Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/DeepTarget

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 22.04.2 LTS)/x86_64	ERROR	skipped	skipped	skipped
lconway	macOS 12.6.5 Monterey/x86_64	OK	ERROR	OK	OK

nebbiolo2 Summary

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Package: DeepTarget

Version: 0.99.0

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DeepTarget

BuildTime: 0 minutes 42.94 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: DeepTarget_20230804142905

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DeepTarget. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 1.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘DeepTarget/DESCRIPTION’ ... OK
* preparing ‘DeepTarget’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘V_analyses.Rmd’ using rmarkdown

Quitting from lines 58-68 [Computing Similarity Between Drug Treatment and Gene Knockout] (V_analyses.Rmd)
Error: processing vignette 'V_analyses.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘V_analyses.Rmd’

SUMMARY: processing the following file failed:
  ‘V_analyses.Rmd’

Error: Vignette re-building failed.
Execution halted

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output

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lconway Summary

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Package: DeepTarget

Version: 0.99.0

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DeepTarget

BuildTime: 0 minutes 40.01 seconds

CheckCommand: BiocCheckGitClone('DeepTarget') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3066/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3066/DeepTarget_20230804142905/DeepTarget.install-out.txt DeepTarget_0.99.0.tar.gz && BiocCheck('DeepTarget_0.99.0.tar.gz', `new-package`=TRUE)

CheckTime: 2 minutes 39.43 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DeepTarget_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 21.51 seconds

PackageFileSize: 2741.45 KiB

BuildID:: DeepTarget_20230804142905

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DeepTarget. Starting Build package. Starting Check package. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. 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.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘DeepTarget/DESCRIPTION’ ... OK
* preparing ‘DeepTarget’:
* 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 ‘DeepTarget_0.99.0.tar.gz’

lconway CHECK output

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

 BiocCheckGitClone('DeepTarget')

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

─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3066/DeepTarget_20230804142905/DeepTarget
─ 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...
    * ERROR: Do not use Author/Maintainer fields. Use Authors@R.
* Checking CITATION...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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

