nebbiolo1 Summary
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Package: NanoStringExperiment |
Version: 0.99.0 |
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 27.02 seconds |
CheckCommand: BiocCheckGitClone('NanoStringExperiment') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings NanoStringExperiment_0.99.0.tar.gz && BiocCheck('NanoStringExperiment_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 41.02 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2059.07 KiB |
BuildID:: NanoStringExperiment_20220418144104 |
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_0.99.0.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('NanoStringExperiment')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2602/NanoStringExperiment_20220418144104/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/NanoStringExperiment_20220418144104/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 ‘0.99.0’
* 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 ... [20s/20s] 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 ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘NanoStringExperiment’ for: ‘classVersion’, ‘design<-’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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: ‘methods’
package 'methods' is used but not declared
* 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’
pData,NanoStringExperiment: no visible global function definition for
‘metadata’
pData<-,NanoStringExperiment-ANY: no visible global function definition
for ‘metadata’
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’
show,NanoStringExperiment: no visible global function definition for
‘classVersion’
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 classVersion 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] WARNING
checkRd: (7) NanoStringExperiment-class.Rd:79: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:81: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:83: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:85: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:87: Tag \code is invalid in a \code block
* 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: \code{annotation} \code{assayData} \code{design}
\code{dimLabels} \code{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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘testAnnotation.rds’ ‘testAssayData.rds’ ‘testDimLabels.rds’
‘testExp.rds’ ‘testExperimentData.rds’ ‘testFeatureData.rds’
‘testPhenoData.rds’ ‘testProtocolData.rds’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] ERROR
Running examples in ‘NanoStringExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sData
> ### Title: Access sample metadata
> ### Aliases: sData sData,NanoStringExperiment-method svarLabels
> ### svarLabels,NanoStringExperiment-method
> ### phenoData,NanoStringExperiment-method
> ### phenoData<-,NanoStringExperiment,ANY-method
> ### phenoData<-,DataFrame,ANY-method
> ### protocolData,NanoStringExperiment-method
> ### protocolData<-,NanoStringExperiment,ANY-method
> ### protocolData<-,DataFrame,ANY-method pData,NanoStringExperiment-method
> ### pData,DataFrame-method pData<-,NanoStringExperiment,ANY-method
> ### pData<-,DataFrame,ANY-method varLabels,NanoStringExperiment-method
> ### varLabels,DataFrame-method varLabels<-,NanoStringExperiment-method
>
> ### ** Examples
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> sData(testExp)
DataFrame with 88 rows and 26 columns
slide name scan name
<character> <character>
DSP-1001250002642-A02.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A03.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A04.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A05.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A06.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
... ... ...
DSP-1001250002642-H01.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H02.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H03.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H04.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H05.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
roi segment area FileVersion
<numeric> <character> <numeric> <character>
DSP-1001250002642-A02.dcc 1 Geometric Segment 31318.7 0.1
DSP-1001250002642-A03.dcc 2 Geometric Segment 31318.7 0.1
DSP-1001250002642-A04.dcc 3 Geometric Segment 31318.7 0.1
DSP-1001250002642-A05.dcc 4 Geometric Segment 31318.7 0.1
DSP-1001250002642-A06.dcc 5 Geometric Segment 31318.7 0.1
... ... ... ... ...
DSP-1001250002642-H01.dcc 18 Geometric Segment 31318.7 0.1
DSP-1001250002642-H02.dcc 19 Geometric Segment 31318.7 0.1
DSP-1001250002642-H03.dcc 20 Geometric Segment 31318.7 0.1
DSP-1001250002642-H04.dcc 21 Geometric Segment 31318.7 0.1
DSP-1001250002642-H05.dcc 22 Geometric Segment 31318.7 0.1
SoftwareVersion Date SampleID
<character> <Date> <character>
DSP-1001250002642-A02.dcc 1.0.0 2020-07-14 DSP-1001250002642-A02
DSP-1001250002642-A03.dcc 1.0.0 2020-07-14 DSP-1001250002642-A03
DSP-1001250002642-A04.dcc 1.0.0 2020-07-14 DSP-1001250002642-A04
DSP-1001250002642-A05.dcc 1.0.0 2020-07-14 DSP-1001250002642-A05
DSP-1001250002642-A06.dcc 1.0.0 2020-07-14 DSP-1001250002642-A06
... ... ... ...
