Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘eheat/DESCRIPTION’ ... OK
* preparing ‘eheat’:
* 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 ‘eheat_0.99.3.tar.gz’

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 BiocCheckGitClone('eheat')

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─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: eheat
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3465/a64358824c51120997f1854ab226ed722d33d4bc/eheat
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      eheat.Rproj
* 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...
    * 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 results ──
1 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3465/a64358824c51120997f1854ab226ed722d33d4bc/eheat.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eheat/DESCRIPTION’ ... OK
* this is package ‘eheat’ version ‘0.99.3’
* 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 serialization versions ... OK
* checking whether package ‘eheat’ 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] WARNING
Loading required package: ComplexHeatmap
Loading required package: grid
========================================
ComplexHeatmap version 2.21.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

Loading required package: ggplot2
Error: package or namespace load failed for ‘eheat’ in loadNamespace(package, lib.loc):
 there is no package called ‘eheat’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [2s/2s] NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) : there is no package called ‘eheat’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: suppressPackageStartupMessages ... withCallingHandlers -> <Anonymous> -> Rd_db -> find.package
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Warning in gzfile(file, "rb") :
  cannot open compressed file '', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> readRDS -> gzfile
Execution halted
* checking for missing documentation entries ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> dirname -> find.package
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Execution halted
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘eheat’
Execution halted
* 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: 8 WARNINGs, 7 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3465/a64358824c51120997f1854ab226ed722d33d4bc/eheat.Rcheck/00check.log’
for details.





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 BiocCheck('eheat_0.99.3.tar.gz')

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─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: eheat
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/Rtmp6SpzTy/file23a2ff20f2ad61/eheat
─ installDir: /tmp/Rtmp6SpzTy/file23a2ff7e30157d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3465/a64358824c51120997f1854ab226ed722d33d4bc/eheat.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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Sequencing
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up of less
      than 3 sentences. Provide a more detailed description of the
      package.
* 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (10%).
* 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 eheat...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 2 times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 9 functions greater than 50 lines.
* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man page(s).
* Checking package NEWS...
* Checking unit tests...
    * 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...
    * NOTE: Consider shorter lines; 29 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 204 lines
      (5%) 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 is in the Support Site Watched Tags.

─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 7 NOTES

See the eheat.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.