 R CMD CHECK

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

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3066/DeepTarget_20230804142905/DeepTarget.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepTarget’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'rlang', 'tictoc', 'fgsea', 'ggplot2', 'ggpubr', 'statar',
  'interactions', 'reshape2', 'parallel', 'pROC', 'ggrepel', 'grid',
  'gridExtra', 'stringb', 'DEGreport', 'readxl', 'stringr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DeepTarget’ 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [19s/20s] NOTE
DMB: no visible binding for global variable ‘Drugname’
DMB: no visible binding for global variable ‘GOI’
DMB: no visible binding for global variable ‘GES.c’
DMB: no visible binding for global variable ‘DRS.c’
DTR: no visible binding for global variable ‘DOI’
DTR: no visible binding for global variable ‘GOI’
DoInteractExp: no visible binding for global variable ‘Drug.sim’
DoInteractMutant: no visible binding for global variable
  ‘Drug.targeted.sim’
DoPWY: no visible binding for global variable ‘Drug.Metadata’
GetSim: no visible binding for global variable ‘DrugName’
GetSim: no visible binding for global variable ‘drugResponseScore’
GetSim: no visible binding for global variable ‘GeneEffectScores’
PredMaxSim: no visible binding for global variable ‘Drug.Metadata’
PredTarget: no visible binding for global variable ‘sim’
PredTarget: no visible binding for global variable ‘Drug.Metadata’
colorBar: no visible global function definition for ‘rect’
colorBar: no visible global function definition for ‘text’
colorBar: no visible global function definition for ‘segments’
cor.test_trimmed_v0.default : pkendall: no visible binding for global
  variable ‘C_pKendall’
cor.test_trimmed_v0.default : pspearman: no visible binding for global
  variable ‘C_pRho’
line2user: no visible global function definition for ‘par’
line2user: no visible global function definition for ‘grconvertX’
line2user: no visible global function definition for ‘grconvertY’
plotCor: no visible binding for global variable ‘Drugname’
plotCor: no visible binding for global variable ‘GOI’
plotCor: no visible binding for global variable ‘GES.c’
plotCor: no visible binding for global variable ‘DRS.c’
plotSim: no visible binding for global variable ‘d.Pval’
plotSim: no visible binding for global variable ‘d.corr’
plotSim: no visible global function definition for ‘colorRampPalette’
plotSim: no visible global function definition for ‘text’
Undefined global functions or variables:
  C_pKendall C_pRho DOI DRS.c Drug.Metadata Drug.sim Drug.targeted.sim
  DrugName Drugname GES.c GOI GeneEffectScores colorRampPalette d.Pval
  d.corr drugResponseScore grconvertX grconvertY par rect segments sim
  text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "grconvertX", "grconvertY", "par", "rect",
             "segments", "text")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] NOTE
prepare_Rd: DMB.Rd:37-39: Dropping empty section \details
prepare_Rd: DMB.Rd:49-51: Dropping empty section \note
prepare_Rd: DMB.Rd:43-45: Dropping empty section \references
prepare_Rd: DMB.Rd:53-55: Dropping empty section \seealso
prepare_Rd: DTR.Rd:40-42: Dropping empty section \details
prepare_Rd: DTR.Rd:52-54: Dropping empty section \note
prepare_Rd: DTR.Rd:46-48: Dropping empty section \references
prepare_Rd: DTR.Rd:58-60: Dropping empty section \seealso
prepare_Rd: DoInteractExp.Rd:25-27: Dropping empty section \details
prepare_Rd: DoInteractExp.Rd:40-42: Dropping empty section \note
prepare_Rd: DoInteractExp.Rd:34-36: Dropping empty section \references
prepare_Rd: DoInteractExp.Rd:44-46: Dropping empty section \seealso
prepare_Rd: DoInteractMutant.Rd:21-23: Dropping empty section \details
prepare_Rd: DoInteractMutant.Rd:37-39: Dropping empty section \note
prepare_Rd: DoInteractMutant.Rd:31-33: Dropping empty section \references
prepare_Rd: DoInteractMutant.Rd:43-45: Dropping empty section \seealso
prepare_Rd: DoPWY.Rd:22-24: Dropping empty section \details
prepare_Rd: DoPWY.Rd:39-41: Dropping empty section \note
prepare_Rd: DoPWY.Rd:33-35: Dropping empty section \references
prepare_Rd: DoPWY.Rd:45-47: Dropping empty section \seealso
prepare_Rd: GetSim.Rd:25-27: Dropping empty section \details
prepare_Rd: GetSim.Rd:37-39: Dropping empty section \note
prepare_Rd: GetSim.Rd:31-33: Dropping empty section \references
prepare_Rd: GetSim.Rd:43-45: Dropping empty section \seealso
prepare_Rd: OntargetM.Rd:41-43: Dropping empty section \references
prepare_Rd: PredMaxSim.Rd:22-24: Dropping empty section \details
prepare_Rd: PredMaxSim.Rd:34-36: Dropping empty section \note
prepare_Rd: PredMaxSim.Rd:28-30: Dropping empty section \references
prepare_Rd: PredMaxSim.Rd:40-42: Dropping empty section \seealso
prepare_Rd: PredTarget.Rd:24-26: Dropping empty section \details
prepare_Rd: PredTarget.Rd:36-38: Dropping empty section \note
prepare_Rd: PredTarget.Rd:30-32: Dropping empty section \references
prepare_Rd: PredTarget.Rd:42-44: Dropping empty section \seealso
prepare_Rd: colorBar.Rd:46-48: Dropping empty section \details
prepare_Rd: colorBar.Rd:49-55: Dropping empty section \value
prepare_Rd: colorBar.Rd:62-64: Dropping empty section \note
prepare_Rd: colorBar.Rd:56-58: Dropping empty section \references
prepare_Rd: colorBar.Rd:68-70: Dropping empty section \seealso
prepare_Rd: cor.test_trimmed_v0.Rd:22-24: Dropping empty section \details
prepare_Rd: cor.test_trimmed_v0.Rd:25-31: Dropping empty section \value
prepare_Rd: cor.test_trimmed_v0.Rd:38-40: Dropping empty section \note
prepare_Rd: cor.test_trimmed_v0.Rd:35-37: Dropping empty section \author
prepare_Rd: cor.test_trimmed_v0.Rd:32-34: Dropping empty section \references
prepare_Rd: cor.test_trimmed_v0.Rd:44-46: Dropping empty section \seealso
prepare_Rd: errHandle.Rd:19-21: Dropping empty section \details
prepare_Rd: errHandle.Rd:22-28: Dropping empty section \value
prepare_Rd: errHandle.Rd:35-37: Dropping empty section \note
prepare_Rd: errHandle.Rd:32-34: Dropping empty section \author
prepare_Rd: errHandle.Rd:29-31: Dropping empty section \references
prepare_Rd: errHandle.Rd:41-43: Dropping empty section \seealso
prepare_Rd: fdrCor.Rd:19-21: Dropping empty section \details
prepare_Rd: fdrCor.Rd:22-28: Dropping empty section \value
prepare_Rd: fdrCor.Rd:35-37: Dropping empty section \note
prepare_Rd: fdrCor.Rd:32-34: Dropping empty section \author
prepare_Rd: fdrCor.Rd:29-31: Dropping empty section \references
prepare_Rd: fdrCor.Rd:41-43: Dropping empty section \seealso
prepare_Rd: line2user.Rd:21-23: Dropping empty section \details
prepare_Rd: line2user.Rd:24-30: Dropping empty section \value
prepare_Rd: line2user.Rd:37-39: Dropping empty section \note
prepare_Rd: line2user.Rd:31-33: Dropping empty section \references
prepare_Rd: line2user.Rd:43-45: Dropping empty section \seealso
prepare_Rd: plotCor.Rd:33-35: Dropping empty section \details
prepare_Rd: plotCor.Rd:45-47: Dropping empty section \note
prepare_Rd: plotCor.Rd:42-44: Dropping empty section \author
prepare_Rd: plotCor.Rd:39-41: Dropping empty section \references
prepare_Rd: plotCor.Rd:51-53: Dropping empty section \seealso
prepare_Rd: plotSim.Rd:28-30: Dropping empty section \details
prepare_Rd: plotSim.Rd:31-37: Dropping empty section \value
prepare_Rd: plotSim.Rd:44-46: Dropping empty section \note
prepare_Rd: plotSim.Rd:38-40: Dropping empty section \references
prepare_Rd: plotSim.Rd:50-52: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'DMB.Rd':
  \usage lines wider than 90 characters:
     DMB(DN = Drugname, GN= GOI, Pred = Pred, Mutant = Mutant, DRS = DRS, GES = GES, plot = TRUE)