DSP-1001250002642-H01.dcc 1.0.0 2020-07-14 DSP-1001250002642-H01
DSP-1001250002642-H02.dcc 1.0.0 2020-07-14 DSP-1001250002642-H02
DSP-1001250002642-H03.dcc 1.0.0 2020-07-14 DSP-1001250002642-H03
DSP-1001250002642-H04.dcc 1.0.0 2020-07-14 DSP-1001250002642-H04
DSP-1001250002642-H05.dcc 1.0.0 2020-07-14 DSP-1001250002642-H05
Plate_ID Well SeqSetId
<character> <character> <character>
DSP-1001250002642-A02.dcc 1001250002642 A02 VH00121:3:AAAG2YWM5
DSP-1001250002642-A03.dcc 1001250002642 A03 VH00121:3:AAAG2YWM5
DSP-1001250002642-A04.dcc 1001250002642 A04 VH00121:3:AAAG2YWM5
DSP-1001250002642-A05.dcc 1001250002642 A05 VH00121:3:AAAG2YWM5
DSP-1001250002642-A06.dcc 1001250002642 A06 VH00121:3:AAAG2YWM5
... ... ... ...
DSP-1001250002642-H01.dcc 1001250002642 H01 VH00121:3:AAAG2YWM5
DSP-1001250002642-H02.dcc 1001250002642 H02 VH00121:3:AAAG2YWM5
DSP-1001250002642-H03.dcc 1001250002642 H03 VH00121:3:AAAG2YWM5
DSP-1001250002642-H04.dcc 1001250002642 H04 VH00121:3:AAAG2YWM5
DSP-1001250002642-H05.dcc 1001250002642 H05 VH00121:3:AAAG2YWM5
Raw Trimmed Stitched Aligned umiQ30
<numeric> <numeric> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc 646250 646250 616150 610390 0.9785
DSP-1001250002642-A03.dcc 629241 629241 603243 597280 0.9784
DSP-1001250002642-A04.dcc 831083 831083 798188 791804 0.9785
DSP-1001250002642-A05.dcc 884485 884485 849060 842133 0.9796
DSP-1001250002642-A06.dcc 781936 781936 751930 744669 0.9779
... ... ... ... ... ...
DSP-1001250002642-H01.dcc 629039 629039 602911 597491 0.9781
DSP-1001250002642-H02.dcc 477362 477362 458755 454228 0.9777
DSP-1001250002642-H03.dcc 463000 463000 444246 439841 0.9774
DSP-1001250002642-H04.dcc 724749 724749 695359 688631 0.9787
DSP-1001250002642-H05.dcc 818093 818093 784654 777211 0.9775
rtsQ30 DeduplicatedReads aoi
<numeric> <integer> <character>
DSP-1001250002642-A02.dcc 0.9804 312060 Geometric Segment-ao..
DSP-1001250002642-A03.dcc 0.9811 305528 Geometric Segment-ao..
DSP-1001250002642-A04.dcc 0.9801 394981 Geometric Segment-ao..
DSP-1001250002642-A05.dcc 0.9814 424162 Geometric Segment-ao..
DSP-1001250002642-A06.dcc 0.9803 355121 Geometric Segment-ao..
... ... ... ...
DSP-1001250002642-H01.dcc 0.9807 303429 Geometric Segment-ao..
DSP-1001250002642-H02.dcc 0.9800 226097 Geometric Segment-ao..
DSP-1001250002642-H03.dcc 0.9793 230026 Geometric Segment-ao..
DSP-1001250002642-H04.dcc 0.9814 348555 Geometric Segment-ao..
DSP-1001250002642-H05.dcc 0.9796 381441 Geometric Segment-ao..
cell_line roi_rep pool_rep slide_rep
<character> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc HS578T 1 1 1
DSP-1001250002642-A03.dcc HS578T 2 1 1
DSP-1001250002642-A04.dcc HEL 1 1 1
DSP-1001250002642-A05.dcc HEL 2 1 1
DSP-1001250002642-A06.dcc U118MG 1 1 1
... ... ... ... ...
DSP-1001250002642-H01.dcc MALME3M 2 2 2
DSP-1001250002642-H02.dcc COLO201 1 2 2
DSP-1001250002642-H03.dcc COLO201 2 2 2
DSP-1001250002642-H04.dcc HUT78 1 2 2
DSP-1001250002642-H05.dcc HUT78 2 2 2
NTC_ID NTC
<character> <integer>
DSP-1001250002642-A02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A05.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A06.dcc DSP-1001250002642-A0.. 7
... ... ...
DSP-1001250002642-H01.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H05.dcc DSP-1001250002642-A0.. 7
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> sData(testExp)
DataFrame with 88 rows and 26 columns
slide name scan name
<character> <character>
DSP-1001250002642-A02.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A03.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A04.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A05.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A06.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
... ... ...
DSP-1001250002642-H01.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H02.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H03.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H04.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H05.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
roi segment area FileVersion
<numeric> <character> <numeric> <character>
DSP-1001250002642-A02.dcc 1 Geometric Segment 31318.7 0.1
DSP-1001250002642-A03.dcc 2 Geometric Segment 31318.7 0.1
DSP-1001250002642-A04.dcc 3 Geometric Segment 31318.7 0.1
DSP-1001250002642-A05.dcc 4 Geometric Segment 31318.7 0.1
DSP-1001250002642-A06.dcc 5 Geometric Segment 31318.7 0.1
... ... ... ... ...
