nebbiolo1 Summary
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Package: ReUseData |
Version: 0.99.15 |
RVersion: 4.3
|
BiocVersion: 3.17
|
BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData |
BuildTime: 0 minutes 26.09 seconds |
CheckCommand: BiocCheckGitClone('ReUseData') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2868/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.install-out.txt ReUseData_0.99.15.tar.gz && BiocCheck('ReUseData_0.99.15.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 11.74 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 299.08 KiB |
BuildID:: ReUseData_20230109184221 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ReUseData. Starting Build package. Starting Check 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. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* 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 ‘ReUseData_0.99.15.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('ReUseData')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.15
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData
─ 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘0.99.15’
* 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 ‘ReUseData’ 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 ... [4s/4s] 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 ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘Rcwl:::env_Rcwl’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [13s/13s] 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 ... [34s/37s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataUpdate 8.097 0.312 8.489
getCloudData 6.320 0.392 8.303
dataHub-class 4.744 0.225 5.301
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
[14s/15s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.Rcheck/00check.log’
for details.
===============================
BiocCheck('ReUseData_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.15
─ sourceDir: /tmp/RtmpEYjIqD/file10896718be934d/ReUseData
─ installDir: /tmp/RtmpEYjIqD/file108967671fce1a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.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:
WorkflowManagement
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...
* 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...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* 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 ReUseData...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* ERROR: Avoid references to external hosting platforms
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 41 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 36% 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; 45 lines (2%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 120 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.
* 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 ──
2 ERRORS | 0 WARNINGS | 15 NOTES
See the ReUseData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
Package: ReUseData |
Version: 0.99.15 |
RVersion: 4.3
|
BiocVersion: 3.17
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData |
BuildTime: 0 minutes 38.94 seconds |
CheckCommand: BiocCheckGitClone('ReUseData') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2868/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.install-out.txt ReUseData_0.99.15.tar.gz && BiocCheck('ReUseData_0.99.15.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 38.88 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ReUseData_0.99.15.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 14.85 seconds |
PackageFileSize: 298.79 KiB |
BuildID:: ReUseData_20230109184221 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ReUseData. 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. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* 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 ‘ReUseData_0.99.15.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('ReUseData')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.15
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData
─ 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/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘0.99.15’
* 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 ‘ReUseData’ 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘Rcwl:::env_Rcwl’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] 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 ... [39s/48s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataUpdate 11.538 1.194 12.889
getCloudData 5.484 0.341 7.069
dataHub-class 4.924 0.342 11.594
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [19s/20s]
[19s/20s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 38 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_data.R:10'): recipe evaluation works ─────────────────────────
dirname(res$output) (`actual`) not equal to `outdir` (`expected`).
actual vs expected
- "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpQBpGxz/test_SharedData"
+ "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQBpGxz/test_SharedData"
── Failure ('test_recipes.R:30'): recipe evaluation works ──────────────────────
dirname(res$output) (`actual`) not equal to tempdir() (`expected`).
`actual`: "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpQBpGxz"
`expected`: "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQBpGxz"
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 38 ]
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/5s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.Rcheck/00check.log’
for details.
===============================
BiocCheck('ReUseData_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.15
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpxXdNo4/file158935017b63/ReUseData
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpxXdNo4/file1589361c42667
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/9f55ce8a6bf52b03fe551f00023c860a7c7b6936/ReUseData.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:
WorkflowManagement
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...
* 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...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* 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 ReUseData...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* ERROR: Avoid references to external hosting platforms
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 41 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 36% 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; 45 lines (2%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 120 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.
* 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 ──
2 ERRORS | 0 WARNINGS | 15 NOTES
See the ReUseData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ReUseData_0.99.15.tar.gz'
>>>>>>>
* installing *source* package ‘ReUseData’ ...
** 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 (ReUseData)