Rd file 'DTR.Rd':
  \usage lines wider than 90 characters:
     DTR(DN = DOI, GN = GOI, Pred = Pred, Exp = Exp, DRS = DRS, GES = GES, CutOff= 3,plot = TRUE)

These lines will be truncated in the PDF manual.
* 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/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/23s] OK
* 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 ... [4s/4s] OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3066/DeepTarget_20230804142905/DeepTarget.Rcheck/00check.log’
for details.






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

 BiocCheck('DeepTarget_0.99.0.tar.gz')

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

─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZxO7Hy/file132476d42d12/DeepTarget
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpZxO7Hy/file132474de67574
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3066/DeepTarget_20230804142905/DeepTarget.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 3.5.0 to 4.3.0.
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Pathways, GeneExpression, RNASeq, ImmunoOncology,
      DifferentialExpression, GeneSetEnrichment, ReportWriting
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import stats in DESCRIPTION as well as NAMESPACE.
* 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 DeepTarget...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
* 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...
    * NOTE: Auto-generated '%% ~' comments found in Rd man pages.
    * WARNING: Empty or missing \value sections found in man pages.
* 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; 123 lines (6%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 268 lines
      (13%) 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: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/

─ BiocCheck results ──
3 ERRORS | 4 WARNINGS | 14 NOTES

See the DeepTarget.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 DeepTarget_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DeepTarget’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (DeepTarget)