DSP-1001250002642-H01.dcc 18 Geometric Segment 31318.7 0.1
DSP-1001250002642-H02.dcc 19 Geometric Segment 31318.7 0.1
DSP-1001250002642-H03.dcc 20 Geometric Segment 31318.7 0.1
DSP-1001250002642-H04.dcc 21 Geometric Segment 31318.7 0.1
DSP-1001250002642-H05.dcc 22 Geometric Segment 31318.7 0.1
SoftwareVersion Date SampleID
<character> <Date> <character>
DSP-1001250002642-A02.dcc 1.0.0 2020-07-14 DSP-1001250002642-A02
DSP-1001250002642-A03.dcc 1.0.0 2020-07-14 DSP-1001250002642-A03
DSP-1001250002642-A04.dcc 1.0.0 2020-07-14 DSP-1001250002642-A04
DSP-1001250002642-A05.dcc 1.0.0 2020-07-14 DSP-1001250002642-A05
DSP-1001250002642-A06.dcc 1.0.0 2020-07-14 DSP-1001250002642-A06
... ... ... ...
DSP-1001250002642-H01.dcc 1.0.0 2020-07-14 DSP-1001250002642-H01
DSP-1001250002642-H02.dcc 1.0.0 2020-07-14 DSP-1001250002642-H02
DSP-1001250002642-H03.dcc 1.0.0 2020-07-14 DSP-1001250002642-H03
DSP-1001250002642-H04.dcc 1.0.0 2020-07-14 DSP-1001250002642-H04
DSP-1001250002642-H05.dcc 1.0.0 2020-07-14 DSP-1001250002642-H05
Plate_ID Well SeqSetId
<character> <character> <character>
DSP-1001250002642-A02.dcc 1001250002642 A02 VH00121:3:AAAG2YWM5
DSP-1001250002642-A03.dcc 1001250002642 A03 VH00121:3:AAAG2YWM5
DSP-1001250002642-A04.dcc 1001250002642 A04 VH00121:3:AAAG2YWM5
DSP-1001250002642-A05.dcc 1001250002642 A05 VH00121:3:AAAG2YWM5
DSP-1001250002642-A06.dcc 1001250002642 A06 VH00121:3:AAAG2YWM5
... ... ... ...
DSP-1001250002642-H01.dcc 1001250002642 H01 VH00121:3:AAAG2YWM5
DSP-1001250002642-H02.dcc 1001250002642 H02 VH00121:3:AAAG2YWM5
DSP-1001250002642-H03.dcc 1001250002642 H03 VH00121:3:AAAG2YWM5
DSP-1001250002642-H04.dcc 1001250002642 H04 VH00121:3:AAAG2YWM5
DSP-1001250002642-H05.dcc 1001250002642 H05 VH00121:3:AAAG2YWM5
Raw Trimmed Stitched Aligned umiQ30
<numeric> <numeric> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc 646250 646250 616150 610390 0.9785
DSP-1001250002642-A03.dcc 629241 629241 603243 597280 0.9784
DSP-1001250002642-A04.dcc 831083 831083 798188 791804 0.9785
DSP-1001250002642-A05.dcc 884485 884485 849060 842133 0.9796
DSP-1001250002642-A06.dcc 781936 781936 751930 744669 0.9779
... ... ... ... ... ...
DSP-1001250002642-H01.dcc 629039 629039 602911 597491 0.9781
DSP-1001250002642-H02.dcc 477362 477362 458755 454228 0.9777
DSP-1001250002642-H03.dcc 463000 463000 444246 439841 0.9774
DSP-1001250002642-H04.dcc 724749 724749 695359 688631 0.9787
DSP-1001250002642-H05.dcc 818093 818093 784654 777211 0.9775
rtsQ30 DeduplicatedReads aoi
<numeric> <integer> <character>
DSP-1001250002642-A02.dcc 0.9804 312060 Geometric Segment-ao..
DSP-1001250002642-A03.dcc 0.9811 305528 Geometric Segment-ao..
DSP-1001250002642-A04.dcc 0.9801 394981 Geometric Segment-ao..
DSP-1001250002642-A05.dcc 0.9814 424162 Geometric Segment-ao..
DSP-1001250002642-A06.dcc 0.9803 355121 Geometric Segment-ao..
... ... ... ...
DSP-1001250002642-H01.dcc 0.9807 303429 Geometric Segment-ao..
DSP-1001250002642-H02.dcc 0.9800 226097 Geometric Segment-ao..
DSP-1001250002642-H03.dcc 0.9793 230026 Geometric Segment-ao..
DSP-1001250002642-H04.dcc 0.9814 348555 Geometric Segment-ao..
