nebbiolo1 Summary
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| Package: alabaster.vcf |
| Version: 0.99.0 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data alabaster.vcf |
| BuildTime: 0 minutes 56.03 seconds |
| CheckCommand: BiocCheckGitClone('alabaster.vcf') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2894/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf.install-out.txt alabaster.vcf_0.99.0.tar.gz && BiocCheck('alabaster.vcf_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 25.00 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 223.72 KiB |
| BuildID:: alabaster.vcf_20230131154540 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: alabaster.vcf. 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
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===============================
R CMD BUILD
===============================
* checking for file ‘alabaster.vcf/DESCRIPTION’ ... OK
* preparing ‘alabaster.vcf’:
* 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 ‘alabaster.vcf_0.99.0.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('alabaster.vcf')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.vcf
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf
─ 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/2894/alabaster.vcf_20230131154540/alabaster.vcf.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.vcf/DESCRIPTION’ ... OK
* this is package ‘alabaster.vcf’ version ‘0.99.0’
* 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 ‘alabaster.vcf’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [36s/36s] 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 ... [13s/13s] ERROR
Running examples in ‘alabaster.vcf-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadVCF
> ### Title: Load a VCF object
> ### Aliases: loadVCF
>
> ### ** Examples
>
> fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
> vcf <- readVcf(fl, genome="hg19")
>
> tmp <- tempfile()
> dir.create(tmp)
> info <- stageObject(vcf, dir=tmp, path="experiment-1")
Error in value[[3L]](cond) : failed to stage 'header(<CollapsedVCF>)'
- there is no package called ‘jsonvalidate’
Calls: stageObject ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
[14s/14s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Failure ('test-VCFHeader.R:12'): VCFHeader stage/load works as expected ─────
`.writeMetadata(info, dir = tmp)` threw an error.
Message: there is no package called 'jsonvalidate'
Class: packageNotFoundError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(.writeMetadata(info, dir = tmp), NA) at test-VCFHeader.R:12:4
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─alabaster.base::.writeMetadata(info, dir = tmp)
7. └─base::loadNamespace(x)
8. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
9. └─base (local) withOneRestart(expr, restarts[[1L]])
10. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1 ]
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 ... [2s/2s] OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf.Rcheck/00check.log’
for details.
===============================
BiocCheck('alabaster.vcf_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.vcf
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmpjygd2e/file37501626d29ef0/alabaster.vcf
─ installDir: /tmp/Rtmpjygd2e/file375016210a10ad
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf.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:
Sequencing, VariantAnnotation
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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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 alabaster.vcf...
* Checking coding practice...
* 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; 52 lines (10%) 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 | 4 NOTES
See the alabaster.vcf.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: alabaster.vcf |
| Version: 0.99.0 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data alabaster.vcf |
| BuildTime: 0 minutes 58.26 seconds |
| CheckCommand: BiocCheckGitClone('alabaster.vcf') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2894/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf.install-out.txt alabaster.vcf_0.99.0.tar.gz && BiocCheck('alabaster.vcf_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 39.19 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh alabaster.vcf_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 38.28 seconds |
| PackageFileSize: 223.59 KiB |
| BuildID:: alabaster.vcf_20230131154540 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: alabaster.vcf. 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 ‘alabaster.vcf/DESCRIPTION’ ... OK
* preparing ‘alabaster.vcf’:
* 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 ‘alabaster.vcf_0.99.0.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('alabaster.vcf')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.vcf
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf
─ 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/2894/alabaster.vcf_20230131154540/alabaster.vcf.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 ‘alabaster.vcf/DESCRIPTION’ ... OK
* this is package ‘alabaster.vcf’ version ‘0.99.0’
* 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 ‘alabaster.vcf’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [37s/38s] 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 ... [13s/13s] ERROR
Running examples in ‘alabaster.vcf-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadVCF
> ### Title: Load a VCF object
> ### Aliases: loadVCF
>
> ### ** Examples
>
> fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
> vcf <- readVcf(fl, genome="hg19")
>
> tmp <- tempfile()
> dir.create(tmp)
> info <- stageObject(vcf, dir=tmp, path="experiment-1")
Error in value[[3L]](cond) : failed to stage 'header(<CollapsedVCF>)'
- there is no package called ‘jsonvalidate’
Calls: stageObject ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[15s/15s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Failure ('test-VCFHeader.R:12'): VCFHeader stage/load works as expected ─────
`.writeMetadata(info, dir = tmp)` threw an error.
Message: there is no package called 'jsonvalidate'
Class: packageNotFoundError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(.writeMetadata(info, dir = tmp), NA) at test-VCFHeader.R:12:4
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─alabaster.base::.writeMetadata(info, dir = tmp)
7. └─base::loadNamespace(x)
8. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
9. └─base (local) withOneRestart(expr, restarts[[1L]])
10. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1 ]
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: 2 ERRORs, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf.Rcheck/00check.log’
for details.
===============================
BiocCheck('alabaster.vcf_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.vcf
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBM1sDb/file1354a472795f/alabaster.vcf
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBM1sDb/file1354a543890a
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.vcf_20230131154540/alabaster.vcf.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:
Sequencing, VariantAnnotation
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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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 alabaster.vcf...
* Checking coding practice...
* 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; 52 lines (10%) 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 | 4 NOTES
See the alabaster.vcf.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 alabaster.vcf_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘alabaster.vcf’ ...
** 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 (alabaster.vcf)