nebbiolo1 Summary
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Package: NanoStringExperiment |
Version: 0.99.1 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoStringExperiment |
BuildTime: 0 minutes 26.60 seconds |
CheckCommand: BiocCheckGitClone('NanoStringExperiment') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings NanoStringExperiment_0.99.1.tar.gz && BiocCheck('NanoStringExperiment_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 0.21 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2058.73 KiB |
BuildID:: NanoStringExperiment_20220420095724 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: NanoStringExperiment. 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. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘NanoStringExperiment/DESCRIPTION’ ... OK
* preparing ‘NanoStringExperiment’:
* 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 ‘NanoStringExperiment_0.99.1.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('NanoStringExperiment')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be git tracked.
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment.Rcheck’
* using R version 4.2.0 beta (2022-04-12 r82161)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoStringExperiment’ version ‘0.99.1’
* 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 ‘NanoStringExperiment’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s/18s] NOTE
.NanoStringExperiment: no visible global function definition for ‘new’
copyRowNames: no visible global function definition for ‘DataFrame’
as.list,NanoStringExperiment: no visible global function definition for
‘as’
controlSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
endogenousSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
experimentData,NanoStringExperiment: no visible global function
definition for ‘metadata’
housekeepingSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
munge,NanoStringExperiment: no visible global function definition for
‘update’
munge,NanoStringExperiment: no visible global function definition for
‘DataFrame’
munge,NanoStringExperiment: no visible global function definition for
‘as’
negativeControlSubset,NanoStringExperiment: no visible binding for
global variable ‘CodeClass’
nonControlSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
phenoData,NanoStringExperiment: no visible global function definition
for ‘metadata’
phenoData<-,NanoStringExperiment-ANY: no visible global function
definition for ‘metadata’
positiveControlSubset,NanoStringExperiment: no visible binding for
global variable ‘CodeClass’
protocolData,NanoStringExperiment: no visible global function
definition for ‘metadata’
protocolData<-,NanoStringExperiment-ANY: no visible global function
definition for ‘metadata’
signatureSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
varLabels,NanoStringExperiment: no visible global function definition
for ‘metadata’
varLabels<-,NanoStringExperiment: no visible global function definition
for ‘metadata’
with,NanoStringExperiment: no visible global function definition for
‘as’
Undefined global functions or variables:
CodeClass DataFrame as metadata new update
Consider adding
importFrom("methods", "as", "new")
importFrom("stats", "update")
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 ... WARNING
S4 class codoc mismatches from documentation object 'NanoStringExperiment-class':
Slots for class 'NanoStringExperiment'
Code: .__classVersion__ NAMES annotation assayData assays colData
design dimLabels elementMetadata metadata signatures
Inherited: colData assays NAMES elementMetadata metadata
Docs: annotation assayData design dimLabels signatures
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'NanoStringExperiment-class'
‘object’ ‘assayData’ ‘phenoData’ ‘protocolData’ ‘featureData’
‘experimentData’ ‘annotation’ ‘dimLabels’ ‘signatures’ ‘design’ ‘...’
Undocumented arguments in documentation object 'annotation,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'as.list,NanoStringExperiment-method'
‘x’ ‘...’
Undocumented arguments in documentation object 'assayData,NanoStringExperiment-method'
‘object’ ‘elt’ ‘...’ ‘value’
Undocumented arguments in documentation object 'assayDataApply'
‘X’ ‘MARGIN’ ‘FUN’ ‘...’ ‘elt’
Undocumented arguments in documentation object 'classVersion,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'controlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'controlSubset'
‘object’
Undocumented arguments in documentation object 'design'
‘object’ ‘value’
Undocumented arguments in documentation object 'dimLabels,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'endogenousSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'endogenousSubset'
‘object’
Undocumented arguments in documentation object 'esApply,NanoStringExperiment-method'
‘X’ ‘MARGIN’ ‘FUN’ ‘...’
Undocumented arguments in documentation object 'esBy'
‘X’ ‘GROUP’ ‘FUN’ ‘...’ ‘simplify’
Undocumented arguments in documentation object 'experimentData,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'fData,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'featureNames,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'housekeepingSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'housekeepingSubset'
‘object’
Undocumented arguments in documentation object 'munge,NanoStringExperiment-method'
‘data’ ‘mapping’ ‘extradata’ ‘elt’ ‘...’