DSP-1001250002642-H05.dcc 0.9796 381441 Geometric Segment-ao..
cell_line roi_rep pool_rep slide_rep
<character> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc HS578T 1 1 1
DSP-1001250002642-A03.dcc HS578T 2 1 1
DSP-1001250002642-A04.dcc HEL 1 1 1
DSP-1001250002642-A05.dcc HEL 2 1 1
DSP-1001250002642-A06.dcc U118MG 1 1 1
... ... ... ... ...
DSP-1001250002642-H01.dcc MALME3M 2 2 2
DSP-1001250002642-H02.dcc COLO201 1 2 2
DSP-1001250002642-H03.dcc COLO201 2 2 2
DSP-1001250002642-H04.dcc HUT78 1 2 2
DSP-1001250002642-H05.dcc HUT78 2 2 2
NTC_ID NTC
<character> <integer>
DSP-1001250002642-A02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A05.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A06.dcc DSP-1001250002642-A0.. 7
... ... ...
DSP-1001250002642-H01.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H05.dcc DSP-1001250002642-A0.. 7
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> svarLabels(testExp)
[1] "slide name" "scan name" "roi"
[4] "segment" "area" "FileVersion"
[7] "SoftwareVersion" "Date" "SampleID"
[10] "Plate_ID" "Well" "SeqSetId"
[13] "Raw" "Trimmed" "Stitched"
[16] "Aligned" "umiQ30" "rtsQ30"
[19] "DeduplicatedReads" "aoi" "cell_line"
[22] "roi_rep" "pool_rep" "slide_rep"
[25] "NTC_ID" "NTC"
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> svarLabels(testExp)
[1] "slide name" "scan name" "roi"
[4] "segment" "area" "FileVersion"
[7] "SoftwareVersion" "Date" "SampleID"
[10] "Plate_ID" "Well" "SeqSetId"
[13] "Raw" "Trimmed" "Stitched"
[16] "Aligned" "umiQ30" "rtsQ30"
[19] "DeduplicatedReads" "aoi" "cell_line"
[22] "roi_rep" "pool_rep" "slide_rep"
[25] "NTC_ID" "NTC"
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> phenoData(testExp)
DataFrame with 88 rows and 5 columns
slide name scan name
<character> <character>
DSP-1001250002642-A02.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A03.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A04.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A05.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A06.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
... ... ...
DSP-1001250002642-H01.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H02.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H03.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H04.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H05.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
roi segment area
<numeric> <character> <numeric>
DSP-1001250002642-A02.dcc 1 Geometric Segment 31318.7
DSP-1001250002642-A03.dcc 2 Geometric Segment 31318.7
DSP-1001250002642-A04.dcc 3 Geometric Segment 31318.7
DSP-1001250002642-A05.dcc 4 Geometric Segment 31318.7
DSP-1001250002642-A06.dcc 5 Geometric Segment 31318.7
... ... ... ...
DSP-1001250002642-H01.dcc 18 Geometric Segment 31318.7
DSP-1001250002642-H02.dcc 19 Geometric Segment 31318.7
DSP-1001250002642-H03.dcc 20 Geometric Segment 31318.7
DSP-1001250002642-H04.dcc 21 Geometric Segment 31318.7
DSP-1001250002642-H05.dcc 22 Geometric Segment 31318.7
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> phenoData(testExp) <- phenoData(testExp)[, 1:2]
Warning in recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
Error in ans[npos] <- rep(no, length.out = len)[npos] :
incompatible types (from S4 to logical) in subassignment type fix
Calls: phenoData<- -> phenoData<- -> ifelse
Execution halted
* 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: 1 ERROR, 6 WARNINGs, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2602/NanoStringExperiment_20220418144104/NanoStringExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('NanoStringExperiment_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmpe87lO6/file2b41867cf99bf0/NanoStringExperiment
─ installDir: /tmp/Rtmpe87lO6/file2b418646a7a82b
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2602/NanoStringExperiment_20220418144104/NanoStringExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
Warning: no function found corresponding to methods exports from ‘NanoStringExperiment’ for: ‘classVersion’, ‘design<-’
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 2 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 3.6 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...
