nebbiolo1 Summary
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| Package: TDbasedUFEadv |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TDbasedUFEadv |
| BuildTime: 4 minutes 2.05 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: TDbasedUFEadv_20230307123801 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TDbasedUFEadv. 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: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘TDbasedUFEadv/DESCRIPTION’ ... OK
* preparing ‘TDbasedUFEadv’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Enrichment.Rmd’ using rmarkdown
trying URL 'https://stringdb-static.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz'
Content type 'application/octet-stream' length 21726816 bytes (20.7 MB)
==================================================
downloaded 20.7 MB
trying URL 'https://stringdb-static.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
Content type 'application/octet-stream' length 1901833 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'Enrichment.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘Enrichment.Rmd’
--- re-building ‘QuickStart.Rmd’ using rmarkdown
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'QuickStart.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘QuickStart.Rmd’
--- re-building ‘QuickStart2.Rmd’ using rmarkdown
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'QuickStart2.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘QuickStart2.Rmd’
--- re-building ‘TDbasedUFEadv.Rmd’ using rmarkdown
--- finished re-building ‘TDbasedUFEadv.Rmd’
SUMMARY: processing the following files failed:
‘Enrichment.Rmd’ ‘QuickStart.Rmd’ ‘QuickStart2.Rmd’
Error: Vignette re-building failed.
Execution halted
nebbiolo1 CHECK output
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nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: TDbasedUFEadv |
| Version: 0.99.2 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TDbasedUFEadv |
| BuildTime: 8 minutes 22.99 seconds |
| CheckCommand: BiocCheckGitClone('TDbasedUFEadv') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2944/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2944/a886ac19242502cc91fb8de1b84a01d3399ac1a1/TDbasedUFEadv.install-out.txt TDbasedUFEadv_0.99.2.tar.gz && BiocCheck('TDbasedUFEadv_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.95 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh TDbasedUFEadv_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 38.52 seconds |
| PackageFileSize: 3828.29 KiB |
| BuildID:: TDbasedUFEadv_20230307123801 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TDbasedUFEadv. 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. WARNING: check time exceeded 10 min. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘TDbasedUFEadv/DESCRIPTION’ ... OK
* preparing ‘TDbasedUFEadv’:
* 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 ‘TDbasedUFEadv_0.99.2.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('TDbasedUFEadv')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: TDbasedUFEadv
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2944/a886ac19242502cc91fb8de1b84a01d3399ac1a1/TDbasedUFEadv
─ 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/2944/a886ac19242502cc91fb8de1b84a01d3399ac1a1/TDbasedUFEadv.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TDbasedUFEadv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TDbasedUFEadv’ 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 serialization versions ... OK
* checking whether package ‘TDbasedUFEadv’ 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 ... [27s/30s] OK
* checking whether the package can be loaded with stated dependencies ... [26s/29s] OK
* checking whether the package can be unloaded cleanly ... [26s/29s] OK
* checking whether the namespace can be loaded with stated dependencies ... [26s/29s] OK
* checking whether the namespace can be unloaded cleanly ... [27s/29s] OK
* checking loading without being on the library search path ... [27s/30s] 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 ... [84s/94s] 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 files in ‘vignettes’ ... OK
* checking examples ... [221s/260s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
prepareCondDrugandDisease 73.470 3.818 86.986
selectFeatureTransRect 54.177 0.731 67.477
prepareexpDrugandDisease 40.332 1.001 51.117
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('TDbasedUFEadv_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: TDbasedUFEadv
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmplg9U8b/filef3571cd70885/TDbasedUFEadv
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmplg9U8b/filef35751564d0f
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2944/a886ac19242502cc91fb8de1b84a01d3399ac1a1/TDbasedUFEadv.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...
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TDbasedUFEadv...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
* Checking package NEWS...
* 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 multiples of 4 spaces for line indents; 97 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.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 3 NOTES
See the TDbasedUFEadv.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir TDbasedUFEadv_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘TDbasedUFEadv’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package keeps a record of temporary installation path
* DONE (TDbasedUFEadv)