lconway Summary
[top]
| Package: BiocBook |
| Version: 0.99.10 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocBook |
| BuildTime: 0 minutes 40.04 seconds |
| CheckCommand: BiocCheckGitClone('BiocBook') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3118/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.install-out.txt BiocBook_0.99.10.tar.gz && BiocCheck('BiocBook_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 57.26 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh BiocBook_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 4.37 seconds |
| PackageFileSize: 900.83 KiB |
| BuildID:: BiocBook_20231006063212 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BiocBook. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* preparing ‘BiocBook’:
* 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 ‘BiocBook_0.99.10.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('BiocBook')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: BiocBook
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* this is package ‘BiocBook’ version ‘0.99.10’
* 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 ‘BiocBook’ 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 ... [1s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
* checking loading without being on the library search path ... [1s/2s] 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 ... [6s/8s] 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 files in ‘vignettes’ ... OK
* checking examples ... [5s/42s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BiocBook-editing 2.412 0.255 24.548
BiocBook 0.192 0.099 14.403
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/21s]
[5s/21s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
error in evaluating the argument 'object' in selecting a method for function 'releases': object 'bb' not found
── Error ('test-BiocBook.R:19:5'): init work ───────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'path': object 'bb' not found
Backtrace:
▆
1. ├─testthat::expect_invisible(add_preamble(bb, open = FALSE)) at test-BiocBook.R:19:4
2. │ └─base::withVisible(call)
3. ├─BiocBook::add_preamble(bb, open = FALSE)
4. │ └─BiocBook:::.add_page(...)
5. │ └─BiocBook:::.find_path(file.path("pages", file), book)
6. │ ├─rprojroot::find_root_file(...)
7. │ │ └─rprojroot::find_root(criterion = criterion, path = path)
8. │ │ └─rprojroot:::get_start_path(path, criterion$subdir)
9. │ │ └─base::normalizePath(path, winslash = "/", mustWork = TRUE)
10. │ │ └─base::path.expand(path)
11. │ └─BiocGenerics::path(book)
12. └─base::.handleSimpleError(...)
13. └─base (local) h(simpleError(msg, call))
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 6 ]
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 ... [4s/4s] OK
* DONE
Status: 1 ERROR
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.Rcheck/00check.log’
for details.
===============================
BiocCheck('BiocBook_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: BiocBook
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpKi5TTS/file3259736f3480/BiocBook
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpKi5TTS/file32594fc48623
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.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...
* 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 by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 BiocBook...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 93 lines (6%) are > 80 characters
long.
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 name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the BiocBook.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir BiocBook_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘BiocBook’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BiocBook)
nebbiolo2 Summary
[top]
| Package: BiocBook |
| Version: 0.99.10 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocBook |
| BuildTime: 0 minutes 38.01 seconds |
| CheckCommand: BiocCheckGitClone('BiocBook') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3118/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.install-out.txt BiocBook_0.99.10.tar.gz && BiocCheck('BiocBook_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 20.16 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 900.88 KiB |
| BuildID:: BiocBook_20231006063212 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BiocBook. 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. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* preparing ‘BiocBook’:
* 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 ‘BiocBook_0.99.10.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('BiocBook')
===============================
Error in BiocCheckGitClone(args, `quit-with-status` = TRUE) :
cannot open file '/home/pkgbuild/packagebuilder/workers/jobs/3118/R-libs/BiocManager/R/BiocManager.rdb': No such file or directory
Execution halted
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* this is package ‘BiocBook’ version ‘0.99.10’
* 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 ‘BiocBook’ 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [9s/10s] 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 files in ‘vignettes’ ... OK
* checking examples ... [10s/45s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BiocBook-editing 5.119 0.311 25.965
BiocBook 0.336 0.020 14.370
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/28s]
[8s/29s] OK
* 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 ... [2s/2s] OK
* DONE
Status: OK
===============================
BiocCheck('BiocBook_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: BiocBook
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/RtmpNr2LgT/file12411b2dfcf934/BiocBook
─ installDir: /tmp/RtmpNr2LgT/file12411b2bfc5d0e
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3118/c6a5fbda6d27ddad2def810f87bd6fdb5d536394/BiocBook.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...
* 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 by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 BiocBook...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 93 lines (6%) are > 80 characters
long.
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 name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the BiocBook.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]