merida1 Summary
[top]
Package: ATACCoGAPS |
Version: 0.99.10 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ATACCoGAPS |
BuildTime: 2 minutes 35.44 seconds |
CheckCommand: BiocCheckGitClone('ATACCoGAPS') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ATACCoGAPS_0.99.10.tar.gz && BiocCheck('ATACCoGAPS_0.99.10.tar.gz', `new-package`=TRUE) |
CheckTime: 9 minutes 5.00 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ATACCoGAPS_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 24.00 seconds |
PackageFileSize: 2842.79 KiB |
BuildID:: ATACCoGAPS_20220513164627 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ATACCoGAPS. 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. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* preparing ‘ATACCoGAPS’:
* 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 ‘ATACCoGAPS_0.99.10.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('ATACCoGAPS')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* this is package ‘ATACCoGAPS’ version ‘0.99.10’
* 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 whether package ‘ATACCoGAPS’ can be installed ... [24s/24s] 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 ... 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 ... NOTE
Namespaces in Imports field not imported from:
‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Mmusculus.UCSC.mm10’
‘Homo.sapiens’ ‘JASPAR2016’ ‘Mus.musculus’ ‘dplyr’ ‘msigdbr’
‘tidyverse’
All declared Imports should be used.
Package in Depends field not imported from: ‘CoGAPS’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
RNAseqTFValidation: no visible global function definition for ‘head’
cgapsPlot: no visible global function definition for ‘rainbow’
cgapsPlot: no visible global function definition for ‘par’
cgapsPlot: no visible global function definition for ‘legend’
findOverlap: no visible global function definition for ‘queryHits’
geneAccessibility: no visible global function definition for
‘subjectHits’
heatmapGeneAccessibility: no visible global function definition for
‘rainbow’
heatmapPatternMarkers: no visible global function definition for
‘rainbow’
heatmapPatternMatrix: no visible global function definition for
‘rainbow’
paths: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
head legend p.adjust par queryHits rainbow subjectHits
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "legend", "par")
importFrom("stats", "p.adjust")
importFrom("utils", "head")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [281s/378s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
applyGREAT 63.488 14.210 174.539
simpleMotifTFMatch 71.380 6.005 77.382
motifPatternMatch 39.350 1.309 40.657
pathwayMatch 25.453 0.311 25.763
genePatternMatch 22.356 0.348 22.703
foldAccessibility 8.691 0.169 8.859
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘viridis’
* 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: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS.Rcheck/00check.log’
for details.
===============================
BiocCheck('ATACCoGAPS_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpunb9Bv/filebec17af7029c/ATACCoGAPS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpunb9Bv/filebec137b57ac7
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 10 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
* 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 3.5.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
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:
Transcription, Sequencing, Microarray, Pathways, Bayesian,
Clustering, GeneExpression, RNASeq, ImmunoOncology,
DifferentialExpression, GeneSetEnrichment, MultipleComparison,
GO, DimensionReduction, TimeCourse
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 msigdbr, tidyverse, JASPAR2016, Homo.sapiens,
Mus.musculus, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, dplyr in NAMESPACE as well as
DESCRIPTION.
* 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 ATACCoGAPS...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* WARNING: Remove set.seed usage (found 4 times)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.8% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* 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; 102 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 676 lines
(26%) are not.
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.
─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 15 NOTES
See the ATACCoGAPS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ATACCoGAPS_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘ATACCoGAPS’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ATACCoGAPS)
nebbiolo1 Summary
[top]
Package: ATACCoGAPS |
Version: 0.99.10 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ATACCoGAPS |
BuildTime: 1 minutes 52.67 seconds |
CheckCommand: BiocCheckGitClone('ATACCoGAPS') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings ATACCoGAPS_0.99.10.tar.gz && BiocCheck('ATACCoGAPS_0.99.10.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 7.68 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2842.95 KiB |
BuildID:: ATACCoGAPS_20220513164627 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ATACCoGAPS. 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. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* preparing ‘ATACCoGAPS’:
* 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 ‘ATACCoGAPS_0.99.10.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('ATACCoGAPS')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.10
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output 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/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* this is package ‘ATACCoGAPS’ version ‘0.99.10’
* 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 whether package ‘ATACCoGAPS’ can be installed ... [17s/17s] 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 ... 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 ... NOTE
Namespaces in Imports field not imported from:
‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Mmusculus.UCSC.mm10’
‘Homo.sapiens’ ‘JASPAR2016’ ‘Mus.musculus’ ‘dplyr’ ‘msigdbr’
‘tidyverse’
All declared Imports should be used.
Package in Depends field not imported from: ‘CoGAPS’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s/11s] NOTE
RNAseqTFValidation: no visible global function definition for ‘head’
cgapsPlot: no visible global function definition for ‘rainbow’
cgapsPlot: no visible global function definition for ‘par’
cgapsPlot: no visible global function definition for ‘legend’
findOverlap: no visible global function definition for ‘queryHits’
geneAccessibility: no visible global function definition for
‘subjectHits’
heatmapGeneAccessibility: no visible global function definition for
‘rainbow’
heatmapPatternMarkers: no visible global function definition for
‘rainbow’
heatmapPatternMatrix: no visible global function definition for
‘rainbow’
paths: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
head legend p.adjust par queryHits rainbow subjectHits
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "legend", "par")
importFrom("stats", "p.adjust")
importFrom("utils", "head")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [195s/315s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simpleMotifTFMatch 54.742 0.600 55.343
applyGREAT 49.538 0.941 170.484
motifPatternMatch 25.080 2.037 27.118
pathwayMatch 18.756 0.240 18.996
genePatternMatch 15.580 0.155 15.736
foldAccessibility 6.215 0.184 6.400
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘viridis’
* 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS.Rcheck/00check.log’
for details.
===============================
BiocCheck('ATACCoGAPS_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/RtmpkLSxq7/file3ebb072279f2e9/ATACCoGAPS
─ installDir: /tmp/RtmpkLSxq7/file3ebb071d41b49b
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2557/dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1/ATACCoGAPS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 10 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
* 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 3.5.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
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:
Transcription, Sequencing, Microarray, Pathways, Bayesian,
Clustering, GeneExpression, RNASeq, ImmunoOncology,
DifferentialExpression, GeneSetEnrichment, MultipleComparison,
GO, DimensionReduction, TimeCourse
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 msigdbr, tidyverse, JASPAR2016, Homo.sapiens,
Mus.musculus, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, dplyr in NAMESPACE as well as
DESCRIPTION.
* 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 ATACCoGAPS...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* WARNING: Remove set.seed usage (found 4 times)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.8% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* 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; 102 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 676 lines
(26%) are not.
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.
─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 15 NOTES
See the ATACCoGAPS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]