Warning: no function found corresponding to methods exports from ‘NanoStringExperiment’ for: ‘classVersion’, ‘design<-’
* 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 ──
1 ERRORS | 0 WARNINGS | 7 NOTES
See the NanoStringExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
Package: NanoStringExperiment |
Version: 0.99.0 |
RVersion:
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data NanoStringExperiment |
BuildTime: 0 minutes 41.87 seconds |
CheckCommand: BiocCheckGitClone('NanoStringExperiment') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NanoStringExperiment_0.99.0.tar.gz && BiocCheck('NanoStringExperiment_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 58.86 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh NanoStringExperiment_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 29.50 seconds |
PackageFileSize: 2059.74 KiB |
BuildID:: NanoStringExperiment_20220418144104 |
PreProcessing: Installing dependencies. Checking Git Clone. Installing package: NanoStringExperiment. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: 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_0.99.0.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('NanoStringExperiment')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2602/NanoStringExperiment_20220418144104/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/NanoStringExperiment_20220418144104/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 ‘0.99.0’
* 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 ... [29s/29s] 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 ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘NanoStringExperiment’ for: ‘classVersion’, ‘design<-’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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: ‘methods’
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s/28s] 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’
pData,NanoStringExperiment: no visible global function definition for
‘metadata’
pData<-,NanoStringExperiment-ANY: no visible global function definition
for ‘metadata’
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’
show,NanoStringExperiment: no visible global function definition for
‘classVersion’
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 classVersion 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] WARNING
checkRd: (7) NanoStringExperiment-class.Rd:79: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:81: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:83: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:85: Tag \code is invalid in a \code block
checkRd: (7) NanoStringExperiment-class.Rd:87: Tag \code is invalid in a \code block
* 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: \code{annotation} \code{assayData} \code{design}
\code{dimLabels} \code{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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘testAnnotation.rds’ ‘testAssayData.rds’ ‘testDimLabels.rds’
‘testExp.rds’ ‘testExperimentData.rds’ ‘testFeatureData.rds’
‘testPhenoData.rds’ ‘testProtocolData.rds’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] ERROR
Running examples in ‘NanoStringExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sData
> ### Title: Access sample metadata
> ### Aliases: sData sData,NanoStringExperiment-method svarLabels
> ### svarLabels,NanoStringExperiment-method
> ### phenoData,NanoStringExperiment-method
> ### phenoData<-,NanoStringExperiment,ANY-method
> ### phenoData<-,DataFrame,ANY-method
> ### protocolData,NanoStringExperiment-method
> ### protocolData<-,NanoStringExperiment,ANY-method
> ### protocolData<-,DataFrame,ANY-method pData,NanoStringExperiment-method
> ### pData,DataFrame-method pData<-,NanoStringExperiment,ANY-method
> ### pData<-,DataFrame,ANY-method varLabels,NanoStringExperiment-method
> ### varLabels,DataFrame-method varLabels<-,NanoStringExperiment-method
>
> ### ** Examples
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> sData(testExp)
DataFrame with 88 rows and 26 columns
slide name scan name
<character> <character>
DSP-1001250002642-A02.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A03.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A04.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A05.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A06.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
... ... ...
DSP-1001250002642-H01.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H02.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H03.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H04.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H05.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
roi segment area FileVersion
<numeric> <character> <numeric> <character>
DSP-1001250002642-A02.dcc 1 Geometric Segment 31318.7 0.1
DSP-1001250002642-A03.dcc 2 Geometric Segment 31318.7 0.1
DSP-1001250002642-A04.dcc 3 Geometric Segment 31318.7 0.1
DSP-1001250002642-A05.dcc 4 Geometric Segment 31318.7 0.1
DSP-1001250002642-A06.dcc 5 Geometric Segment 31318.7 0.1
... ... ... ... ...
DSP-1001250002642-H01.dcc 18 Geometric Segment 31318.7 0.1
DSP-1001250002642-H02.dcc 19 Geometric Segment 31318.7 0.1
DSP-1001250002642-H03.dcc 20 Geometric Segment 31318.7 0.1
DSP-1001250002642-H04.dcc 21 Geometric Segment 31318.7 0.1
DSP-1001250002642-H05.dcc 22 Geometric Segment 31318.7 0.1
SoftwareVersion Date SampleID
<character> <Date> <character>
DSP-1001250002642-A02.dcc 1.0.0 2020-07-14 DSP-1001250002642-A02
DSP-1001250002642-A03.dcc 1.0.0 2020-07-14 DSP-1001250002642-A03
DSP-1001250002642-A04.dcc 1.0.0 2020-07-14 DSP-1001250002642-A04
DSP-1001250002642-A05.dcc 1.0.0 2020-07-14 DSP-1001250002642-A05
DSP-1001250002642-A06.dcc 1.0.0 2020-07-14 DSP-1001250002642-A06
... ... ... ...
