===============================
BiocCheckGitClone('SVMDO')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: SVMDO
─ PackageVersion: 0.99.18
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2848/50be8b5ae059d47f8d994c35b069501545393114/SVMDO
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc 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/2848/50be8b5ae059d47f8d994c35b069501545393114/SVMDO.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘0.99.18’
* 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 ‘SVMDO’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [28s/28s] NOTE
Found the following assignments to the global environment:
File ‘SVMDO/R/classification_server.R’:
assign("final_discriminative_gene_set", final_gene_list, envir = .GlobalEnv)
assign("final_discriminative_gene_set", final_gene_list, envir = .GlobalEnv)
File ‘SVMDO/R/deg_server.R’:
assign("tissue_type_list", assigning_tissue_type_list, envir = .GlobalEnv)
assign("tissue_type_list", assigning_tissue_type_list, envir = .GlobalEnv)
assign("tcga_id_list", assigning_tcga_id_list, envir = .GlobalEnv)
assign("sorted_new_bound_form_A_test", sorted_new_bound_form_A,
envir = .GlobalEnv)
assign("sorted_new_bound_form_B_test", sorted_new_bound_form_B,
envir = .GlobalEnv)
assign("complete_deg_gene_list_test", complete_deg_gene_list,
envir = .GlobalEnv)
assign("total_exp_dataset_test", c, envir = .GlobalEnv)
assign("top_genes_test", changed_whole_data_test, envir = .GlobalEnv)
assign("sorted_new_bound_form_A", sorted_new_bound_form_A, envir = .GlobalEnv)
assign("sorted_new_bound_form_B", sorted_new_bound_form_B, envir = .GlobalEnv)
assign("complete_deg_gene_list", complete_deg_gene_list, envir = .GlobalEnv)
assign("total_exp_dataset", c, envir = .GlobalEnv)
File ‘SVMDO/R/do_based_gene_filtration_server.R’:
assign("new_tissue_type_list", assigning_new_tissue_type_list,
envir = .GlobalEnv)
assign("tcga_sample_comb", assigning_tcga_sample_comb, envir = .GlobalEnv)
assign("disease_filtered_gene_data", assigning_disease_filtered_gene_data,
envir = .GlobalEnv)
File ‘SVMDO/R/gene_directory_selection_server.R’:
assign("direct_val_gene_list", getwd(), envir = .GlobalEnv)
assign("direct_val_gene_list", global$datapath, envir = .GlobalEnv)
File ‘SVMDO/R/plot_list_server.R’:
assign("fit_list", fit_list, envir = .GlobalEnv)
assign("modulename_list", modulename_list, envir = .GlobalEnv)
assign("hr_list", hr_list, envir = .GlobalEnv)
assign("p_list", p_list, envir = .GlobalEnv)
assign("max_plots", length(fit_list), envir = .GlobalEnv)
assign("plot_prep_sign", 1, envir = .GlobalEnv)
File ‘SVMDO/R/survival_analysis_server.R’:
assign(paste0("fit1", "_", a), fit1, envir = .GlobalEnv)
assign(paste0("modulename", "_", a), modulename, envir = .GlobalEnv)
assign(paste0("hr", "_", a), hr, envir = .GlobalEnv)
assign(paste0("p", "_", a), p, envir = .GlobalEnv)
File ‘SVMDO/R/top_val_based_deg_filtration_server.R’:
assign("top_genes", changed_whole_data, envir = .GlobalEnv)
* 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 files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/17s]
[17s/17s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2848/50be8b5ae059d47f8d994c35b069501545393114/SVMDO.Rcheck/00check.log’
for details.
===============================
BiocCheck('SVMDO_0.99.18.tar.gz')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: SVMDO
─ PackageVersion: 0.99.18
─ sourceDir: /tmp/Rtmp8GRqng/file2834e9109ae0ae/SVMDO
─ installDir: /tmp/Rtmp8GRqng/file2834e97b554e11
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2848/50be8b5ae059d47f8d994c35b069501545393114/SVMDO.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SVMDO...
* Checking coding practice...
* 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 7 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* 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; 189 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 700 lines
(24%) 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 | 1 WARNINGS | 4 NOTES
See the SVMDO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.