merida1 Summary
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Package: ATACCoGAPS |
Version: 0.99.4 |
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 41.09 seconds |
CheckCommand: BiocCheckGitClone('ATACCoGAPS') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ATACCoGAPS_0.99.4.tar.gz && BiocCheck('ATACCoGAPS_0.99.4.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 4.41 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ATACCoGAPS_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 25.00 seconds |
PackageFileSize: 4289.38 KiB |
BuildID:: ATACCoGAPS_20220509152646 |
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: 1. 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_0.99.4.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('ATACCoGAPS')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/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/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/ATACCoGAPS.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* 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 ‘0.99.4’
* 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 ... [25s/25s] 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 ... WARNING
'::' or ':::' import not declared from: ‘stringr’
Namespaces in Imports field not imported from:
‘Homo.sapiens’ ‘JASPAR2016’ ‘Mus.musculus’ ‘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 ... [17s/17s] 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 ... NOTE
Rd file 'RNAseqTFValidation.Rd':
\examples lines wider than 100 characters:
gseaList = RNAseqTFValidation(TFMatchResult$RegulatoryNetworks, RNACoGAPS, c(1,3), c(2,7), matrix = FALSE)
Rd file 'applyGREAT.Rd':
\examples lines wider than 100 characters:
GOenrichment <- applyGREAT(cogapsResult = schepCogapsResult, granges = schepGranges, genome = "hg19")
Rd file 'foldAccessibility.Rd':
\examples lines wider than 100 characters:
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
foldAccessibility(peaksAccessibility = accessiblePeaks$TAL1, cellTypeList = schepCellTypes, cellType = "K562 Erythroleukemia", binaryMa ... [TRUNCATED]
Rd file 'geneAccessibility.Rd':
\examples lines wider than 100 characters:
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
Rd file 'genePatternMatch.Rd':
\examples lines wider than 100 characters:
genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)
Rd file 'heatmapGeneAccessibility.Rd':
\examples lines wider than 100 characters:
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
Rd file 'motifSummarization.Rd':
\examples lines wider than 100 characters:
motifSummTest = motifSummarization(motifList = motifs, scATACData = scatac, granges = peakGranges, genome = "hg19", cellNames = cells, ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘exampleMotifList’ ‘schepCellTypes’ ‘schepCogapsResult’
‘schepGranges’ ‘schepPeaks’ ‘subsetSchepData’ ‘tfData’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' import not declared from: ‘dplyr’
'library' or 'require' call not declared from: ‘dplyr’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
schepCogapsResult.rda 1.5Mb 743Kb xz
schepGranges.rda 20Kb 14Kb xz
schepPeaks.rda 45Kb 26Kb xz
subsetSchepData.rda 902Kb 450Kb bzip2
tfData.rda 466Kb 197Kb xz
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [102s/226s] ERROR
Running examples in ‘ATACCoGAPS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genePatternMatch
> ### Title: Match genes to pattern differentiating peaks
> ### Aliases: genePatternMatch
>
> ### ** Examples
>
> data("schepCogapsResult")
> data(schepGranges)
>
> genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)
[1] Number of peaks used for each pattern:
Pattern 1 Pattern 2 Pattern 3 Pattern 4 Pattern 5 Pattern 6 Pattern 7 Pattern 8
80 640 906 2055 35 501 28 776
Pattern 9
15
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'genes': object 'Homo.sapiens' not found
Calls: genePatternMatch -> suppressMessages -> withCallingHandlers
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
‘dplyr’ ‘viridis’
'library' or 'require' call not declared from: ‘dplyr’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2557/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/ATACCoGAPS.Rcheck/00check.log’
for details.
===============================
BiocCheck('ATACCoGAPS_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpElNnhO/file826f36af273e/ATACCoGAPS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpElNnhO/file826f5ecd6849
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/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 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: Avoid T/F variables; If logical, use TRUE/FALSE
* 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...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.12% 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; 108 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 664 lines
(28%) 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...
