lconway Summary
[top]
| Package: adverSCarial |
| Version: 0.99.36 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data adverSCarial |
| BuildTime: 0 minutes 15.14 seconds |
| CheckCommand: BiocCheckGitClone('adverSCarial') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2983/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.install-out.txt adverSCarial_0.99.36.tar.gz && BiocCheck('adverSCarial_0.99.36.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 30.13 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh adverSCarial_0.99.36.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 2.29 seconds |
| PackageFileSize: 144.12 KiB |
| BuildID:: adverSCarial_20230531054546 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: adverSCarial. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. 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. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* preparing ‘adverSCarial’:
* 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 ‘adverSCarial_0.99.36.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('adverSCarial')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.36
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial
─ 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* 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 ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘0.99.36’
* 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 ‘adverSCarial’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [3s/3s] NOTE
.advModificationsFunction: no visible global function definition for
‘is’
.advModificationsFunction : <anonymous>: no visible global function
definition for ‘is’
.advModificationsNotFunction: no visible global function definition for
‘is’
.advModificationsNotFunction: no visible global function definition for
‘counts’
.advModificationsNotFunction : <anonymous>: no visible global function
definition for ‘is’
.randWalkGetSeed: no visible global function definition for
‘SingleCellExperiment’
.randWalkTryNewVector: no visible global function definition for
‘SingleCellExperiment’
MClassifier: no visible global function definition for ‘is’
advChar: no visible global function definition for ‘new’
advGridMinChange: no visible global function definition for ‘is’
advGridMinChange: no visible global function definition for ‘counts’
advGridMinChange: no visible global function definition for
‘SingleCellExperiment’
advList: no visible global function definition for ‘new’
advMaxChange: no visible global function definition for ‘is’
advMaxChange: no visible global function definition for ‘counts’
advMaxChange: no visible global function definition for ‘new’
advMinChange: no visible global function definition for ‘is’
advMinChange: no visible global function definition for ‘counts’
advMinChange: no visible binding for '<<-' assignment to
‘lastResLength’
advMinChange : <anonymous>: no visible binding for global variable
‘lastResLength’
advMinChange : <anonymous>: no visible binding for '<<-' assignment to
‘lastResLength’
advMinChange: no visible global function definition for ‘new’
advModifications: no visible global function definition for ‘is’
advModifications: no visible global function definition for ‘counts’
advModifications: no visible global function definition for
‘SingleCellExperiment’
advRandWalkMinChange: no visible global function definition for ‘is’
advRandWalkMinChange: no visible global function definition for
‘counts’
matrixFromSCE: no visible global function definition for ‘is’
matrixFromSCE: no visible global function definition for ‘colData’
maxChangeOverview: no visible global function definition for ‘is’
maxChangeOverview: no visible global function definition for ‘counts’
minChangeOverview: no visible global function definition for ‘is’
minChangeOverview: no visible global function definition for ‘counts’
predictWithNewValue: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for
‘SingleCellExperiment’
sceConvertToHGNC: no visible global function definition for ‘colData’
Undefined global functions or variables:
SingleCellExperiment colData counts is lastResLength new
Consider adding
importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [60s/68s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MClassifier 17.629 1.788 26.611
matrixFromSCE 9.640 1.065 11.257
sceConvertToHGNC 9.416 1.217 11.145
advChar 8.852 1.608 10.461
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [1s/1s]
[1s/1s] 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: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.Rcheck/00check.log’
for details.
===============================
BiocCheck('adverSCarial_0.99.36.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.36
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpK5QfYl/file7edd363868e8/adverSCarial
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpK5QfYl/file7eddbf11ecc
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.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...
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:
GeneExpression, ATACSeq, GeneTarget
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...
* 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...
* WARNING: Import methods in NAMESPACE as well as DESCRIPTION.