Undocumented arguments in documentation object 'munge'
‘data’ ‘...’
Undocumented arguments in documentation object 'negativeControlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'negativeControlSubset'
‘object’
Undocumented arguments in documentation object 'nonControlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'nonControlSubset'
‘object’
Undocumented arguments in documentation object 'normalize'
‘object’ ‘...’
Undocumented arguments in documentation object 'positiveControlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'positiveControlSubset'
‘object’
Undocumented arguments in documentation object 'sData'
‘object’ ‘value’
Undocumented arguments in documentation object 'sampleNames,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'setQCFlags'
‘object’ ‘...’
Undocumented arguments in documentation object 'signatureSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'signatureSubset'
‘object’
Undocumented arguments in documentation object 'signatures,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'signatures'
‘object’ ‘value’
Undocumented arguments in documentation object 'summary,NanoStringExperiment-method'
‘object’ ‘MARGIN’ ‘GROUP’ ‘log2scale’ ‘elt’ ‘signatureScores’ ‘...’
Undocumented arguments in documentation object 'with,NanoStringExperiment-method'
‘data’ ‘expr’ ‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
exampleNSEData.RData 2.1Mb 629Kb xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/34s] 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 ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('NanoStringExperiment_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmp7avzHg/file336d5458c3762/NanoStringExperiment
─ installDir: /tmp/Rtmp7avzHg/file336d544c5ab2ea
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* ERROR: Packages providing 1 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is 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 3.6 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:
Coverage
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...
* 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 NanoStringExperiment...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 1
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
normalize.Rd, setQCFlags.Rd
* 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 multiples of 4 spaces for line indents; 91 lines
(2%) 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.
* 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 ──
2 ERRORS | 0 WARNINGS | 7 NOTES
See the NanoStringExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
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Package: NanoStringExperiment |
Version: 0.99.1 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data NanoStringExperiment |
BuildTime: 1 minutes 5.12 seconds |
CheckCommand: BiocCheckGitClone('NanoStringExperiment') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NanoStringExperiment_0.99.1.tar.gz && BiocCheck('NanoStringExperiment_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 55.05 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh NanoStringExperiment_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 54.15 seconds |
PackageFileSize: 2059.41 KiB |
BuildID:: NanoStringExperiment_20220420095724 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: NanoStringExperiment. 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. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘NanoStringExperiment/DESCRIPTION’ ... OK
* preparing ‘NanoStringExperiment’:
* 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 ‘NanoStringExperiment_0.99.1.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('NanoStringExperiment')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be git tracked.
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment.Rcheck’
* using R version 4.2.0 beta (2022-04-12 r82161)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoStringExperiment’ version ‘0.99.1’
* 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 ‘NanoStringExperiment’ can be installed ... [50s/51s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [47s/47s] NOTE
.NanoStringExperiment: no visible global function definition for ‘new’
copyRowNames: no visible global function definition for ‘DataFrame’
as.list,NanoStringExperiment: no visible global function definition for
‘as’
controlSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
endogenousSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
experimentData,NanoStringExperiment: no visible global function
definition for ‘metadata’
housekeepingSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
munge,NanoStringExperiment: no visible global function definition for
‘update’
munge,NanoStringExperiment: no visible global function definition for
‘DataFrame’
munge,NanoStringExperiment: no visible global function definition for
‘as’
negativeControlSubset,NanoStringExperiment: no visible binding for
global variable ‘CodeClass’
nonControlSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
phenoData,NanoStringExperiment: no visible global function definition
for ‘metadata’
phenoData<-,NanoStringExperiment-ANY: no visible global function
definition for ‘metadata’
positiveControlSubset,NanoStringExperiment: no visible binding for
global variable ‘CodeClass’
protocolData,NanoStringExperiment: no visible global function
definition for ‘metadata’
protocolData<-,NanoStringExperiment-ANY: no visible global function
definition for ‘metadata’
signatureSubset,NanoStringExperiment: no visible binding for global
variable ‘CodeClass’
varLabels,NanoStringExperiment: no visible global function definition
for ‘metadata’
varLabels<-,NanoStringExperiment: no visible global function definition
for ‘metadata’
with,NanoStringExperiment: no visible global function definition for
‘as’
Undefined global functions or variables:
CodeClass DataFrame as metadata new update
Consider adding
importFrom("methods", "as", "new")
importFrom("stats", "update")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [1s/1s] 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 ... WARNING
S4 class codoc mismatches from documentation object 'NanoStringExperiment-class':
Slots for class 'NanoStringExperiment'
Code: .__classVersion__ NAMES annotation assayData assays colData
design dimLabels elementMetadata metadata signatures
Inherited: colData assays NAMES elementMetadata metadata
Docs: annotation assayData design dimLabels signatures
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'NanoStringExperiment-class'
‘object’ ‘assayData’ ‘phenoData’ ‘protocolData’ ‘featureData’
‘experimentData’ ‘annotation’ ‘dimLabels’ ‘signatures’ ‘design’ ‘...’
