Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/spbtest3
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 20.04.4 LTS)/x86_64   OK     ERROR     skipped     OK  
lconway macOS 12.2.1 Monterey/x86_64   OK     ERROR     OK     OK  

nebbiolo2 Summary

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Package: spbtest3
Version: 0.99.119
RVersion: 4.2
BiocVersion: 3.16
BuildCommand: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spbtest3
BuildTime: 0 minutes 7.75 seconds
CheckCommand: BiocCheckGitClone('spbtest3') && /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/51/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.install-out.txt spbtest3_0.99.119.tar.gz && BiocCheck('spbtest3_0.99.119.tar.gz', `new-package`=TRUE)
CheckTime: 0 minutes 14.19 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 476.30 KiB
BuildID:: spbtest3_20220627174525
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spbtest3. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* preparing ‘spbtest3’:
* 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 ‘spbtest3_0.99.119.tar.gz’


nebbiolo2 CHECK output

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===============================

 BiocCheckGitClone('spbtest3')

===============================

─ BiocCheckVersion: 1.33.10
─ BiocVersion: 3.16
─ Package: spbtest3
─ PackageVersion: 0.99.119
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
    * ERROR: Use Authors@R field not Author/Maintainer fields. Do not
      use both.
* Checking CITATION...

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

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




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* this is package ‘spbtest3’ version ‘0.99.119’
* 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 ‘spbtest3’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [2s/2s] NOTE
test9: no visible global function definition for ‘sleep’
Undefined global functions or variables:
  sleep
Consider adding
  importFrom("datasets", "sleep")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'test'
  ‘x’

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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [0s/0s]
 [1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spbtest3)
  > 
  > test_check("spbtest3")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-utils.R:4:5): sbptest3 ────────────────────────────────────────
  `res` not equal to FALSE.
  1 element mismatch
  ── Error (test-utils.R:11:5): sbptestV2 ────────────────────────────────────────
  Error in `sleep(700)`: could not find function "sleep"
  Backtrace:
      ▆
   1. └─spbtest3:::test9() at test-utils.R:11:4
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* 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 ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.Rcheck/00check.log’
for details.





===============================

 BiocCheck('spbtest3_0.99.119.tar.gz')

===============================

─ BiocCheckVersion: 1.33.10
─ BiocVersion: 3.16
─ Package: spbtest3
─ PackageVersion: 0.99.119
─ sourceDir: /tmp/RtmpwgoNAO/file206c6d4eb0cc40/spbtest3
─ installDir: /tmp/RtmpwgoNAO/file206c6d465a6c07
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
      it is part of a data set loaded with data(), or perhaps part of
      an object referenced in with() or within().
* 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...
    * WARNING: Description field in the DESCRIPTION file is too concise
* 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...
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spbtest3...
* Checking coding practice...
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
Warning in cond & parsedf$token[which(cond) - 1] != shQuote(lookback) :
  longer object length is not a multiple of shorter object length
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Remove set.seed usage (found 1 times)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 67% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* 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; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 4 lines
      (2%) 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.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.

─ BiocCheck results ──
1 ERRORS | 6 WARNINGS | 10 NOTES

See the spbtest3.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo2 BUILD BIN output

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lconway Summary

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Package: spbtest3
Version: 0.99.119
RVersion: 4.2
BiocVersion: 3.16
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spbtest3
BuildTime: 0 minutes 10.90 seconds
CheckCommand: BiocCheckGitClone('spbtest3') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/51/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.install-out.txt spbtest3_0.99.119.tar.gz && BiocCheck('spbtest3_0.99.119.tar.gz', `new-package`=TRUE)
CheckTime: 0 minutes 18.73 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh spbtest3_0.99.119.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 1.72 seconds
PackageFileSize: 632.65 KiB
BuildID:: spbtest3_20220627174525
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spbtest3. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0.

lconway BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* preparing ‘spbtest3’:
* 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 ‘spbtest3_0.99.119.tar.gz’


lconway CHECK output

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===============================

 BiocCheckGitClone('spbtest3')

===============================

─ BiocCheckVersion: 1.33.10
─ BiocVersion: 3.16
─ Package: spbtest3
─ PackageVersion: 0.99.119
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
    * ERROR: Use Authors@R field not Author/Maintainer fields. Do not
      use both.
* Checking CITATION...

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

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




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* this is package ‘spbtest3’ version ‘0.99.119’
* 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 ‘spbtest3’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... [2s/2s] NOTE
test9: no visible global function definition for ‘sleep’
Undefined global functions or variables:
  sleep
Consider adding
  importFrom("datasets", "sleep")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'test'
  ‘x’

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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [1s/1s]
 [1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spbtest3)
  > 
  > test_check("spbtest3")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-utils.R:4:5): sbptest3 ────────────────────────────────────────
  `res` not equal to FALSE.
  1 element mismatch
  ── Error (test-utils.R:11:5): sbptestV2 ────────────────────────────────────────
  Error in `sleep(700)`: could not find function "sleep"
  Backtrace:
      ▆
   1. └─spbtest3:::test9() at test-utils.R:11:4
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* 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 ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.Rcheck/00check.log’
for details.





===============================

 BiocCheck('spbtest3_0.99.119.tar.gz')

===============================

─ BiocCheckVersion: 1.33.10
─ BiocVersion: 3.16
─ Package: spbtest3
─ PackageVersion: 0.99.119
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpAfq83y/file46ac5eec98ad/spbtest3
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpAfq83y/file46ac746d5f37
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/51/bdf8a707a3b482dd0c9c9748162cd34898e73396/spbtest3.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
      it is part of a data set loaded with data(), or perhaps part of
      an object referenced in with() or within().
* 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...
    * WARNING: Description field in the DESCRIPTION file is too concise
* 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...
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spbtest3...
* Checking coding practice...
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
Warning in cond & parsedf$token[which(cond) - 1] != shQuote(lookback) :
  longer object length is not a multiple of shorter object length
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Remove set.seed usage (found 1 times)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 67% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* 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; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 4 lines
      (2%) 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.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.

─ BiocCheck results ──
1 ERRORS | 6 WARNINGS | 10 NOTES

See the spbtest3.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

lconway BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir spbtest3_0.99.119.tar.gz'
>>>>>>> 

* installing *source* package ‘spbtest3’ ...
** 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 (spbtest3)