* 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 adverSCarial...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/vign01_adverSCarial.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid '<<-' if possible (found 2 times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 156 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 140 lines
(3%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 10 NOTES
See the adverSCarial.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 adverSCarial_0.99.36.tar.gz'
>>>>>>>
* installing *source* package ‘adverSCarial’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (adverSCarial)
nebbiolo2 Summary
[top]
| Package: adverSCarial |
| Version: 0.99.36 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data adverSCarial |
| BuildTime: 0 minutes 24.37 seconds |
| CheckCommand: BiocCheckGitClone('adverSCarial') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2983/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.install-out.txt adverSCarial_0.99.36.tar.gz && BiocCheck('adverSCarial_0.99.36.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 49.69 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 144.04 KiB |
| BuildID:: adverSCarial_20230531054546 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: adverSCarial. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* preparing ‘adverSCarial’:
* 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 ‘adverSCarial_0.99.36.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('adverSCarial')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.36
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial
─ 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘0.99.36’
* 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 ‘adverSCarial’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] NOTE
.advModificationsFunction: no visible global function definition for
‘is’
.advModificationsFunction : <anonymous>: no visible global function
definition for ‘is’
.advModificationsNotFunction: no visible global function definition for
‘is’
.advModificationsNotFunction: no visible global function definition for
‘counts’
.advModificationsNotFunction : <anonymous>: no visible global function
definition for ‘is’
.randWalkGetSeed: no visible global function definition for
‘SingleCellExperiment’
.randWalkTryNewVector: no visible global function definition for
‘SingleCellExperiment’
MClassifier: no visible global function definition for ‘is’
advChar: no visible global function definition for ‘new’
advGridMinChange: no visible global function definition for ‘is’
advGridMinChange: no visible global function definition for ‘counts’
advGridMinChange: no visible global function definition for
‘SingleCellExperiment’
advList: no visible global function definition for ‘new’
advMaxChange: no visible global function definition for ‘is’
advMaxChange: no visible global function definition for ‘counts’
advMaxChange: no visible global function definition for ‘new’
advMinChange: no visible global function definition for ‘is’
advMinChange: no visible global function definition for ‘counts’
advMinChange: no visible binding for '<<-' assignment to
‘lastResLength’
advMinChange : <anonymous>: no visible binding for global variable
‘lastResLength’
advMinChange : <anonymous>: no visible binding for '<<-' assignment to
‘lastResLength’
advMinChange: no visible global function definition for ‘new’
advModifications: no visible global function definition for ‘is’
advModifications: no visible global function definition for ‘counts’
advModifications: no visible global function definition for
‘SingleCellExperiment’
advRandWalkMinChange: no visible global function definition for ‘is’
advRandWalkMinChange: no visible global function definition for
‘counts’
matrixFromSCE: no visible global function definition for ‘is’
matrixFromSCE: no visible global function definition for ‘colData’
maxChangeOverview: no visible global function definition for ‘is’
maxChangeOverview: no visible global function definition for ‘counts’
minChangeOverview: no visible global function definition for ‘is’
minChangeOverview: no visible global function definition for ‘counts’
predictWithNewValue: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for
‘SingleCellExperiment’
sceConvertToHGNC: no visible global function definition for ‘colData’
Undefined global functions or variables:
SingleCellExperiment colData counts is lastResLength new
Consider adding
importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [86s/88s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MClassifier 26.557 2.186 29.561
sceConvertToHGNC 14.446 2.126 17.092
matrixFromSCE 14.570 1.840 17.098
advChar 12.189 0.724 12.914
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [1s/1s]
[1s/1s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.Rcheck/00check.log’
for details.
===============================
BiocCheck('adverSCarial_0.99.36.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.36
─ sourceDir: /tmp/RtmpTiJgsI/file1f21ee4d748bb3/adverSCarial
─ installDir: /tmp/RtmpTiJgsI/file1f21ee18d794a6
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2983/52988ca146488fdba3436b3a071849a27e9914e9/adverSCarial.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...
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:
GeneExpression, ATACSeq, GeneTarget
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...
* 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...
* WARNING: Import methods in NAMESPACE as well as DESCRIPTION.
* 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 adverSCarial...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
Found @ in vignettes/vign01_adverSCarial.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid '<<-' if possible (found 2 times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 156 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 140 lines
(3%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 10 NOTES
See the adverSCarial.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]