* 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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
3 ERRORS | 3 WARNINGS | 14 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_0.99.4.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: 0.99.4 |
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 52.44 seconds |
CheckCommand: BiocCheckGitClone('ATACCoGAPS') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings ATACCoGAPS_0.99.4.tar.gz && BiocCheck('ATACCoGAPS_0.99.4.tar.gz', `new-package`=TRUE) |
CheckTime: 5 minutes 34.60 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 4289.54 KiB |
BuildID:: ATACCoGAPS_20220509152646 |
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: 1. |
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_0.99.4.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('ATACCoGAPS')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2557/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/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/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/ATACCoGAPS.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* 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 ‘0.99.4’
* 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 ... WARNING
'::' or ':::' import not declared from: ‘stringr’
Namespaces in Imports field not imported from:
‘Homo.sapiens’ ‘JASPAR2016’ ‘Mus.musculus’ ‘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 ... NOTE
Rd file 'RNAseqTFValidation.Rd':
\examples lines wider than 100 characters:
gseaList = RNAseqTFValidation(TFMatchResult$RegulatoryNetworks, RNACoGAPS, c(1,3), c(2,7), matrix = FALSE)
Rd file 'applyGREAT.Rd':
\examples lines wider than 100 characters:
GOenrichment <- applyGREAT(cogapsResult = schepCogapsResult, granges = schepGranges, genome = "hg19")
Rd file 'foldAccessibility.Rd':
\examples lines wider than 100 characters:
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
foldAccessibility(peaksAccessibility = accessiblePeaks$TAL1, cellTypeList = schepCellTypes, cellType = "K562 Erythroleukemia", binaryMa ... [TRUNCATED]
Rd file 'geneAccessibility.Rd':
\examples lines wider than 100 characters:
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
Rd file 'genePatternMatch.Rd':
\examples lines wider than 100 characters:
genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)
Rd file 'heatmapGeneAccessibility.Rd':
\examples lines wider than 100 characters:
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
Rd file 'motifSummarization.Rd':
\examples lines wider than 100 characters:
motifSummTest = motifSummarization(motifList = motifs, scATACData = scatac, granges = peakGranges, genome = "hg19", cellNames = cells, ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘exampleMotifList’ ‘schepCellTypes’ ‘schepCogapsResult’
‘schepGranges’ ‘schepPeaks’ ‘subsetSchepData’ ‘tfData’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' import not declared from: ‘dplyr’
'library' or 'require' call not declared from: ‘dplyr’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
schepCogapsResult.rda 1.5Mb 743Kb xz
schepGranges.rda 20Kb 14Kb xz
schepPeaks.rda 45Kb 26Kb xz
subsetSchepData.rda 902Kb 450Kb bzip2
tfData.rda 466Kb 197Kb xz
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/204s] ERROR
Running examples in ‘ATACCoGAPS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genePatternMatch
> ### Title: Match genes to pattern differentiating peaks
> ### Aliases: genePatternMatch
>
> ### ** Examples
>
> data("schepCogapsResult")
> data(schepGranges)
>
> genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)
[1] Number of peaks used for each pattern:
Pattern 1 Pattern 2 Pattern 3 Pattern 4 Pattern 5 Pattern 6 Pattern 7 Pattern 8
80 640 906 2055 35 501 28 776
Pattern 9
15
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'genes': object 'Homo.sapiens' not found
Calls: genePatternMatch -> suppressMessages -> withCallingHandlers
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
‘dplyr’ ‘viridis’
'library' or 'require' call not declared from: ‘dplyr’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2557/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/ATACCoGAPS.Rcheck/00check.log’
for details.
===============================
BiocCheck('ATACCoGAPS_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpSHKWkI/file3165079c7c5a6/ATACCoGAPS
─ installDir: /tmp/RtmpSHKWkI/file31650547edca0
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2557/e4d6a0a74dbcfba3acf35d289ad2df09ddb6054a/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 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: Avoid T/F variables; If logical, use TRUE/FALSE
* 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...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.12% 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; 108 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 664 lines
(28%) 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...
* 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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
3 ERRORS | 3 WARNINGS | 14 NOTES
See the ATACCoGAPS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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