Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* 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_0.99.2.tar.gz’

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 BiocCheckGitClone('omada')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: omada
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2668/omada_20220606141204/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

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2668/omada_20220606141204/omada.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘0.99.2’
* 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’ ‘clValid’ ‘clusterCrit’ ‘diceR’ ‘dplyr’ ‘fpc’ ‘ggplot2’
  ‘glmnet’ ‘kernlab’ ‘pdfCluster’ ‘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 ... [7s/7s] NOTE
clusterVoting: no visible global function definition for ‘prepare_data’
clusterVoting: no visible global function definition for ‘specc’
clusterVoting: no visible global function definition for ‘dist’
clusterVoting: no visible global function definition for ‘hclust’
clusterVoting: no visible global function definition for ‘cutree’
clusterVoting: no visible global function definition for ‘kmeans’
clusterVoting: no visible global function definition for ‘intCriteria’
clusterVoting: no visible global function definition for ‘compactness’
clusterVoting: no visible global function definition for ‘ggplot’
clusterVoting: no visible global function definition for ‘aes’
clusterVoting: no visible binding for global variable ‘k’
clusterVoting: no visible binding for global variable ‘Frequency’
clusterVoting: no visible global function definition for ‘geom_col’
clusterVoting: no visible global function definition for
  ‘scale_fill_brewer’
clusteringMethodSelection: no visible global function definition for
  ‘melt’
clusteringMethodSelection: no visible global function definition for
  ‘ggplot’
clusteringMethodSelection: no visible global function definition for
  ‘aes’
clusteringMethodSelection: no visible binding for global variable
  ‘clusters’
clusteringMethodSelection: no visible binding for global variable
  ‘value’
clusteringMethodSelection: no visible global function definition for
  ‘geom_line’
clusteringMethodSelection: no visible binding for global variable
  ‘methods’
clusteringMethodSelection: no visible global function definition for
  ‘geom_hline’
clusteringMethodSelection: no visible global function definition for
  ‘geom_text’
clusteringMethodSelection: no visible global function definition for
  ‘ylab’
feasibilityAnalysis: no visible global function definition for ‘rnorm’
feasibilityAnalysis: no visible global function definition for
  ‘clusterboot’
feasibilityAnalysis: no visible binding for global variable ‘speccCBI’
feasibilityAnalysisDataBased: no visible global function definition for
  ‘sd’
feasibilityAnalysisDataBased: no visible global function definition for
  ‘rnorm’
feasibilityAnalysisDataBased: no visible global function definition for
  ‘clusterboot’
feasibilityAnalysisDataBased: no visible binding for global variable
  ‘speccCBI’
featureSelection: no visible binding for global variable ‘var’
featureSelection: no visible global function definition for
  ‘clusterboot’
featureSelection: no visible binding for global variable ‘speccCBI’
featureSelection: no visible global function definition for ‘ggplot’
featureSelection: no visible global function definition for ‘aes’
featureSelection: no visible binding for global variable ‘featureSet’
featureSelection: no visible binding for global variable ‘means’
featureSelection: no visible global function definition for ‘geom_line’
featureSelection: no visible global function definition for
  ‘geom_point’
featureSelection: no visible global function definition for ‘ylab’
featureSelection: no visible global function definition for ‘xlab’
featureSelection: no visible global function definition for ‘theme’
featureSelection: no visible global function definition for
  ‘element_text’
featureSelection: no visible global function definition for ‘theme_bw’
geneSignatures: no visible global function definition for ‘left_join’
geneSignatures: no visible global function definition for ‘cv.glmnet’
geneSignatures: no visible global function definition for ‘glmnet’
geneSignatures: no visible global function definition for ‘coef’
geneSignatures: no visible global function definition for ‘%>%’
geneSignatures: no visible global function definition for ‘filter’
geneSignatures: no visible global function definition for ‘across’
geneSignatures: no visible global function definition for ‘where’
geneSignatures: no visible global function definition for ‘melt’
geneSignatures: no visible global function definition for ‘ggplot’
geneSignatures: no visible global function definition for ‘aes’
geneSignatures: no visible binding for global variable ‘features’
geneSignatures: no visible binding for global variable ‘value’
geneSignatures: no visible binding for global variable ‘variable’
geneSignatures: no visible global function definition for ‘geom_bar’
geneSignatures: no visible global function definition for ‘theme’
