.412
get_cluster_voting_memberships                   18.250  0.076  18.326
get_feature_selection_optimal_features           17.877  0.064  17.942
get_sample_memberships                           17.872  0.016  17.889
plot_partition_agreement                         17.606  0.044  17.651
get_cluster_voting_scores                        17.512  0.024  17.537
get_cluster_voting_k_votes                       17.385  0.112  17.497
plot_signature_feature                           17.375  0.020  17.396
omada                                            13.873  0.024  13.897
plot_cluster_voting                              13.611  0.048  13.660
get_optimal_number_of_features                    5.887  0.023   5.911
get_optimal_features                              5.715  0.001   5.715
featureSelection                                  5.385  0.056   5.441
plot_average_stabilities                          5.416  0.000   5.416
get_optimal_parameter_used                        5.198  0.008   5.206
get_optimal_stability_score                       5.026  0.004   5.030
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [46s/46s]
 [46s/46s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2668/c1ad01731d9d66a843fdab0132bdc8dd9093859f/omada.Rcheck/00check.log’
for details.






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

 BiocCheck('omada_0.99.15.tar.gz')

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

─ BiocCheckVersion: 1.33.10
─ BiocVersion: 3.16
─ Package: omada
─ PackageVersion: 0.99.15
─ sourceDir: /tmp/Rtmphd1ey7/file205d837c5da1f/omada
─ installDir: /tmp/Rtmphd1ey7/file205d835122cfaf
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2668/c1ad01731d9d66a843fdab0132bdc8dd9093859f/omada.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 11 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.1 to 4.2.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of omada...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 85 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      documentexported objects.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 32 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 418 lines
      (13%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 12 NOTES

See the omada.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo2 BUILD BIN output

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