nebbiolo1 Summary
[top]
| Package: MouseAgingData |
| Version: 0.99.2 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MouseAgingData |
| BuildTime: 1 minutes 35.93 seconds |
| CheckCommand: BiocCheckGitClone('MouseAgingData') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3293/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.install-out.txt MouseAgingData_0.99.2.tar.gz && BiocCheck('MouseAgingData_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 0.68 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 914.84 KiB |
| BuildID:: MouseAgingData_20240212233431 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MouseAgingData. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file MouseAgingData/DESCRIPTION ... OK
* preparing MouseAgingData:
* 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 MouseAgingData_0.99.2.tar.gz
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('MouseAgingData')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: MouseAgingData
PackageVersion: 0.99.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData
platform: unix
isTarBall: FALSE
* Checking valid files...
* WARNING: System files in '/inst' should not be Git tracked.
inst/.DS_Store
* ERROR: System files found that should not be Git tracked.
MouseAgingData.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* 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
1 ERRORS | 1 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MouseAgingData/DESCRIPTION ... OK
* this is package MouseAgingData version 0.99.2
* 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
WARNING: omitting pointless dependence on 'R' without a version requirement
* checking serialization versions ... OK
* checking whether package MouseAgingData can be installed ... WARNING
Found the following significant warnings:
WARNING: omitting pointless dependence on 'R' without a version requirement
See /home/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.Rcheck/00install.out for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ...WARNING: omitting pointless dependence on 'R' without a version requirement
OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [16s/20s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
BiocGenerics S4Vectors methods
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] NOTE
parabiosis10X: no visible global function definition for 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 ... [26s/27s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parabiosis10X 13.618 1.606 15.793
* 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: 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.Rcheck/00check.log
for details.
===============================
BiocCheck('MouseAgingData_0.99.2.tar.gz')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: MouseAgingData
PackageVersion: 0.99.2
sourceDir: /tmp/RtmpJMMGKq/file8d4045239547/MouseAgingData
installDir: /tmp/RtmpJMMGKq/file8d4044d5e23e9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
ExperimentData
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (80%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import BiocGenerics, methods, S4Vectors in NAMESPACE as
well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
* ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
* 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 MouseAgingData...
* 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...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 9 lines
(2%) 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.
* ERROR: Add package to Watched Tags in your Support Site profile;
visit https://support.bioconductor.org/accounts/edit/profile
BiocCheck results
3 ERRORS | 2 WARNINGS | 4 NOTES
See the MouseAgingData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: MouseAgingData |
| Version: 0.99.2 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MouseAgingData |
| BuildTime: 3 minutes 5.07 seconds |
| CheckCommand: BiocCheckGitClone('MouseAgingData') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3293/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.install-out.txt MouseAgingData_0.99.2.tar.gz && BiocCheck('MouseAgingData_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 8 minutes 53.11 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MouseAgingData_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 8.54 seconds |
| PackageFileSize: 880.58 KiB |
| BuildID:: MouseAgingData_20240212233431 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MouseAgingData. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file MouseAgingData/DESCRIPTION ... OK
* preparing MouseAgingData:
* 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 MouseAgingData_0.99.2.tar.gz
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('MouseAgingData')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: MouseAgingData
PackageVersion: 0.99.2
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData
platform: unix
isTarBall: FALSE
* Checking valid files...
* WARNING: System files in '/inst' should not be Git tracked.
inst/.DS_Store
* ERROR: System files found that should not be Git tracked.
MouseAgingData.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* 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
1 ERRORS | 1 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* 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 MouseAgingData/DESCRIPTION ... OK
* this is package MouseAgingData version 0.99.2
* 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
WARNING: omitting pointless dependence on 'R' without a version requirement
* checking serialization versions ... OK
* checking whether package MouseAgingData can be installed ... WARNING
Found the following significant warnings:
WARNING: omitting pointless dependence on 'R' without a version requirement
See /Users/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.Rcheck/00install.out for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ...WARNING: omitting pointless dependence on 'R' without a version requirement
OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [20s/23s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/22s] OK
* checking whether the package can be unloaded cleanly ... [20s/22s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/21s] OK
* checking loading without being on the library search path ... [20s/22s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
BiocGenerics S4Vectors methods
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [61s/71s] NOTE
parabiosis10X: no visible global function definition for query
Undefined global functions or variables:
query
* checking Rd files ... [1s/1s] 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 ... [44s/59s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parabiosis10X 19.234 2.997 33.45
* 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 ... [11s/14s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
/Users/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.Rcheck/00check.log
for details.
===============================
BiocCheck('MouseAgingData_0.99.2.tar.gz')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: MouseAgingData
PackageVersion: 0.99.2
sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpGVmY5c/file1591f1b153f6a/MouseAgingData
installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpGVmY5c/file1591f758ab2b5
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3293/5f0489df0731ee9a52e5265bbbd21dbfe50acc90/MouseAgingData.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
ExperimentData
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (80%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import BiocGenerics, methods, S4Vectors in NAMESPACE as
well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
* ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
* 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 MouseAgingData...
* 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...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 9 lines
(2%) 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.
* ERROR: Add package to Watched Tags in your Support Site profile;
visit https://support.bioconductor.org/accounts/edit/profile
BiocCheck results
3 ERRORS | 2 WARNINGS | 4 NOTES
See the MouseAgingData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MouseAgingData_0.99.2.tar.gz'
>>>>>>>
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package MouseAgingData ...
** 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 (MouseAgingData)