lconway Summary
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| Package: DeepTarget |
| Version: 0.99.2 |
| 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: 1 minutes 3.19 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/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.install-out.txt DeepTarget_0.99.2.tar.gz && BiocCheck('DeepTarget_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 1.71 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh DeepTarget_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 22.69 seconds |
| PackageFileSize: 2744.16 KiB |
| BuildID:: DeepTarget_20230829151019 |
| 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_0.99.2.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('DeepTarget')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
vignettes/.RData
vignettes/.Rhistory
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/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 ‘0.99.2’
* 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 ... NOTE
Found the following hidden files and directories:
vignettes/.RData
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 ‘DeepTarget’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.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 ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [22s/23s] 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 ... [31s/27s] 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 ... [5s/5s] OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.Rcheck/00check.log’
for details.
===============================
BiocCheck('DeepTarget_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp1RnhWD/file33f1748dd1b2/DeepTarget
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp1RnhWD/file33f15525898e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/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...
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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.
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
* 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; 127 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; 269 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...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 3 WARNINGS | 15 NOTES
See the DeepTarget.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 DeepTarget_0.99.2.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
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
** testing if installed package keeps a record of temporary installation path
* DONE (DeepTarget)
nebbiolo2 Summary
[top]
| Package: DeepTarget |
| Version: 0.99.2 |
| 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 55.20 seconds |
| CheckCommand: BiocCheckGitClone('DeepTarget') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3066/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.install-out.txt DeepTarget_0.99.2.tar.gz && BiocCheck('DeepTarget_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 47.98 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2727.78 KiB |
| BuildID:: DeepTarget_20230829151019 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: DeepTarget. Starting Build package. Starting Check 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. |
nebbiolo2 BUILD SRC output
[top]
===============================
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_0.99.2.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('DeepTarget')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
vignettes/.RData
vignettes/.Rhistory
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepTarget’ version ‘0.99.2’
* 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 ... NOTE
Found the following hidden files and directories:
vignettes/.RData
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 ‘DeepTarget’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.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 ... 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 ... [9s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [30s/30s] 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 ... [35s/30s] 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 ... [3s/3s] OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/DeepTarget.Rcheck/00check.log’
for details.
===============================
BiocCheck('DeepTarget_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: DeepTarget
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpP3Dx7v/filee55c4491854ae/DeepTarget
─ installDir: /tmp/RtmpP3Dx7v/filee55c429e8cb89
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3066/2b99f7f2d3d58bc4e9b2f980edf35b300f09b5a4/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...
* 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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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.
Warning: replacing previous import ‘stats::var’ by ‘pROC::var’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::cov’ by ‘pROC::cov’ when loading ‘DeepTarget’
Warning: replacing previous import ‘stats::smooth’ by ‘pROC::smooth’ when loading ‘DeepTarget’
* 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; 127 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; 269 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...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 3 WARNINGS | 15 NOTES
See the DeepTarget.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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