===============================
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’
===============================
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.