nebbiolo2 Summary
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| Package: spatialSimGP |
| Version: 0.99.0 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialSimGP |
| BuildTime: 1 minutes 14.45 seconds |
| CheckCommand: BiocCheckGitClone('spatialSimGP') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3544/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP.install-out.txt spatialSimGP_0.99.0.tar.gz && BiocCheck('spatialSimGP_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 17.70 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 332.59 KiB |
| BuildID:: spatialSimGP_20240920092058 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spatialSimGP. 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 ‘spatialSimGP/DESCRIPTION’ ... OK
* preparing ‘spatialSimGP’:
* 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 ‘spatialSimGP_0.99.0.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('spatialSimGP')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP
→ BiocVersion: 3.20
→ Package: spatialSimGP
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP
→ 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/3544/spatialSimGP_20240920092058/spatialSimGP.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 ‘spatialSimGP/DESCRIPTION’ ... OK
* this is package ‘spatialSimGP’ version ‘0.99.0’
* 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 ‘spatialSimGP’ 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [22s/22s] 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 ... [23s/23s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
spatial_simulate 13.627 0.805 14.819
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [23s/24s]
[24s/24s] 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: OK
===============================
BiocCheck('spatialSimGP_0.99.0.tar.gz')
===============================
── Installing spatialSimGP ─────────────────────────────────────────────────────
✔ Package installed successfully
── spatialSimGP session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpx0wreP/filecae1b3004be20/spatialSimGP
→ BiocVersion: 3.20
→ Package: spatialSimGP
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmpx0wreP/filecae1b3004be20/spatialSimGP
→ installDir: /tmp/Rtmpx0wreP/filecae1b304cd23a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spatialSimGP ───────────────────────────────────────────
* 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 (67%).
* 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 spatialSimGP...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• spatial_simulate() (R/spatial_simulate.R): 121 lines
* 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; 20 lines (4%) are > 80 characters long.
First few lines:
• R/spatial_simulate.R#L5 #' @details This function simulates a Sp ...
• ...
• vignettes/spatialSimGP.Rmd#L77 $$(C_{ij}(\boldsymbol{\theta})) = \sigma ...
i NOTE: Consider multiples of 4 spaces for line indents; 78 lines (17%) are
not.
First few lines:
• R/spatial_simulate.R#L57 range_sigma ...
• ...
• vignettes/spatialSimGP.Rmd#L241 theme(plot.title = element_text(face = ...
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 | • 3 NOTES
i See the spatialSimGP.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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teran2 Summary
[top]
| Package: spatialSimGP |
| Version: 0.99.0 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialSimGP |
| BuildTime: 0 minutes 47.29 seconds |
| CheckCommand: BiocCheckGitClone('spatialSimGP') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3544/R-libs --install=check:/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP.install-out.txt spatialSimGP_0.99.0.tar.gz && BiocCheck('spatialSimGP_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 42.72 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 694.50 KiB |
| BuildID:: spatialSimGP_20240920092058 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spatialSimGP. 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 ‘spatialSimGP/DESCRIPTION’ ... OK
* preparing ‘spatialSimGP’:
* 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 ‘spatialSimGP_0.99.0.tar.gz’
teran2 CHECK output
[top]
===============================
BiocCheckGitClone('spatialSimGP')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP
→ BiocVersion: 3.20
→ Package: spatialSimGP
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP
→ 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/3544/spatialSimGP_20240920092058/spatialSimGP.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 ‘spatialSimGP/DESCRIPTION’ ... OK
* this is package ‘spatialSimGP’ version ‘0.99.0’
* 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 ‘spatialSimGP’ 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [18s/18s] 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 ... [18s/19s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
spatial_simulate 10.13 0.892 11.685
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [18s/18s]
[18s/18s] 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('spatialSimGP_0.99.0.tar.gz')
===============================
── Installing spatialSimGP ─────────────────────────────────────────────────────
✔ Package installed successfully
── spatialSimGP session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpS95Zte/file3a2f3fc59112/spatialSimGP
→ BiocVersion: 3.20
→ Package: spatialSimGP
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3544/spatialSimGP_20240920092058/spatialSimGP.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpS95Zte/file3a2f3fc59112/spatialSimGP
→ installDir: /tmp/RtmpS95Zte/file3a2f367375e21
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spatialSimGP ───────────────────────────────────────────
* 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 (67%).
* 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 spatialSimGP...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• spatial_simulate() (R/spatial_simulate.R): 121 lines
* 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; 20 lines (4%) are > 80 characters long.
First few lines:
• R/spatial_simulate.R#L5 #' @details This function simulates a Sp ...
• ...
• vignettes/spatialSimGP.Rmd#L77 $$(C_{ij}(\boldsymbol{\theta})) = \sigma ...
i NOTE: Consider multiples of 4 spaces for line indents; 78 lines (17%) are
not.
First few lines:
• R/spatial_simulate.R#L57 range_sigma ...
• ...
• vignettes/spatialSimGP.Rmd#L241 theme(plot.title = element_text(face = ...
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 | • 3 NOTES
i See the spatialSimGP.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
teran2 BUILD BIN output
[top]