nebbiolo1 Summary
[top]
| Package: homosapienDEE2CellScore |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data homosapienDEE2CellScore |
| BuildTime: 3 minutes 45.57 seconds |
| CheckCommand: BiocCheckGitClone('homosapienDEE2CellScore') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3101/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.install-out.txt homosapienDEE2CellScore_0.99.3.tar.gz && BiocCheck('homosapienDEE2CellScore_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 19.49 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 191.74 KiB |
| BuildID:: homosapienDEE2CellScore_20240205215202 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: homosapienDEE2CellScore. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file homosapienDEE2CellScore/DESCRIPTION ... OK
* preparing homosapienDEE2CellScore:
* 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 homosapienDEE2CellScore_0.99.3.tar.gz
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('homosapienDEE2CellScore')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: homosapienDEE2CellScore
PackageVersion: 0.99.3
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore
platform: unix
isTarBall: FALSE
* Checking valid files...
* 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
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.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 homosapienDEE2CellScore/DESCRIPTION ... OK
* this is package homosapienDEE2CellScore 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 serialization versions ... OK
* checking whether package homosapienDEE2CellScore 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking whether startup messages can be suppressed ... [11s/12s] 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 ... [36s/37s] OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
HomosapienDEE2_QC_PASS_Agg HomosapienDEE2_QC_PASS_Deseq2
HomosapienDEE2_QC_PASS_Rank HomosapienDEE2_QC_PASS_Raw
HomosapienDEE2_QC_WARN_Agg HomosapienDEE2_QC_WARN_Deseq2
HomosapienDEE2_QC_WARN_Rank HomosapienDEE2_QC_WARN_Raw
buildData buildRaw cols downloadAllTheData readInSEZip
srx_agg_se writeOutSEZip
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking files in vignettes ... OK
* checking examples ... NONE
* 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
See
/home/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.Rcheck/00check.log
for details.
===============================
BiocCheck('homosapienDEE2CellScore_0.99.3.tar.gz')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: homosapienDEE2CellScore
PackageVersion: 0.99.3
sourceDir: /tmp/Rtmp0lhNaS/file1c46c751d5cbb3/homosapienDEE2CellScore
installDir: /tmp/Rtmp0lhNaS/file1c46c7497a1016
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.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...
* 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...
* NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (78%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of homosapienDEE2CellScore...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 147 lines (26%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 175 lines
(31%) 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...
* ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
1 ERRORS | 0 WARNINGS | 12 NOTES
See the homosapienDEE2CellScore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
| Package: homosapienDEE2CellScore |
| Version: 0.99.3 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data homosapienDEE2CellScore |
| BuildTime: 8 minutes 25.87 seconds |
| CheckCommand: BiocCheckGitClone('homosapienDEE2CellScore') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3101/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.install-out.txt homosapienDEE2CellScore_0.99.3.tar.gz && BiocCheck('homosapienDEE2CellScore_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 14.29 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh homosapienDEE2CellScore_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 17.98 seconds |
| PackageFileSize: 191.76 KiB |
| BuildID:: homosapienDEE2CellScore_20240205215202 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: homosapienDEE2CellScore. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 1. Checking git clone status: 0. 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 homosapienDEE2CellScore/DESCRIPTION ... OK
* preparing homosapienDEE2CellScore:
* 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 homosapienDEE2CellScore_0.99.3.tar.gz
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('homosapienDEE2CellScore')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: homosapienDEE2CellScore
PackageVersion: 0.99.3
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore
platform: unix
isTarBall: FALSE
* Checking valid files...
* 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
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.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 homosapienDEE2CellScore/DESCRIPTION ... OK
* this is package homosapienDEE2CellScore 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 serialization versions ... OK
* checking whether package homosapienDEE2CellScore 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [22s/24s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/22s] OK
* checking whether the package can be unloaded cleanly ... [20s/23s] OK
* checking whether the namespace can be loaded with stated dependencies ... [19s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [20s/27s] OK
* checking loading without being on the library search path ... [20s/21s] OK
* checking whether startup messages can be suppressed ... [19s/20s] 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 ... [60s/63s] OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
HomosapienDEE2_QC_PASS_Agg HomosapienDEE2_QC_PASS_Deseq2
HomosapienDEE2_QC_PASS_Rank HomosapienDEE2_QC_PASS_Raw
HomosapienDEE2_QC_WARN_Agg HomosapienDEE2_QC_WARN_Deseq2
HomosapienDEE2_QC_WARN_Rank HomosapienDEE2_QC_WARN_Raw
buildData buildRaw cols downloadAllTheData readInSEZip
srx_agg_se writeOutSEZip
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking files in vignettes ... OK
* checking examples ... NONE
* 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 ... [6s/6s] OK
* DONE
Status: 1 WARNING
See
/Users/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.Rcheck/00check.log
for details.
===============================
BiocCheck('homosapienDEE2CellScore_0.99.3.tar.gz')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: homosapienDEE2CellScore
PackageVersion: 0.99.3
sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpsZVXuT/filedce124fc8b44/homosapienDEE2CellScore
installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpsZVXuT/filedce13901fbad
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3101/9c060e34768671b32a16d0270302cb9d3a6042d1/homosapienDEE2CellScore.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...
* 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...
* NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (78%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of homosapienDEE2CellScore...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 147 lines (26%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 175 lines
(31%) 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...
* ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
1 ERRORS | 0 WARNINGS | 12 NOTES
See the homosapienDEE2CellScore.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 homosapienDEE2CellScore_0.99.3.tar.gz'
>>>>>>>
* installing *source* package homosapienDEE2CellScore ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package homosapienDEE2CellScore
*** 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 (homosapienDEE2CellScore)