DSP-1001250002642-H01.dcc 1.0.0 2020-07-14 DSP-1001250002642-H01
DSP-1001250002642-H02.dcc 1.0.0 2020-07-14 DSP-1001250002642-H02
DSP-1001250002642-H03.dcc 1.0.0 2020-07-14 DSP-1001250002642-H03
DSP-1001250002642-H04.dcc 1.0.0 2020-07-14 DSP-1001250002642-H04
DSP-1001250002642-H05.dcc 1.0.0 2020-07-14 DSP-1001250002642-H05
Plate_ID Well SeqSetId
<character> <character> <character>
DSP-1001250002642-A02.dcc 1001250002642 A02 VH00121:3:AAAG2YWM5
DSP-1001250002642-A03.dcc 1001250002642 A03 VH00121:3:AAAG2YWM5
DSP-1001250002642-A04.dcc 1001250002642 A04 VH00121:3:AAAG2YWM5
DSP-1001250002642-A05.dcc 1001250002642 A05 VH00121:3:AAAG2YWM5
DSP-1001250002642-A06.dcc 1001250002642 A06 VH00121:3:AAAG2YWM5
... ... ... ...
DSP-1001250002642-H01.dcc 1001250002642 H01 VH00121:3:AAAG2YWM5
DSP-1001250002642-H02.dcc 1001250002642 H02 VH00121:3:AAAG2YWM5
DSP-1001250002642-H03.dcc 1001250002642 H03 VH00121:3:AAAG2YWM5
DSP-1001250002642-H04.dcc 1001250002642 H04 VH00121:3:AAAG2YWM5
DSP-1001250002642-H05.dcc 1001250002642 H05 VH00121:3:AAAG2YWM5
Raw Trimmed Stitched Aligned umiQ30
<numeric> <numeric> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc 646250 646250 616150 610390 0.9785
DSP-1001250002642-A03.dcc 629241 629241 603243 597280 0.9784
DSP-1001250002642-A04.dcc 831083 831083 798188 791804 0.9785
DSP-1001250002642-A05.dcc 884485 884485 849060 842133 0.9796
DSP-1001250002642-A06.dcc 781936 781936 751930 744669 0.9779
... ... ... ... ... ...
DSP-1001250002642-H01.dcc 629039 629039 602911 597491 0.9781
DSP-1001250002642-H02.dcc 477362 477362 458755 454228 0.9777
DSP-1001250002642-H03.dcc 463000 463000 444246 439841 0.9774
DSP-1001250002642-H04.dcc 724749 724749 695359 688631 0.9787
DSP-1001250002642-H05.dcc 818093 818093 784654 777211 0.9775
rtsQ30 DeduplicatedReads aoi
<numeric> <integer> <character>
DSP-1001250002642-A02.dcc 0.9804 312060 Geometric Segment-ao..
DSP-1001250002642-A03.dcc 0.9811 305528 Geometric Segment-ao..
DSP-1001250002642-A04.dcc 0.9801 394981 Geometric Segment-ao..
DSP-1001250002642-A05.dcc 0.9814 424162 Geometric Segment-ao..
DSP-1001250002642-A06.dcc 0.9803 355121 Geometric Segment-ao..
... ... ... ...
DSP-1001250002642-H01.dcc 0.9807 303429 Geometric Segment-ao..
DSP-1001250002642-H02.dcc 0.9800 226097 Geometric Segment-ao..
DSP-1001250002642-H03.dcc 0.9793 230026 Geometric Segment-ao..
DSP-1001250002642-H04.dcc 0.9814 348555 Geometric Segment-ao..
DSP-1001250002642-H05.dcc 0.9796 381441 Geometric Segment-ao..
cell_line roi_rep pool_rep slide_rep
<character> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc HS578T 1 1 1
DSP-1001250002642-A03.dcc HS578T 2 1 1
DSP-1001250002642-A04.dcc HEL 1 1 1
DSP-1001250002642-A05.dcc HEL 2 1 1
DSP-1001250002642-A06.dcc U118MG 1 1 1
... ... ... ... ...
DSP-1001250002642-H01.dcc MALME3M 2 2 2
DSP-1001250002642-H02.dcc COLO201 1 2 2
DSP-1001250002642-H03.dcc COLO201 2 2 2
DSP-1001250002642-H04.dcc HUT78 1 2 2
DSP-1001250002642-H05.dcc HUT78 2 2 2
NTC_ID NTC
<character> <integer>
DSP-1001250002642-A02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A05.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A06.dcc DSP-1001250002642-A0.. 7
... ... ...
DSP-1001250002642-H01.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H05.dcc DSP-1001250002642-A0.. 7
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> sData(testExp)
DataFrame with 88 rows and 26 columns
slide name scan name
<character> <character>
DSP-1001250002642-A02.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A03.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A04.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A05.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A06.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
... ... ...
DSP-1001250002642-H01.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H02.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H03.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H04.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H05.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
roi segment area FileVersion
<numeric> <character> <numeric> <character>
DSP-1001250002642-A02.dcc 1 Geometric Segment 31318.7 0.1
DSP-1001250002642-A03.dcc 2 Geometric Segment 31318.7 0.1
DSP-1001250002642-A04.dcc 3 Geometric Segment 31318.7 0.1
DSP-1001250002642-A05.dcc 4 Geometric Segment 31318.7 0.1
DSP-1001250002642-A06.dcc 5 Geometric Segment 31318.7 0.1
... ... ... ... ...
