teran2 Summary
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| Package: rhinotypeR |
| Version: 0.99.5 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rhinotypeR |
| BuildTime: 0 minutes 22.86 seconds |
| CheckCommand: BiocCheckGitClone('rhinotypeR') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/R-libs --install=check:/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.install-out.txt rhinotypeR_0.99.5.tar.gz && BiocCheck('rhinotypeR_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 46.88 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2414.88 KiB |
| BuildID:: rhinotypeR_20240917212957 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: rhinotypeR. 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. Adding Build Product Information to Database.Checking Package status: 0. |
teran2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘rhinotypeR/DESCRIPTION’ ... OK
* preparing ‘rhinotypeR’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘rhinotypeR_0.99.5.tar.gz’
teran2 CHECK output
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===============================
BiocCheckGitClone('rhinotypeR')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR
→ BiocVersion: 3.20
→ Package: rhinotypeR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhinotypeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhinotypeR’ version ‘0.99.5’
* 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 whether package ‘rhinotypeR’ 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [9s/9s] NOTE
plotFrequency: no visible binding for global variable ‘query’
Undefined global functions or variables:
query
* 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 ... [27s/27s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [19s/19s]
[19s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.Rcheck/00check.log’
for details.
===============================
BiocCheck('rhinotypeR_0.99.5.tar.gz')
===============================
── Installing rhinotypeR ───────────────────────────────────────────────────────
✔ Package installed successfully
── rhinotypeR session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvKMC4H/file3d2538764b68d8/rhinotypeR
→ BiocVersion: 3.20
→ Package: rhinotypeR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpvKMC4H/file3d2538764b68d8/rhinotypeR
→ installDir: /tmp/RtmpvKMC4H/file3d2538a97fcbb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rhinotypeR ─────────────────────────────────────────────
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (100%).
* Checking for pinned package versions in DESCRIPTION...
* 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 rhinotypeR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 61 lines (7%) are > 80 characters long.
First few lines:
• R/02_preProcessFastaFiles.R#L2 # Compare lengths among input sequences ...
• ...
• vignettes/rhinotypeR.Rmd#L141 The rhinotypeR package simplifies the pr ...
i NOTE: Consider multiples of 4 spaces for line indents; 452 lines (50%) are
not.
First few lines:
• R/01_getPrototypeSeqs.R#L4 ...
• ...
• vignettes/rhinotypeR.Rmd#L91 ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 2 NOTES
i See the rhinotypeR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
teran2 BUILD BIN output
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nebbiolo2 Summary
[top]
| Package: rhinotypeR |
| Version: 0.99.5 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rhinotypeR |
| BuildTime: 0 minutes 25.95 seconds |
| CheckCommand: BiocCheckGitClone('rhinotypeR') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3454/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.install-out.txt rhinotypeR_0.99.5.tar.gz && BiocCheck('rhinotypeR_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 0.55 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1697.92 KiB |
| BuildID:: rhinotypeR_20240917212957 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: rhinotypeR. 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. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘rhinotypeR/DESCRIPTION’ ... OK
* preparing ‘rhinotypeR’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘rhinotypeR_0.99.5.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('rhinotypeR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR
→ BiocVersion: 3.20
→ Package: rhinotypeR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhinotypeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhinotypeR’ version ‘0.99.5’
* 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 whether package ‘rhinotypeR’ 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] 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 ... [9s/9s] NOTE
plotFrequency: no visible binding for global variable ‘query’
Undefined global functions or variables:
query
* 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/34s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotFrequency 5.411 0.005 5.417
plotDistances 5.243 0.017 5.261
pairwiseDistances 5.094 0.074 5.170
assignTypes 4.967 0.068 5.036
plotTree 5.006 0.001 5.007
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/22s]
[22s/22s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.Rcheck/00check.log’
for details.
===============================
BiocCheck('rhinotypeR_0.99.5.tar.gz')
===============================
── Installing rhinotypeR ───────────────────────────────────────────────────────
✔ Package installed successfully
── rhinotypeR session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUCDUMP/file844557f4ead3e/rhinotypeR
→ BiocVersion: 3.20
→ Package: rhinotypeR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3454/bb62b97f02749a4d1520971b732e13b440cc5a7f/rhinotypeR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpUCDUMP/file844557f4ead3e/rhinotypeR
→ installDir: /tmp/RtmpUCDUMP/file8445566405b8c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rhinotypeR ─────────────────────────────────────────────
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (100%).
* Checking for pinned package versions in DESCRIPTION...
* 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 rhinotypeR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 61 lines (7%) are > 80 characters long.
First few lines:
• R/02_preProcessFastaFiles.R#L2 # Compare lengths among input sequences ...
• ...
• vignettes/rhinotypeR.Rmd#L141 The rhinotypeR package simplifies the pr ...
i NOTE: Consider multiples of 4 spaces for line indents; 452 lines (50%) are
not.
First few lines:
• R/01_getPrototypeSeqs.R#L4 ...
• ...
• vignettes/rhinotypeR.Rmd#L91 ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 2 NOTES
i See the rhinotypeR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]