===============================
R CMD BUILD
===============================
* checking for file ‘crumblr/DESCRIPTION’ ... OK
* preparing ‘crumblr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: crumblr
* saving partial Rd database
* 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
* building ‘crumblr_0.99.13.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff’
===============================
BiocCheckGitClone('crumblr')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/crumblr_20250118002015/crumblr
→ BiocVersion: 3.21
→ Package: crumblr
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/crumblr_20250118002015/crumblr.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/crumblr_20250118002015/crumblr
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• man/.Rapp.history
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3699/crumblr_20250118002015/crumblr.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crumblr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crumblr’ version ‘0.99.13’
* 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 ... NOTE
Found the following non-portable file paths:
crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
crumblr/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
crumblr/docs/deps/bootstrap-5.1.3/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
crumblr/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘crumblr’ 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 ... [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 ... [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 ... [27s/27s] OK
* checking Rd files ... [9s/9s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [104s/104s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
diffTree 28.520 0.431 28.959
treeTest 15.150 0.001 15.152
plotTreeTestBeta 14.378 0.004 14.404
plotTreeTest 14.334 0.010 14.344
plotForest-methods 13.614 0.138 13.754
* 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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3699/crumblr_20250118002015/crumblr.Rcheck/00check.log’
for details.
===============================
BiocCheck('crumblr_0.99.13.tar.gz')
===============================
── Installing crumblr ──────────────────────────────────────────────────────────
✔ Package installed successfully
── crumblr session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr
→ BiocVersion: 3.21
→ Package: crumblr
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/crumblr_20250118002015/crumblr.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr
→ installDir: /tmp/RtmpJYbbDE/file37658e734e81b4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on crumblr ────────────────────────────────────────────────
* 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 4.2.0 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...
i NOTE: Consider adding these automatically suggested biocViews: Clustering,
DimensionReduction
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/crumblr_theory.Rmd
• vignettes/crumblr.Rmd
• vignettes/integration.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/vignettes/crumblr_theory.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/vignettes/crumblr.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/vignettes/integration.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/clr.Rd:49: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
* Checking for library/require of crumblr...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/crumblr.R (line 155, column 12)
• ...
• R/tree.R (line 267, column 14)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• dmn.mle() (R/dmn.mle.R): 84 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/clr.Rd:49: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/buildClusterTree.Rd
• ...
• man/treeTest.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/clr.Rd:49: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• buildClusterTree.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/clr.Rd:49: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpJYbbDE/file37658e6ce9c50c/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 101 lines (6%) are > 80 characters long.
First few lines:
• R/crumblr.R#L11 #' @details The CLR of a vector \code{x} ...
• ...
• vignettes/integration.Rmd#L121 Given the results here, we see that CD8 ...
i NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
First few lines:
• R/data.R#L11 #' \item \code{info} is metadata for ea ...
• ...
• vignettes/integration.Rmd#L35 ``` ...
i NOTE: Consider multiples of 4 spaces for line indents; 358 lines (20%) are
not.
First few lines:
• R/crumblr.R#L46 if (!is.data.frame(counts) & !is.matri ...
• ...
• vignettes/integration.Rmd#L96 ...
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 | ⚠ 1 WARNINGS | i 11 NOTES
i See the crumblr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.