DSP-1001250002642-H01.dcc 18 Geometric Segment 31318.7 0.1
DSP-1001250002642-H02.dcc 19 Geometric Segment 31318.7 0.1
DSP-1001250002642-H03.dcc 20 Geometric Segment 31318.7 0.1
DSP-1001250002642-H04.dcc 21 Geometric Segment 31318.7 0.1
DSP-1001250002642-H05.dcc 22 Geometric Segment 31318.7 0.1
SoftwareVersion Date SampleID
<character> <Date> <character>
DSP-1001250002642-A02.dcc 1.0.0 2020-07-14 DSP-1001250002642-A02
DSP-1001250002642-A03.dcc 1.0.0 2020-07-14 DSP-1001250002642-A03
DSP-1001250002642-A04.dcc 1.0.0 2020-07-14 DSP-1001250002642-A04
DSP-1001250002642-A05.dcc 1.0.0 2020-07-14 DSP-1001250002642-A05
DSP-1001250002642-A06.dcc 1.0.0 2020-07-14 DSP-1001250002642-A06
... ... ... ...
DSP-1001250002642-H01.dcc 1.0.0 2020-07-14 DSP-1001250002642-H01
DSP-1001250002642-H02.dcc 1.0.0 2020-07-14 DSP-1001250002642-H02
DSP-1001250002642-H03.dcc 1.0.0 2020-07-14 DSP-1001250002642-H03
DSP-1001250002642-H04.dcc 1.0.0 2020-07-14 DSP-1001250002642-H04
DSP-1001250002642-H05.dcc 1.0.0 2020-07-14 DSP-1001250002642-H05
Plate_ID Well SeqSetId
<character> <character> <character>
DSP-1001250002642-A02.dcc 1001250002642 A02 VH00121:3:AAAG2YWM5
DSP-1001250002642-A03.dcc 1001250002642 A03 VH00121:3:AAAG2YWM5
DSP-1001250002642-A04.dcc 1001250002642 A04 VH00121:3:AAAG2YWM5
DSP-1001250002642-A05.dcc 1001250002642 A05 VH00121:3:AAAG2YWM5
DSP-1001250002642-A06.dcc 1001250002642 A06 VH00121:3:AAAG2YWM5
... ... ... ...
DSP-1001250002642-H01.dcc 1001250002642 H01 VH00121:3:AAAG2YWM5
DSP-1001250002642-H02.dcc 1001250002642 H02 VH00121:3:AAAG2YWM5
DSP-1001250002642-H03.dcc 1001250002642 H03 VH00121:3:AAAG2YWM5
DSP-1001250002642-H04.dcc 1001250002642 H04 VH00121:3:AAAG2YWM5
DSP-1001250002642-H05.dcc 1001250002642 H05 VH00121:3:AAAG2YWM5
Raw Trimmed Stitched Aligned umiQ30
<numeric> <numeric> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc 646250 646250 616150 610390 0.9785
DSP-1001250002642-A03.dcc 629241 629241 603243 597280 0.9784
DSP-1001250002642-A04.dcc 831083 831083 798188 791804 0.9785
DSP-1001250002642-A05.dcc 884485 884485 849060 842133 0.9796
DSP-1001250002642-A06.dcc 781936 781936 751930 744669 0.9779
... ... ... ... ... ...
DSP-1001250002642-H01.dcc 629039 629039 602911 597491 0.9781
DSP-1001250002642-H02.dcc 477362 477362 458755 454228 0.9777
DSP-1001250002642-H03.dcc 463000 463000 444246 439841 0.9774
DSP-1001250002642-H04.dcc 724749 724749 695359 688631 0.9787
DSP-1001250002642-H05.dcc 818093 818093 784654 777211 0.9775
rtsQ30 DeduplicatedReads aoi
<numeric> <integer> <character>
DSP-1001250002642-A02.dcc 0.9804 312060 Geometric Segment-ao..
DSP-1001250002642-A03.dcc 0.9811 305528 Geometric Segment-ao..
DSP-1001250002642-A04.dcc 0.9801 394981 Geometric Segment-ao..
DSP-1001250002642-A05.dcc 0.9814 424162 Geometric Segment-ao..
DSP-1001250002642-A06.dcc 0.9803 355121 Geometric Segment-ao..
... ... ... ...
DSP-1001250002642-H01.dcc 0.9807 303429 Geometric Segment-ao..
DSP-1001250002642-H02.dcc 0.9800 226097 Geometric Segment-ao..
DSP-1001250002642-H03.dcc 0.9793 230026 Geometric Segment-ao..
DSP-1001250002642-H04.dcc 0.9814 348555 Geometric Segment-ao..
