Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘StatescopeR/DESCRIPTION’ ... OK
* preparing ‘StatescopeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘StatescopeR_0.99.23.tar.gz’

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 BiocCheckGitClone('StatescopeR')

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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR
→ BiocVersion: 3.22
→ Package: StatescopeR
→ PackageVersion: 0.99.23
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘StatescopeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘StatescopeR’ version ‘0.99.23’
* 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 ‘StatescopeR’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [31s/31s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/24s] ERROR
Running examples in ‘StatescopeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BLADE_deconvolution
> ### Title: Run BLADE deconvolution
> ### Aliases: BLADE_deconvolution
> 
> ### ** Examples
> 
> if (requireNamespace("scRNAseq", quietly = TRUE)) {
+     library(scRNAseq)
+     library(scuttle)
+     ## Load SegerstolpePancreas data set
+     scRNAseq <- SegerstolpePancreasData()
+ 
+     ## remove duplicate genes
+     scRNAseq <- scRNAseq[!duplicated(rownames(scRNAseq)), ]
+     ## Subset to 3 healthy and 3 type 2 diabetes samples
+     scRNAseq = scRNAseq[,scRNAseq$individual %in% c('H2', 'H3', 'H4',
+                                                'T2D1', 'T2D2', 'T2D3')]
+     ## remove cells with no cell type label
+     scRNAseq <- scRNAseq[, !is.na(scRNAseq$`cell type`)]
+ 
+     ## remove very rare cell types (<120 cells in total data set)
+     celltypes_to_remove <- names(table(scRNAseq$`cell type`)
+         [(table(scRNAseq$`cell type`) < 150)])
+     scRNAseq <- scRNAseq[, !scRNAseq$`cell type` %in% celltypes_to_remove]
+ 
+     ## Create pseudobulk and normalize to cp10k
+     pseudobulk <- aggregateAcrossCells(scRNAseq, ids = scRNAseq$individual)
+     normcounts(pseudobulk) <- calculateCPM(pseudobulk)/100
+     pseudobulk = as(pseudobulk, "SummarizedExperiment")
+     rownames(pseudobulk) = rownames(scRNAseq)
+ 
+     ## Load signature
+     load(system.file("extdata", "example_signature.RData",
+         package = "StatescopeR"))
+ 
+     ## Load selected_genes
+     load(system.file("extdata", "example_selected_genes.RData",
+         package = "StatescopeR"))
+ 
+     ##  Load prior
+     load(system.file("extdata", "example_prior.RData",
+         package = "StatescopeR"))
+ 
+     ## Perform Deconvolution with BLADE
+     Statescope <- BLADE_deconvolution(
+         signature, pseudobulk, selected_genes,
+         prior, 1L,
+         Nrep = 1L)
+ 
+     ## show estimated fractions
+     S4Vectors::metadata(Statescope)$fractions
+     }
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Error in as.matrix(prior)[colnames(bulk), colnames(signature$mu)] : 
  subscript out of bounds
Calls: BLADE_deconvolution
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [96s/96s]
 [97s/96s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR.Rcheck/00check.log’
for details.





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 BiocCheck('StatescopeR_0.99.23.tar.gz')

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── Installing StatescopeR ──────────────────────────────────────────────────────
✔ Package installed successfully
── StatescopeR session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzvZSr0/file131a512fb9d4e/StatescopeR
→ BiocVersion: 3.22
→ Package: StatescopeR
→ PackageVersion: 0.99.23
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3838/c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f/StatescopeR.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmpzvZSr0/file131a512fb9d4e/StatescopeR
→ installDir: /tmp/RtmpzvZSr0/file131a517eac5409
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on StatescopeR ────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (50%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* 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 StatescopeR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i See the StatescopeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.