===============================
R CMD BUILD
===============================
* checking for file ‘CPSM/DESCRIPTION’ ... OK
* preparing ‘CPSM’:
* 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
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘CPSM/data/Example_TCGA_LGG_FPKM_data.rda’
‘CPSM/data/Key_Clin_feature_list.rda’
‘CPSM/data/Key_Clin_features_with_PI_list.rda’
‘CPSM/data/Key_PI_list.rda’
‘CPSM/data/Key_univariate_features_list.rda’
‘CPSM/data/Key_univariate_features_with_Clin_list.rda’
‘CPSM/data/New_data.rda’ ‘CPSM/data/Test_Clin.rda’
‘CPSM/data/Test_Norm_data.rda’ ‘CPSM/data/Test_PI_data.rda’
‘CPSM/data/Test_Uni_sig_data.rda’ ‘CPSM/data/Train_Clin.rda’
‘CPSM/data/Train_Data_Nomogram_input.rda’
‘CPSM/data/Train_Norm_data.rda’ ‘CPSM/data/Train_PI_data.rda’
‘CPSM/data/Train_Uni_sig_data.rda’
‘CPSM/data/feature_list_for_Nomogram.rda’
‘CPSM/data/mean_median_survival_time_data.rda’
‘CPSM/data/survCurves_data.rda’ ‘CPSM/data/test_FPKM.rda’
‘CPSM/data/train_FPKM.rda’
* building ‘CPSM_0.99.5.tar.gz’
===============================
BiocCheckGitClone('CPSM')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3518/73769aca29bddb0045148cc11352084be8045a0d/CPSM
→ BiocVersion: 3.21
→ Package: CPSM
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3518/73769aca29bddb0045148cc11352084be8045a0d/CPSM.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3518/73769aca29bddb0045148cc11352084be8045a0d/CPSM
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3518/73769aca29bddb0045148cc11352084be8045a0d/CPSM.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CPSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CPSM’ 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 ‘CPSM’ 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 ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] 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 ... [25s/25s] OK
* checking Rd files ... [2s/2s] 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [34s/34s]
[34s/34s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [18s/18s] OK
* DONE
Status: OK
===============================
BiocCheck('CPSM_0.99.5.tar.gz')
===============================
── Installing CPSM ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── CPSM session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpG0WWYf/file2d081f795968b8/CPSM
→ BiocVersion: 3.21
→ Package: CPSM
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3518/73769aca29bddb0045148cc11352084be8045a0d/CPSM.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpG0WWYf/file2d081f795968b8/CPSM
→ installDir: /tmp/RtmpG0WWYf/file2d081f12f10f10
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CPSM ───────────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 3.5.0 to 4.5.0.
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (5%).
* Checking for pinned package versions in DESCRIPTION...
* 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 CPSM...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/data_process_f.R (line 39, column 13)
• ...
• R/Univariate_sig_features_f.R (line 98, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressWarnings() in R/Nomogram_generate_f.R (line 188, column 8)
• suppressMessages() in R/Nomogram_generate_f.R (line 188, column 25)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• MTLR_pred_model_f() (R/MTLR_pred_model_f.R): 538 lines
• ...
• surv_curve_plots_f() (R/surv_curve_plots_f.R): 86 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...
i NOTE: Consider multiples of 4 spaces for line indents; 588 lines (25%) are
not.
First few lines:
• R/data_process_f.R#L36 # Check if any input variable is empty ...
• ...
• vignettes/CPSM.Rmd#L474 surv_event = "OS" ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the CPSM.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.