geneSignatures: no visible global function definition for
  ‘element_blank’
geneSignatures: no visible global function definition for
  ‘element_text’
geneSignatures: no visible global function definition for ‘geom_hline’
geneSignatures: no visible global function definition for ‘labs’
geneSignatures: no visible global function definition for ‘facet_grid’
optimalClustering: no visible global function definition for
  ‘clusterboot’
optimalClustering: no visible binding for global variable ‘speccCBI’
optimalClustering: no visible binding for global variable ‘hclustCBI’
optimalClustering: no visible binding for global variable ‘kmeansCBI’
partitionAgreement: no visible global function definition for ‘specc’
partitionAgreement: no visible global function definition for ‘dist’
partitionAgreement: no visible global function definition for ‘hclust’
partitionAgreement: no visible global function definition for ‘cutree’
partitionAgreement: no visible global function definition for ‘kmeans’
partitionAgreement: no visible global function definition for
  ‘adj.rand.index’
Undefined global functions or variables:
  %>% Frequency across adj.rand.index aes clusterboot clusters coef
  compactness cutree cv.glmnet dist element_blank element_text
  facet_grid featureSet features filter geom_bar geom_col geom_hline
  geom_line geom_point geom_text ggplot glmnet hclust hclustCBI
  intCriteria k kmeans kmeansCBI labs left_join means melt methods
  prepare_data rnorm scale_fill_brewer sd specc speccCBI theme theme_bw
  value var variable where xlab ylab
Consider adding
  importFrom("stats", "coef", "cutree", "dist", "filter", "hclust",
             "kmeans", "rnorm", "sd", "var")
  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 ... WARNING
Undocumented code objects:
  ‘get_average_feature_k_stabilities’ ‘get_average_stabilities_per_k’
  ‘get_average_stability’ ‘get_cluster_memberships_k’
  ‘get_cluster_voting_k_votes’ ‘get_cluster_voting_memberships’
  ‘get_cluster_voting_metric_votes’ ‘get_cluster_voting_scores’
  ‘get_coefficient_dataset’ ‘get_feature_selection_scores’
  ‘get_generated_dataset’ ‘get_internal_metric_scores’
  ‘get_max_stability’ ‘get_metric_votes_k’ ‘get_optimal_features’
  ‘get_optimal_memberships’ ‘get_optimal_number_of_features’
  ‘get_optimal_parameter_used’ ‘get_optimal_stability_score’
  ‘get_partition_agreement_scores’ ‘get_sample_memberships’
  ‘get_signature_feature_coefs’ ‘get_top30percent_coefficients’
  ‘get_vote_frequencies_k’ ‘plot_average_stabilities’
  ‘plot_cluster_voting’ ‘plot_feature_selection’
  ‘plot_partition_agreement’ ‘plot_signature_feature’
  ‘plot_vote_frequencies’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [211s/211s] OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
feasibilityAnalysis 104.635  1.323 105.963
featureSelection     54.083  0.100  54.186
omada                34.333  0.076  34.410
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [65s/65s]
 [65s/65s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  1/1 mismatches
  [1] 1 - 2 == -1
  ── Failure (test_partitionAgreement.R:61:9): Algorithm combinations ────────────
  length(...) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  ── Failure (test_partitionAgreement.R:61:9): Algorithm combinations ────────────
  length(...) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  ── Failure (test_partitionAgreement.R:61:9): Algorithm combinations ────────────
  length(...) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  ── Failure (test_partitionAgreement.R:61:9): Algorithm combinations ────────────
  length(...) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  
  [ FAIL 33 | WARN 0 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2668/omada_20220606141204/omada.Rcheck/00check.log’
for details.





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 BiocCheck('omada_0.99.2.tar.gz')

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

─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: omada
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpRhtYhL/file28361e746b41cc/omada
─ installDir: /tmp/RtmpRhtYhL/file28361e65311b79
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2668/omada_20220606141204/omada.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
    * ERROR: Packages providing 54 object(s) used in this package
      should be imported in the NAMESPACE file, otherwise packages
      importing this package may fail.
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 23 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: Recommended function length <= 50 lines.There are 4
      functions > 50 lines.
* Checking man page documentation...
* 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; 31 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 459 lines
      (22%) are not.
    See http://bioconductor.org/developers/how-to/coding-style/
    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...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 11 NOTES

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