DSP-1001250002642-H05.dcc 0.9796 381441 Geometric Segment-ao..
cell_line roi_rep pool_rep slide_rep
<character> <numeric> <numeric> <numeric>
DSP-1001250002642-A02.dcc HS578T 1 1 1
DSP-1001250002642-A03.dcc HS578T 2 1 1
DSP-1001250002642-A04.dcc HEL 1 1 1
DSP-1001250002642-A05.dcc HEL 2 1 1
DSP-1001250002642-A06.dcc U118MG 1 1 1
... ... ... ... ...
DSP-1001250002642-H01.dcc MALME3M 2 2 2
DSP-1001250002642-H02.dcc COLO201 1 2 2
DSP-1001250002642-H03.dcc COLO201 2 2 2
DSP-1001250002642-H04.dcc HUT78 1 2 2
DSP-1001250002642-H05.dcc HUT78 2 2 2
NTC_ID NTC
<character> <integer>
DSP-1001250002642-A02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A05.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-A06.dcc DSP-1001250002642-A0.. 7
... ... ...
DSP-1001250002642-H01.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H02.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H03.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H04.dcc DSP-1001250002642-A0.. 7
DSP-1001250002642-H05.dcc DSP-1001250002642-A0.. 7
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> svarLabels(testExp)
[1] "slide name" "scan name" "roi"
[4] "segment" "area" "FileVersion"
[7] "SoftwareVersion" "Date" "SampleID"
[10] "Plate_ID" "Well" "SeqSetId"
[13] "Raw" "Trimmed" "Stitched"
[16] "Aligned" "umiQ30" "rtsQ30"
[19] "DeduplicatedReads" "aoi" "cell_line"
[22] "roi_rep" "pool_rep" "slide_rep"
[25] "NTC_ID" "NTC"
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> svarLabels(testExp)
[1] "slide name" "scan name" "roi"
[4] "segment" "area" "FileVersion"
[7] "SoftwareVersion" "Date" "SampleID"
[10] "Plate_ID" "Well" "SeqSetId"
[13] "Raw" "Trimmed" "Stitched"
[16] "Aligned" "umiQ30" "rtsQ30"
[19] "DeduplicatedReads" "aoi" "cell_line"
[22] "roi_rep" "pool_rep" "slide_rep"
[25] "NTC_ID" "NTC"
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> phenoData(testExp)
DataFrame with 88 rows and 5 columns
slide name scan name
<character> <character>
DSP-1001250002642-A02.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A03.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A04.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A05.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-A06.dcc 6panel-old-slide1 (P.. cw005 (PTL-10891) Sl..
... ... ...
DSP-1001250002642-H01.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H02.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H03.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H04.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
DSP-1001250002642-H05.dcc 6panel-new-slide4 (P.. cw005 (PTL-10891) Sl..
roi segment area
<numeric> <character> <numeric>
DSP-1001250002642-A02.dcc 1 Geometric Segment 31318.7
DSP-1001250002642-A03.dcc 2 Geometric Segment 31318.7
DSP-1001250002642-A04.dcc 3 Geometric Segment 31318.7
DSP-1001250002642-A05.dcc 4 Geometric Segment 31318.7
DSP-1001250002642-A06.dcc 5 Geometric Segment 31318.7
... ... ... ...
DSP-1001250002642-H01.dcc 18 Geometric Segment 31318.7
DSP-1001250002642-H02.dcc 19 Geometric Segment 31318.7
DSP-1001250002642-H03.dcc 20 Geometric Segment 31318.7
DSP-1001250002642-H04.dcc 21 Geometric Segment 31318.7
DSP-1001250002642-H05.dcc 22 Geometric Segment 31318.7
>
> datadir <- system.file("data", package="NanoStringExperiment")
> testExp <- readRDS(file.path(datadir, "testExp.rds"))
> phenoData(testExp) <- phenoData(testExp)[, 1:2]
Warning in recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
Error in ans[npos] <- rep(no, length.out = len)[npos] :
incompatible types (from S4 to logical) in subassignment type fix
Calls: phenoData<- -> phenoData<- -> ifelse
Execution halted
* 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: 1 ERROR, 6 WARNINGs, 4 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2602/NanoStringExperiment_20220418144104/NanoStringExperiment.Rcheck/00check.log’
for details.
===============================
BiocCheck('NanoStringExperiment_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: NanoStringExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXPkaOT/filef0c731689d6f/NanoStringExperiment
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXPkaOT/filef0c7487120d4
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2602/NanoStringExperiment_20220418144104/NanoStringExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
Warning: no function found corresponding to methods exports from ‘NanoStringExperiment’ for: ‘classVersion’, ‘design<-’
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 2 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 3.6 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...
Warning: no function found corresponding to methods exports from ‘NanoStringExperiment’ for: ‘classVersion’, ‘design<-’
* 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 ──
1 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_0.99.0.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)