nebbiolo2 Summary
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| Package: HuBMAPR |
| 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 HuBMAPR |
| BuildTime: 1 minutes 26.83 seconds |
| CheckCommand: BiocCheckGitClone('HuBMAPR') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3532/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.install-out.txt HuBMAPR_0.99.5.tar.gz && BiocCheck('HuBMAPR_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 35.75 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 268.66 KiB |
| BuildID:: HuBMAPR_20240919224527 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HuBMAPR. 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
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===============================
R CMD BUILD
===============================
* checking for file ‘HuBMAPR/DESCRIPTION’ ... OK
* preparing ‘HuBMAPR’:
* 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 ‘HuBMAPR_0.99.5.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('HuBMAPR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR
→ BiocVersion: 3.20
→ Package: HuBMAPR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR/.gitignore'
* 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/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.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 ‘HuBMAPR/DESCRIPTION’ ... OK
* this is package ‘HuBMAPR’ 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 serialization versions ... OK
* checking whether package ‘HuBMAPR’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [4s/4s] 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 ... [8s/67s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
donors 1.850 0.023 31.720
datasets 1.614 0.065 16.038
samples 0.846 0.004 5.546
collection_information 0.201 0.026 5.445
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [9s/61s]
[9s/61s] 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: OK
===============================
BiocCheck('HuBMAPR_0.99.5.tar.gz')
===============================
── Installing HuBMAPR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── HuBMAPR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2BbuAr/file1d020145c28b74/HuBMAPR
→ BiocVersion: 3.20
→ Package: HuBMAPR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmp2BbuAr/file1d020145c28b74/HuBMAPR
→ installDir: /tmp/Rtmp2BbuAr/file1d020156d6c18c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HuBMAPR ────────────────────────────────────────────────
* 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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 HuBMAPR...
* 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...
* 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 | • 1 NOTES
i See the HuBMAPR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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teran2 Summary
[top]
| Package: HuBMAPR |
| 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 HuBMAPR |
| BuildTime: 0 minutes 57.36 seconds |
| CheckCommand: BiocCheckGitClone('HuBMAPR') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/R-libs --install=check:/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.install-out.txt HuBMAPR_0.99.5.tar.gz && BiocCheck('HuBMAPR_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 39.48 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 362.61 KiB |
| BuildID:: HuBMAPR_20240919224527 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HuBMAPR. 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
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘HuBMAPR/DESCRIPTION’ ... OK
* preparing ‘HuBMAPR’:
* 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 ‘HuBMAPR_0.99.5.tar.gz’
teran2 CHECK output
[top]
===============================
BiocCheckGitClone('HuBMAPR')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR
→ BiocVersion: 3.20
→ Package: HuBMAPR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR/.gitignore'
* 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/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.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 ‘HuBMAPR/DESCRIPTION’ ... OK
* this is package ‘HuBMAPR’ 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 serialization versions ... OK
* checking whether package ‘HuBMAPR’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [3s/3s] 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 ... [5s/48s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
datasets 1.016 0.035 14.837
donors 0.984 0.026 18.730
samples 0.551 0.003 8.256
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/90s]
[7s/90s] 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 ... [2s/2s] OK
* DONE
Status: OK
===============================
BiocCheck('HuBMAPR_0.99.5.tar.gz')
===============================
── Installing HuBMAPR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── HuBMAPR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpS1KvWs/file16edb756af2b10/HuBMAPR
→ BiocVersion: 3.20
→ Package: HuBMAPR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3532/e78fa804a03d87feb9631647b0f5684a8a7774d0/HuBMAPR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpS1KvWs/file16edb756af2b10/HuBMAPR
→ installDir: /tmp/RtmpS1KvWs/file16edb73684f06f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HuBMAPR ────────────────────────────────────────────────
* 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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 HuBMAPR...
* 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...
* 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 | • 1 NOTES
i See the HuBMAPR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
teran2 BUILD BIN output
[top]