merida1 Summary
[top]
| Package: SVMDO |
| Version: 0.99.5 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SVMDO |
| BuildTime: 1 minutes 23.57 seconds |
| CheckCommand: BiocCheckGitClone('SVMDO') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2848/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/SVMDO.install-out.txt SVMDO_0.99.5.tar.gz && BiocCheck('SVMDO_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 16.90 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh SVMDO_0.99.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 16.42 seconds |
| PackageFileSize: 2404.09 KiB |
| BuildID:: SVMDO_20230227073252 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SVMDO. Starting Build package. Starting Check package. Starting Build 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. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* preparing ‘SVMDO’:
* 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 ‘SVMDO_0.99.5.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('SVMDO')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SVMDO
─ PackageVersion: 0.99.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/SVMDO.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘0.99.5’
* 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 ... [21s/24s] OK
* checking whether the package can be loaded with stated dependencies ... [21s/24s] OK
* checking whether the package can be unloaded cleanly ... [21s/24s] OK
* checking whether the namespace can be loaded with stated dependencies ... [20s/23s] OK
* checking whether the namespace can be unloaded cleanly ... [21s/24s] OK
* checking loading without being on the library search path ... [21s/24s] 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 ... [69s/77s] 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", 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)
assign("top_genes_test", changed_whole_data, 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/gui_obj_removal_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)
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)
File ‘SVMDO/R/survival_analysis_server.R’:
assign("fit_list", fit_list, envir = .GlobalEnv)
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 ... [1s/1s] 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 ... [24s/26s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [37s/42s]
[38s/42s] 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 ... [10s/11s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/SVMDO.Rcheck/00check.log’
for details.
===============================
BiocCheck('SVMDO_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SVMDO
─ PackageVersion: 0.99.5
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpIKfoxh/file111433cf4ba6c/SVMDO
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpIKfoxh/file1114372ec9432
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/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 55 functions greater than 50 lines.
* Checking man page documentation...
* 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; 154 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 633 lines
(25%) 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 | 4 NOTES
See the SVMDO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SVMDO_0.99.5.tar.gz'
>>>>>>>
* installing *source* package ‘SVMDO’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SVMDO)
nebbiolo1 Summary
[top]
| Package: SVMDO |
| Version: 0.99.5 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SVMDO |
| BuildTime: 0 minutes 31.62 seconds |
| CheckCommand: BiocCheckGitClone('SVMDO') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2848/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/SVMDO.install-out.txt SVMDO_0.99.5.tar.gz && BiocCheck('SVMDO_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 40.17 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2404.23 KiB |
| BuildID:: SVMDO_20230227073252 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SVMDO. 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. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* preparing ‘SVMDO’:
* 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 ‘SVMDO_0.99.5.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('SVMDO')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SVMDO
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/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/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/SVMDO.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* 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 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘0.99.5’
* 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 ... OK
* 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 ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [29s/29s] 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", 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)
assign("top_genes_test", changed_whole_data, 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/gui_obj_removal_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)
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)
File ‘SVMDO/R/survival_analysis_server.R’:
assign("fit_list", fit_list, envir = .GlobalEnv)
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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [18s/18s]
[18s/18s] 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/SVMDO.Rcheck/00check.log’
for details.
===============================
BiocCheck('SVMDO_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: SVMDO
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpHgCjAv/file33e9f5bd87ff6/SVMDO
─ installDir: /tmp/RtmpHgCjAv/file33e9f577cee4de
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2848/8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7/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 55 functions greater than 50 lines.
* Checking man page documentation...
* 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; 154 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 633 lines
(25%) 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 | 4 NOTES
See the SVMDO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]