lconway Summary
[top]
| Package: TENET.AnnotationHub |
| Version: 0.99.0 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TENET.AnnotationHub |
| BuildTime: 1 minutes 11.73 seconds |
| CheckCommand: BiocCheckGitClone('TENET.AnnotationHub') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3473/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.install-out.txt TENET.AnnotationHub_0.99.0.tar.gz && BiocCheck('TENET.AnnotationHub_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 59.19 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh TENET.AnnotationHub_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 6.00 seconds |
| PackageFileSize: 352.23 KiB |
| BuildID:: TENET.AnnotationHub_20240806124332 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TENET.AnnotationHub. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: AnnotationData. 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
[top]
===============================
R CMD BUILD
===============================
* checking for file TENET.AnnotationHub/DESCRIPTION ... OK
* preparing TENET.AnnotationHub:
* 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 TENET.AnnotationHub_0.99.0.tar.gz
lconway CHECK output
[top]
===============================
BiocCheckGitClone('TENET.AnnotationHub')
===============================
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub
BiocVersion: 3.20
Package: TENET.AnnotationHub
PackageVersion: 0.99.0
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.BiocCheck
BiocCheckVersion: 1.41.10
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub
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...
* 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/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.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 TENET.AnnotationHub/DESCRIPTION ... OK
* this is package TENET.AnnotationHub 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 TENET.AnnotationHub 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 ... [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 ... [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 ... [6s/6s] 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 sizes of PDF files under inst/doc ... OK
* checking files in vignettes ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [0s/0s]
[0s/1s] 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('TENET.AnnotationHub_0.99.0.tar.gz')
===============================
* Installing package...
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpFCqqdh/file180c71da6d8aa/TENET.AnnotationHub
BiocVersion: 3.20
Package: TENET.AnnotationHub
PackageVersion: 0.99.0
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.BiocCheck
BiocCheckVersion: 1.41.10
sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpFCqqdh/file180c71da6d8aa/TENET.AnnotationHub
installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpFCqqdh/file180c734da901b
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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
AnnotationData
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
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 TENET.AnnotationHub...
* 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...
* NOTE: Consider shorter lines; 17 lines (2%) are > 80 characters
long.
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 | 0 WARNINGS | 2 NOTES
See the TENET.AnnotationHub.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir TENET.AnnotationHub_0.99.0.tar.gz'
>>>>>>>
* installing *source* package TENET.AnnotationHub ...
** 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 (TENET.AnnotationHub)
nebbiolo2 Summary
[top]
| Package: TENET.AnnotationHub |
| 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 TENET.AnnotationHub |
| BuildTime: 1 minutes 23.85 seconds |
| CheckCommand: BiocCheckGitClone('TENET.AnnotationHub') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3473/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.install-out.txt TENET.AnnotationHub_0.99.0.tar.gz && BiocCheck('TENET.AnnotationHub_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 14.10 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 346.56 KiB |
| BuildID:: TENET.AnnotationHub_20240806124332 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TENET.AnnotationHub. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: AnnotationData. 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 TENET.AnnotationHub/DESCRIPTION ... OK
* preparing TENET.AnnotationHub:
* 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 TENET.AnnotationHub_0.99.0.tar.gz
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('TENET.AnnotationHub')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub
BiocVersion: 3.20
Package: TENET.AnnotationHub
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.BiocCheck
BiocCheckVersion: 1.41.10
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub
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...
* 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/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.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 TENET.AnnotationHub/DESCRIPTION ... OK
* this is package TENET.AnnotationHub 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 TENET.AnnotationHub 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 ... [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 ... [9s/9s] 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/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [0s/0s]
[1s/1s] 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('TENET.AnnotationHub_0.99.0.tar.gz')
===============================
* Installing package...
sourceDir: /tmp/RtmpKODVYf/file3c6d782e7af20/TENET.AnnotationHub
BiocVersion: 3.20
Package: TENET.AnnotationHub
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3473/TENET.AnnotationHub_20240806124332/TENET.AnnotationHub.BiocCheck
BiocCheckVersion: 1.41.10
sourceDir: /tmp/RtmpKODVYf/file3c6d782e7af20/TENET.AnnotationHub
installDir: /tmp/RtmpKODVYf/file3c6d784999ddc7
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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
AnnotationData
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
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 TENET.AnnotationHub...
* 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...
* NOTE: Consider shorter lines; 17 lines (2%) are > 80 characters
long.
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 | 0 WARNINGS | 2 NOTES
See the TENET.AnnotationHub.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]