Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘batchCorr/DESCRIPTION’ ... OK
* preparing ‘batchCorr’:
* 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
* building ‘batchCorr_0.99.2.tar.gz’

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 BiocCheckGitClone('batchCorr')

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→ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3469/75c2c81fc7dcde0d2d6f2ad73e16b4d925273f36/batchCorr
→ BiocVersion: 3.20
→ Package: batchCorr
→ PackageVersion: 0.99.2
→ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3469/75c2c81fc7dcde0d2d6f2ad73e16b4d925273f36/batchCorr.BiocCheck
→ BiocCheckVersion: 1.41.12
→ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3469/75c2c81fc7dcde0d2d6f2ad73e16b4d925273f36/batchCorr
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
i Checking valid files...
✔ Checking valid files... [8ms]

i Checking for stray BiocCheck output folders...
✔ Checking for stray BiocCheck output folders... [10ms]

i Checking for inst/doc folders...
✔ Checking for inst/doc folders... [5ms]

i Checking if DESCRIPTION is well formatted...
✔ Checking if DESCRIPTION is well formatted... [5ms]

i Checking for valid maintainer...
✔ Checking for valid maintainer... [5ms]

i Checking CITATION...
✔ Checking CITATION... [7ms]

i Checking that provided CITATION file is correctly formatted...
✔ Checking that provided CITATION file is correctly formatted... [5ms]

── BiocCheck v1.41.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 0 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3469/75c2c81fc7dcde0d2d6f2ad73e16b4d925273f36/batchCorr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘batchCorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘batchCorr’ version ‘0.99.2’
* 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 ‘batchCorr’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/4s] OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                     old_size new_size compress
  ThreeBatchData.rda    1.0Mb    641Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... [123s/98s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
correctDrift 60.459  0.378  48.120
mergeBatches 60.322  0.355  48.022
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [77s/62s]
 [77s/62s] 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 ... [4s/4s] OK
* DONE

Status: 1 WARNING
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3469/75c2c81fc7dcde0d2d6f2ad73e16b4d925273f36/batchCorr.Rcheck/00check.log’
for details.





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 BiocCheck('batchCorr_0.99.2.tar.gz')

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── Installing batchCorr ────────────────────────────────────────────────────────
✔ Package installed successfully
── batchCorr session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpR4f6iB/file2a327f5cf0de/batchCorr
→ BiocVersion: 3.20
→ Package: batchCorr
→ PackageVersion: 0.99.2
→ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3469/75c2c81fc7dcde0d2d6f2ad73e16b4d925273f36/batchCorr.BiocCheck
→ BiocCheckVersion: 1.41.12
→ sourceDir: /tmp/RtmpR4f6iB/file2a327f5cf0de/batchCorr
→ installDir: /tmp/RtmpR4f6iB/file2a322ec9c025
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on batchCorr ──────────────────────────────────────────────
i Checking for deprecated package usage...
✔ Checking for deprecated package usage... [9ms]

i Checking for remote package usage...
✔ Checking for remote package usage... [15ms]

i Checking for 'LazyData: true' usage...
✔ Checking for 'LazyData: true' usage... [5ms]

i Checking version number...
✔ Checking version number... [5ms]

i Checking for version number mismatch...
✔ Checking for version number mismatch... [5ms]

i Checking new package version number...
✔ Checking new package version number... [5ms]

i Checking R version dependency...
✔ Checking R version dependency... [8ms]

i Checking package size...
✔ Checking package size... [5ms]

i Checking individual file sizes...
✔ Checking individual file sizes... [5ms]

i Checking biocViews...
✔ Checking biocViews... [5ms]

i Checking that biocViews are present...
✔ Checking that biocViews are present... [5ms]

i Checking package type based on biocViews...
✔ Checking package type based on biocViews... [8ms]

→ Software
i Checking for non-trivial biocViews...
✔ Checking for non-trivial biocViews... [5ms]

i Checking that biocViews come from the same category...
✔ Checking that biocViews come from the same category... [6ms]

i Checking biocViews validity...
✔ Checking biocViews validity... [5ms]

i Checking for recommended biocViews...
✔ Checking for recommended biocViews... [5ms]

i N: Consider adding these automatically suggested biocViews: SystemsBiology,
Alignment
i Search 'biocViews' at https://contributions.bioconductor.org
i Checking build system compatibility...
✔ Checking build system compatibility... [5ms]

i Checking for proper Description: field...
✔ Checking for proper Description: field... [9ms]

i Checking if DESCRIPTION is well formatted...
✔ Checking if DESCRIPTION is well formatted... [5ms]

i Checking for whitespace in DESCRIPTION field names...
✔ Checking for whitespace in DESCRIPTION field names... [5ms]

i Checking that Package field matches directory/tarball name...
✔ Checking that Package field matches directory/tarball name... [5ms]

i Checking for Version: field...
✔ Checking for Version: field... [5ms]

i Checking License: for restrictive use...
✔ Checking License: for restrictive use... [5ms]

i Checking for recommended DESCRIPTION fields...
✔ Checking for recommended DESCRIPTION fields... [5ms]

i Checking for Bioconductor software dependencies...
✔ Checking for Bioconductor software dependencies... [5ms]

i Bioconductor dependencies found in Imports & Depends (33%).
i Checking for pinned package versions in DESCRIPTION...
✔ Checking for pinned package versions in DESCRIPTION... [5ms]

i Checking .Rbuildignore...
✔ Checking .Rbuildignore... [5ms]

i Checking for stray BiocCheck output folders...
✔ Checking for stray BiocCheck output folders... [10ms]

i Checking vignette directory...
✔ Checking vignette directory... [5ms]

i Checking whether vignette is built with 'R CMD build'...
✔ Checking whether vignette is built with 'R CMD build'... [8ms]

i Checking package installation calls in R code...
✔ Checking package installation calls in R code... [7ms]

i Checking for library/require of batchCorr...
✔ Checking for library/require of batchCorr... [9ms]

i Checking coding practice...
✔ Checking coding practice... [6ms]

i Checking parsed R code in R directory, examples, vignettes...
✔ Checking parsed R code in R directory, examples, vignettes... [6ms]

i Checking function lengths...
✔ Checking function lengths... [6ms]

i N: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
i Checking man page documentation...
✔ Checking man page documentation... [5ms]

i Checking package NEWS...
✔ Checking package NEWS... [5ms]

i Checking unit tests...
✔ Checking unit tests... [5ms]

i Checking skip_on_bioc() in tests...
✔ Checking skip_on_bioc() in tests... [5ms]

i Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne...
✔ Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne...

i Checking if package already exists in CRAN...
✔ Checking if package already exists in CRAN... [5ms]

i Checking if new package already exists in Bioconductor...
✔ Checking if new package already exists in Bioconductor... [6ms]

i Checking for bioc-devel mailing list subscription...
✔ Checking for bioc-devel mailing list subscription... [6ms]

i Maintainer is subscribed to bioc-devel.
i Checking for support site registration...
✔ Checking for support site registration... [5ms]

i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 2 NOTES
i See the batchCorr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir batchCorr_0.99.2.tar.gz'
>>>>>>> 

* installing *source* package ‘batchCorr’ ...
** using staged installation
** R
** data
** 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 (batchCorr)