nebbiolo1 Summary
[top]
Package: gemma.R |
Version: 0.99.11 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R |
BuildTime: 0 minutes 43.72 seconds |
CheckCommand: BiocCheckGitClone('gemma.R') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings gemma.R_0.99.11.tar.gz && BiocCheck('gemma.R_0.99.11.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 22.96 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 4901.48 KiB |
BuildID:: gemma.R_20220526225826 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: gemma.R. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: ExperimentData. 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 ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* 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 ‘gemma.R_0.99.11.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('gemma.R')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: gemma.R
─ PackageVersion: 0.99.11
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R
─ 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...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ 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/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘0.99.11’
* 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 ‘gemma.R’ can be installed ... [4s/4s] 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 ... [6s/6s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/18s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getDatasetDE 1.182 0.061 5.376
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/86s]
[16s/86s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
▆
1. ├─gemma.R::getDataset("GSE46416", memoised = TRUE) at testCaches.R:35:2
2. │ └─gemma.R::getDatasetExpression(dataset, filter, memoised = memoised)
3. │ ├─gemma.R:::memgetDatasetExpression(...)
4. │ │ ├─base::withVisible(eval(mc, parent.frame()))
5. │ │ └─base::eval(mc, parent.frame())
6. │ │ └─base::eval(mc, parent.frame())
7. │ └─gemma.R `<fn>`(...)
8. │ ├─gemma.R:::.body(...)
9. │ │ └─base::eval(quote(eval(preprocessor)(mData)), envir = envWhere)
10. │ │ └─base::eval(quote(eval(preprocessor)(mData)), envir = envWhere)
11. │ └─eval(preprocessor)(mData)
12. │ └─... %>% ...
13. ├─base::paste0(., collapse = "\n")
14. └─base::readLines(.)
[ FAIL 1 | WARN 1 | SKIP 3 | PASS 71 ]
Error: Test failures
In addition: Warning message:
In .Internal(sys.function(which)) :
closing unused connection 4 (/tmp/RtmpZC82zO/file21e87c676ef381)
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
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R.Rcheck/00check.log’
for details.
===============================
BiocCheck('gemma.R_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: gemma.R
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/RtmpqxaDuc/file22280b48d6336e/gemma.R
─ installDir: /tmp/RtmpqxaDuc/file22280b42cd5be9
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R.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...
* 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...
ExperimentData
* 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:
ENCODE
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 'Apache License (>= 2)' 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 gemma.R...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 4
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.7% of man pages use one of these cases.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* NOTE: skip_on_bioc() found in testthat files: testConvenience.R
testDatasetEndpoints.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 296 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 153 lines
(3%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 9 NOTES
See the gemma.R.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
Package: gemma.R |
Version: 0.99.11 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R |
BuildTime: 0 minutes 51.98 seconds |
CheckCommand: BiocCheckGitClone('gemma.R') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gemma.R_0.99.11.tar.gz && BiocCheck('gemma.R_0.99.11.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 43.86 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh gemma.R_0.99.11.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 13.76 seconds |
PackageFileSize: 4898.95 KiB |
BuildID:: gemma.R_20220526225826 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: gemma.R. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* 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 ‘gemma.R_0.99.11.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('gemma.R')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: gemma.R
─ PackageVersion: 0.99.11
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R
─ 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...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ 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/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘0.99.11’
* 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 ‘gemma.R’ can be installed ... [7s/7s] 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 ... [10s/10s] OK
* checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/84s]
[22s/85s] 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 ... OK
* DONE
Status: OK
===============================
BiocCheck('gemma.R_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: gemma.R
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/RtmpJIjQAw/file130ce55d5042d/gemma.R
─ installDir: /tmp/RtmpJIjQAw/file130ce6963688b
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2533/82e753372ecfc9f6c12aa520d19b930be306e698/gemma.R.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...
* 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...
ExperimentData
* 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:
ENCODE
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 'Apache License (>= 2)' 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 gemma.R...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 4
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.7% of man pages use one of these cases.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* NOTE: skip_on_bioc() found in testthat files: testConvenience.R
testDatasetEndpoints.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 296 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 153 lines
(3%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 9 NOTES
See the gemma.R.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 gemma.R_0.99.11.tar.gz'
>>>>>>>
* installing *source* package ‘gemma.R’ ...
** 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 (gemma.R)