Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/octad.db
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 20.04.4 LTS)/x86_64   OK     WARNINGS     skipped     OK  
merida1 macOS 10.14.6 Mojave/x86_64   OK     WARNINGS     OK     OK  

nebbiolo1 Summary

[top]

Package: octad.db
Version: 0.99.30
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data octad.db
BuildTime: 0 minutes 20.32 seconds
CheckCommand: BiocCheckGitClone('octad.db') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings octad.db_0.99.30.tar.gz && BiocCheck('octad.db_0.99.30.tar.gz', `new-package`=TRUE)
CheckTime: 1 minutes 38.18 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 977.38 KiB
BuildID:: octad.db_20220411044249
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: octad.db. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0.

nebbiolo1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘octad.db/DESCRIPTION’ ... OK
* preparing ‘octad.db’:
* 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 ‘octad.db_0.99.30.tar.gz’

nebbiolo1 CHECK output

[top]

===============================

 BiocCheckGitClone('octad.db')

===============================

This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 1
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/6d903b425b875cb581e1652a30b060529330aa79/octad.db.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad.db/DESCRIPTION’ ... OK
* this is package ‘octad.db’ version ‘0.99.30’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad.db’ can be installed ... [11s/11s] 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument is missing, with no default
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [11s/12s] 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/6d903b425b875cb581e1652a30b060529330aa79/octad.db.Rcheck/00check.log’
for details.






===============================

 BiocCheck('octad.db_0.99.30.tar.gz')

===============================

This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2391/6d903b425b875cb581e1652a30b060529330aa79/octad.db_0.99.30.tar.gz" "/tmp/RtmpStdS1t/file1ea2961b557dc/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1.0 to 4.2.0.
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of octad.db...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 1 times)
        <<- in R/zzz.R (line 19, column 7)
* Checking function lengths...
* Checking man page documentation...
snapshotDate(): 2022-04-06
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 25 lines (11%) are > 80 characters
      long.
    First 6 lines:
      R/octad.db.R:3 #' This is a support package for the main package ```oct...
      R/octad.db.R:8 #'```phenoDF=.eh[["EH7274"]]``` #load data.frame with sa...
      R/octad.db.R:11 #'Besides, the package includes examples of the output ...
      R/octad.db.R:23 #' \url{https://bioconductor.org/packages/octad} or \ur...
      R/octad.db.R:27 #' Zeng, B., Glicksberg, B.S., Newbury, P., Chekalin, E...
      R/octad.db.R:28 #' [https://www.nature.com/articles/s41596-020-00430-z]...
    * NOTE: Consider multiples of 4 spaces for line indents, 7
      lines(3%) are not.
    First 6 lines:
      R/zzz.R:23   .eh <<- ExperimentHub::ExperimentHub()
      R/zzz.R:27   packageStartupMessage("Welcome to octad.db package. This i...
      vignettes/octad.db.Rmd:4   html_document:
      vignettes/octad.db.Rmd:8   %\VignetteIndexEntry{octad}
      vignettes/octad.db.Rmd:9   %\VignetteEngine{knitr::rmarkdown}
      vignettes/octad.db.Rmd:10   %\VignetteEncoding{UTF-8}
    See http://bioconductor.org/developers/how-to/coding-style/
    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 name is in support site watched tags.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 5
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output

nebbiolo1 BUILD BIN output

[top]


                				
 
                
		    
		        			

                			
                			
merida1 Summary
 
                			
[top]

                			
 
                				
 
						        
Package: octad.db
 
                					
Version: 0.99.30
 
                					
RVersion: 4.2
                
 
                					
BiocVersion: 3.15
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data octad.db
 
                					
BuildTime: 0 minutes 59.38 seconds
 
                					
CheckCommand: BiocCheckGitClone('octad.db')  &&  /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings  --no-multiarch  octad.db_0.99.30.tar.gz  &&  BiocCheck('octad.db_0.99.30.tar.gz',  `new-package`=TRUE)

   							
CheckTime: 4 minutes 44.63 seconds

                 					
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh octad.db_0.99.30.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

 							
BuildBinTime: 0 minutes 32.99 seconds

                					
PackageFileSize: 977.30 KiB
 
                					
BuildID:: octad.db_20220411044249
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: octad.db. Starting Build package. Starting Check package. Starting Build package. 
 
                					
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. 
        				
                				
 
                			
 
                			
 
                			    
                				
merida1 BUILD SRC output
 
                    			
[top]

                				
 
                					
===============================

 R CMD BUILD

===============================

* checking for file ‘octad.db/DESCRIPTION’ ... OK
* preparing ‘octad.db’:
* 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 ‘octad.db_0.99.30.tar.gz’



                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
[top]

                				
 
                					
===============================

 BiocCheckGitClone('octad.db')

===============================

This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 1
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2391/6d903b425b875cb581e1652a30b060529330aa79/octad.db.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad.db/DESCRIPTION’ ... OK
* this is package ‘octad.db’ version ‘0.99.30’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad.db’ can be installed ... [32s/33s] 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument is missing, with no default
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [33s/34s] 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2391/6d903b425b875cb581e1652a30b060529330aa79/octad.db.Rcheck/00check.log’
for details.






===============================

 BiocCheck('octad.db_0.99.30.tar.gz')

===============================

This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2391/6d903b425b875cb581e1652a30b060529330aa79/octad.db_0.99.30.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpe9WmRb/filea2924f11a40/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1.0 to 4.2.0.
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of octad.db...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 1 times)
        <<- in R/zzz.R (line 19, column 7)
* Checking function lengths...
* Checking man page documentation...
snapshotDate(): 2022-04-06
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 25 lines (11%) are > 80 characters
      long.
    First 6 lines:
      R/octad.db.R:3 #' This is a support package for the main package ```oct...
      R/octad.db.R:8 #'```phenoDF=.eh[["EH7274"]]``` #load data.frame with sa...
      R/octad.db.R:11 #'Besides, the package includes examples of the output ...
      R/octad.db.R:23 #' \url{https://bioconductor.org/packages/octad} or \ur...
      R/octad.db.R:27 #' Zeng, B., Glicksberg, B.S., Newbury, P., Chekalin, E...
      R/octad.db.R:28 #' [https://www.nature.com/articles/s41596-020-00430-z]...
    * NOTE: Consider multiples of 4 spaces for line indents, 7
      lines(3%) are not.
    First 6 lines:
      R/zzz.R:23   .eh <<- ExperimentHub::ExperimentHub()
      R/zzz.R:27   packageStartupMessage("Welcome to octad.db package. This i...
      vignettes/octad.db.Rmd:4   html_document:
      vignettes/octad.db.Rmd:8   %\VignetteIndexEntry{octad}
      vignettes/octad.db.Rmd:9   %\VignetteEngine{knitr::rmarkdown}
      vignettes/octad.db.Rmd:10   %\VignetteEncoding{UTF-8}
    See http://bioconductor.org/developers/how-to/coding-style/
    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 name is in support site watched tags.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 5
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output


                				
 

                            
 
                                
                				
merida1 BUILD BIN output
 
                    			
[top]

                				
 
                					
===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir octad.db_0.99.30.tar.gz'
>>>>>>> 

* installing *source* package ‘octad.db’ ...
** using staged installation
** R
** data
** 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
snapshotDate(): 2022-04-06
** testing if installed package can be loaded from final location
snapshotDate(): 2022-04-06
** testing if installed package keeps a record of temporary installation path
* DONE (octad.db)