Undocumented arguments in documentation object 'annotation,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'as.list,NanoStringExperiment-method'
‘x’ ‘...’
Undocumented arguments in documentation object 'assayData,NanoStringExperiment-method'
‘object’ ‘elt’ ‘...’ ‘value’
Undocumented arguments in documentation object 'assayDataApply'
‘X’ ‘MARGIN’ ‘FUN’ ‘...’ ‘elt’
Undocumented arguments in documentation object 'classVersion,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'controlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'controlSubset'
‘object’
Undocumented arguments in documentation object 'design'
‘object’ ‘value’
Undocumented arguments in documentation object 'dimLabels,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'endogenousSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'endogenousSubset'
‘object’
Undocumented arguments in documentation object 'esApply,NanoStringExperiment-method'
‘X’ ‘MARGIN’ ‘FUN’ ‘...’
Undocumented arguments in documentation object 'esBy'
‘X’ ‘GROUP’ ‘FUN’ ‘...’ ‘simplify’
Undocumented arguments in documentation object 'experimentData,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'fData,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'featureNames,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'housekeepingSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'housekeepingSubset'
‘object’
Undocumented arguments in documentation object 'munge,NanoStringExperiment-method'
‘data’ ‘mapping’ ‘extradata’ ‘elt’ ‘...’
Undocumented arguments in documentation object 'munge'
‘data’ ‘...’
Undocumented arguments in documentation object 'negativeControlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'negativeControlSubset'
‘object’
Undocumented arguments in documentation object 'nonControlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'nonControlSubset'
‘object’
Undocumented arguments in documentation object 'normalize'
‘object’ ‘...’
Undocumented arguments in documentation object 'positiveControlSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'positiveControlSubset'
‘object’
Undocumented arguments in documentation object 'sData'
‘object’ ‘value’
Undocumented arguments in documentation object 'sampleNames,NanoStringExperiment-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'setQCFlags'
‘object’ ‘...’
Undocumented arguments in documentation object 'signatureSubset,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'signatureSubset'
‘object’
Undocumented arguments in documentation object 'signatures,NanoStringExperiment-method'
‘object’
Undocumented arguments in documentation object 'signatures'
‘object’ ‘value’
Undocumented arguments in documentation object 'summary,NanoStringExperiment-method'
‘object’ ‘MARGIN’ ‘GROUP’ ‘log2scale’ ‘elt’ ‘signatureScores’ ‘...’
Undocumented arguments in documentation object 'with,NanoStringExperiment-method'
‘data’ ‘expr’ ‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
exampleNSEData.RData 2.1Mb 629Kb xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [70s/75s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
esBy 5.543 0.870 6.429
assayData 4.097 1.894 6.426
* 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 ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('NanoStringExperiment_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp2LFK8b/file727b947403f/NanoStringExperiment
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp2LFK8b/file727b68430bc
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2602/ecde1f75a4a89a3ea29549e56561410bae6fd645/NanoStringExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* ERROR: Packages providing 1 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is 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 3.6 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:
Coverage
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...
* 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 NanoStringExperiment...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 1
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
normalize.Rd, setQCFlags.Rd
* 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 multiples of 4 spaces for line indents; 91 lines
(2%) 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...
Unable to connect to mailing list status code 502
* 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 ──
2 ERRORS | 0 WARNINGS | 7 NOTES
See the NanoStringExperiment.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 NanoStringExperiment_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘NanoStringExperiment’ ...
** 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 (NanoStringExperiment)