nebbiolo1 Summary
[top]
| Package: alabaster.string |
| 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.string |
| BuildTime: 0 minutes 14.30 seconds |
| CheckCommand: BiocCheckGitClone('alabaster.string') && /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.string_20230131154129/alabaster.string.install-out.txt alabaster.string_0.99.0.tar.gz && BiocCheck('alabaster.string_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 11.96 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 219.61 KiB |
| BuildID:: alabaster.string_20230131154129 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: alabaster.string. 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 ‘alabaster.string/DESCRIPTION’ ... OK
* preparing ‘alabaster.string’:
* 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.string_0.99.0.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('alabaster.string')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.string
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.string_20230131154129/alabaster.string
─ 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.string_20230131154129/alabaster.string.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.string/DESCRIPTION’ ... OK
* this is package ‘alabaster.string’ 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.string’ 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 ... [3s/3s] 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 ... [3s/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 ... [10s/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 ... [3s/3s] ERROR
Running examples in ‘alabaster.string-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadXStringSet
> ### Title: Load a DNAStringSet
> ### Aliases: loadXStringSet
>
> ### ** Examples
>
> library(Biostrings)
> stuff <- DNAStringSet(c("AAA", "CC", "G", "TTTT"))
>
> tmp <- tempfile()
> dir.create(tmp)
> info <- stageObject(stuff, tmp, path="dna_thing")
Error in loadNamespace(x) : there is no package called ‘jsonvalidate’
Calls: stageObject ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[4s/4s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
2. ├─alabaster.string::stageObject(rstuff, tmp, path = "sequence_thing")
3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test-XStringSet.R:90'): saving and loading works with proteins ──────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'jsonvalidate'
Backtrace:
▆
1. ├─alabaster.base::stageObject(astuff, tmp, path = "sequence_thing") at test-XStringSet.R:90:4
2. ├─alabaster.string::stageObject(astuff, tmp, path = "sequence_thing")
3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 0 ]
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.string_20230131154129/alabaster.string.Rcheck/00check.log’
for details.
===============================
BiocCheck('alabaster.string_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.string
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmp7Ww4Pl/file36abe3226a8b83/alabaster.string
─ installDir: /tmp/Rtmp7Ww4Pl/file36abe313e976eb
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.string_20230131154129/alabaster.string.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, Alignment, SequenceMatching
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.string...
* 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
are 2 functions greater than 50 lines.
* 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; 27 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1 lines
(0%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 6 NOTES
See the alabaster.string.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
| Package: alabaster.string |
| 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.string |
| BuildTime: 0 minutes 15.64 seconds |
| CheckCommand: BiocCheckGitClone('alabaster.string') && /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.string_20230131154129/alabaster.string.install-out.txt alabaster.string_0.99.0.tar.gz && BiocCheck('alabaster.string_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 23.35 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh alabaster.string_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 10.60 seconds |
| PackageFileSize: 219.48 KiB |
| BuildID:: alabaster.string_20230131154129 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: alabaster.string. 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.string/DESCRIPTION’ ... OK
* preparing ‘alabaster.string’:
* 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.string_0.99.0.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('alabaster.string')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.string
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.string_20230131154129/alabaster.string
─ 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.string_20230131154129/alabaster.string.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.string/DESCRIPTION’ ... OK
* this is package ‘alabaster.string’ 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.string’ 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 ... [3s/3s] 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 ... [3s/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 ... [10s/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 ... [3s/3s] ERROR
Running examples in ‘alabaster.string-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadXStringSet
> ### Title: Load a DNAStringSet
> ### Aliases: loadXStringSet
>
> ### ** Examples
>
> library(Biostrings)
> stuff <- DNAStringSet(c("AAA", "CC", "G", "TTTT"))
>
> tmp <- tempfile()
> dir.create(tmp)
> info <- stageObject(stuff, tmp, path="dna_thing")
Error in loadNamespace(x) : there is no package called ‘jsonvalidate’
Calls: stageObject ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[4s/4s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
2. ├─alabaster.string::stageObject(rstuff, tmp, path = "sequence_thing")
3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test-XStringSet.R:90'): saving and loading works with proteins ──────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'jsonvalidate'
Backtrace:
▆
1. ├─alabaster.base::stageObject(astuff, tmp, path = "sequence_thing") at test-XStringSet.R:90:4
2. ├─alabaster.string::stageObject(astuff, tmp, path = "sequence_thing")
3. │ └─alabaster.base::.writeMetadata(meta, dir = dir)
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 0 ]
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.string_20230131154129/alabaster.string.Rcheck/00check.log’
for details.
===============================
BiocCheck('alabaster.string_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: alabaster.string
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpze21jy/file12f4e12fd6480/alabaster.string
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpze21jy/file12f4e4ed01172
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2894/alabaster.string_20230131154129/alabaster.string.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, Alignment, SequenceMatching
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.string...
* 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
are 2 functions greater than 50 lines.
* 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; 27 lines (9%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1 lines
(0%) 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 6 NOTES
See the alabaster.string.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.string_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘alabaster.string’ ...
** 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.string)