lconway Summary
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| Package: seahtrue |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data seahtrue |
| BuildTime: 1 minutes 40.29 seconds |
| CheckCommand: BiocCheckGitClone('seahtrue') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3401/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.install-out.txt seahtrue_0.99.3.tar.gz && BiocCheck('seahtrue_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 55.93 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh seahtrue_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 4.99 seconds |
| PackageFileSize: 3400.11 KiB |
| BuildID:: seahtrue_20240720103226 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seahtrue. 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. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file seahtrue/DESCRIPTION ... OK
* preparing seahtrue:
* 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
* looking to see if a data/datalist file should be added
* building seahtrue_0.99.3.tar.gz
lconway CHECK output
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===============================
BiocCheckGitClone('seahtrue')
===============================
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue
BiocVersion: 3.20
Package: seahtrue
PackageVersion: 0.99.3
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue/.gitignore'
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* 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 results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file seahtrue/DESCRIPTION ... OK
* checking extension type ... Package
* this is package seahtrue version 0.99.3
* 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 seahtrue 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 ... [1s/1s] 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 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 ... [5s/5s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [0s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [131s/131s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sketch_rate 41.810 1.522 43.336
sketch_assimilate_raw 21.053 0.749 21.804
sketch_assimilate_rate 20.693 0.746 21.445
glue_xfplates 20.651 0.770 21.423
sketch_plate 10.443 0.410 10.855
revive_xfplate 10.138 0.370 10.508
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [7s/7s]
[7s/7s] 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 ... [5s/5s] OK
* DONE
Status: OK
===============================
BiocCheck('seahtrue_0.99.3.tar.gz')
===============================
* Installing package...
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptXZAja/file90d48c3b0d9/seahtrue
BiocVersion: 3.20
Package: seahtrue
PackageVersion: 0.99.3
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptXZAja/file90d48c3b0d9/seahtrue
installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptXZAja/file90d278f9be1
isTarBall: TRUE
platform: unix
* 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...
* NOTE: Update R version dependency from 4.2.0 to 4.4.0.
* 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...
* WARNING: 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...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of seahtrue...
* 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 15 functions greater than 50 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...
* NOTE: Consider shorter lines; 59 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 151 lines
(5%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 2 WARNINGS | 4 NOTES
See the seahtrue.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir seahtrue_0.99.3.tar.gz'
>>>>>>>
* installing *source* package seahtrue ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (seahtrue)
nebbiolo2 Summary
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| Package: seahtrue |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data seahtrue |
| BuildTime: 3 minutes 15.22 seconds |
| CheckCommand: BiocCheckGitClone('seahtrue') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3401/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.install-out.txt seahtrue_0.99.3.tar.gz && BiocCheck('seahtrue_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 29.98 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3400.21 KiB |
| BuildID:: seahtrue_20240720103226 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seahtrue. 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 seahtrue/DESCRIPTION ... OK
* preparing seahtrue:
* 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
* looking to see if a data/datalist file should be added
* building seahtrue_0.99.3.tar.gz
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('seahtrue')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue
BiocVersion: 3.20
Package: seahtrue
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue/.gitignore'
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* 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 results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file seahtrue/DESCRIPTION ... OK
* checking extension type ... Package
* this is package seahtrue version 0.99.3
* 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 seahtrue 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] 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 ... [2s/2s] OK
* checking loading without being on the library search path ... [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 ... [7s/7s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [214s/214s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sketch_rate 70.330 0.932 71.262
sketch_assimilate_rate 35.435 0.524 35.959
glue_xfplates 34.413 0.628 35.041
sketch_assimilate_raw 33.693 0.476 34.169
sketch_plate 17.351 0.212 17.564
revive_xfplate 16.867 0.232 17.098
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [10s/10s]
[10s/10s] 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('seahtrue_0.99.3.tar.gz')
===============================
* Installing package...
sourceDir: /tmp/RtmpFXtR7R/file30f90b4ec41ba2/seahtrue
BiocVersion: 3.20
Package: seahtrue
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3401/c1eb115e4ad0d379b20db1dcc229f453deca51eb/seahtrue.BiocCheck
BiocCheckVersion: 1.41.6
sourceDir: /tmp/RtmpFXtR7R/file30f90b4ec41ba2/seahtrue
installDir: /tmp/RtmpFXtR7R/file30f90b46ef2d40
isTarBall: TRUE
platform: unix
* 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...
* NOTE: Update R version dependency from 4.2.0 to 4.4.0.
* 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...
* WARNING: 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...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of seahtrue...
* 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 15 functions greater than 50 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...
* NOTE: Consider shorter lines; 59 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 151 lines
(5%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 2 WARNINGS | 4 NOTES
See the seahtrue.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]