Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘ClusterFoldSimilarity/DESCRIPTION’ ... OK
* preparing ‘ClusterFoldSimilarity’:
* 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 ‘ClusterFoldSimilarity_0.99.4.tar.gz’

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 BiocCheckGitClone('ClusterFoldSimilarity')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ClusterFoldSimilarity
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2900/0dba564e6a476c253de74a541a071e5d559dd81f/ClusterFoldSimilarity
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2900/0dba564e6a476c253de74a541a071e5d559dd81f/ClusterFoldSimilarity.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClusterFoldSimilarity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClusterFoldSimilarity’ version ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ClusterFoldSimilarity’ can be installed ... 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
Malformed Description field: should contain one or more complete sentences.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [3s/3s] NOTE
clusterFoldSimilarity: no visible global function definition for ‘is’
clusterFoldSimilarity: no visible global function definition for
  ‘quantile’
pairwiseClusterFoldChange : <anonymous> : <anonymous>: no visible
  global function definition for ‘quantile’
pairwiseClusterFoldChange : <anonymous> : <anonymous>: no visible
  global function definition for ‘pnorm’
pairwiseClusterFoldChange : <anonymous> : <anonymous>: no visible
  global function definition for ‘var’
pairwiseClusterFoldChange : <anonymous> : <anonymous>: no visible
  global function definition for ‘optim’
pairwiseClusterFoldChange : <anonymous>: no visible global function
  definition for ‘median’
similarityHeatmap: no visible binding for global variable ‘clusterL’
similarityHeatmap: no visible binding for global variable ‘clusterR’
similarityHeatmap: no visible binding for global variable
  ‘similarityValue’
Undefined global functions or variables:
  clusterL clusterR is median optim pnorm quantile similarityValue var
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "median", "optim", "pnorm", "quantile", "var")
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 ... NOTE
Rd file 'clusterFoldSimilarity.Rd':
  \examples lines wider than 100 characters:
     if (requireNamespace("Seurat") & requireNamespace("SingleCellExperiment") & requireNamespace("scRNAseq")){
     singlecell.1.seurat <- CreateSeuratObject(counts = counts(mouse.brain.romanov),meta.data = as.data.frame(colData(mouse.brain.romanov)))
     singlecell.2.seurat <- CreateSeuratObject(counts = counts(mouse.brain.zei),meta.data = as.data.frame(colData(mouse.brain.zei)))

Rd file 'plotClustersGraph.Rd':
  \examples lines wider than 100 characters:
     if (!requireNamespace("SingleCellExperiment", quietly=TRUE)){stop("SingleCellExperiment package not available", call.=FALSE)}
     singlecell.1.seurat <- CreateSeuratObject(counts = counts(mouse.brain.romanov),meta.data = as.data.frame(colData(mouse.brain.romanov)))
     singlecell.2.seurat <- CreateSeuratObject(counts = counts(mouse.brain.zei),meta.data = as.data.frame(colData(mouse.brain.zei)))

Rd file 'similarityHeatmap.Rd':
  \examples lines wider than 100 characters:
     if (!requireNamespace("SingleCellExperiment", quietly=TRUE)){stop("SingleCellExperiment package not available", call.=FALSE)}
     singlecell.1.seurat <- CreateSeuratObject(counts = counts(mouse.brain.romanov),meta.data = as.data.frame(colData(mouse.brain.romanov)))
     singlecell.2.seurat <- CreateSeuratObject(counts = counts(mouse.brain.zei),meta.data = as.data.frame(colData(mouse.brain.zei)))

These lines will be truncated in the PDF manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [20s/48s] ERROR
Running examples in ‘ClusterFoldSimilarity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterFoldSimilarity
> ### Title: Calculate cluster similarity between clusters from different
> ###   single cell samples.
> ### Aliases: clusterFoldSimilarity
> 
> ### ** Examples
> 
> if (requireNamespace("Seurat") & requireNamespace("SingleCellExperiment") & requireNamespace("scRNAseq")){
+ library(ClusterFoldSimilarity)
+ # Mouse brain single-cell RNA-seq 1 from Romanov et. al.
+ mouse.brain.romanov <- scRNAseq::RomanovBrainData(ensembl = TRUE)
+ colnames(mouse.brain.romanov) <- colData(mouse.brain.romanov)$cellID
+ rownames(colData(mouse.brain.romanov)) <- colData(mouse.brain.romanov)$cellID
+ singlecell.1.seurat <- CreateSeuratObject(counts = counts(mouse.brain.romanov),meta.data = as.data.frame(colData(mouse.brain.romanov)))
+ 
+ # Mouse brain single-cell RNA-seq 2 from Zeisel et. al.
+ mouse.brain.zei <- scRNAseq::ZeiselBrainData(ensembl = TRUE)
+ singlecell.2.seurat <- CreateSeuratObject(counts = counts(mouse.brain.zei),meta.data = as.data.frame(colData(mouse.brain.zei)))
+ 
+ # Create a list with the unprocessed single-cell datasets
+ singlecell.object.list <- list(singlecell.1.seurat,singlecell.2.seurat)
+ # Apply the same processing to each dataset and return a list of single-cell analysis
+ singlecell.object.list <- lapply(X = singlecell.object.list, FUN = function(x){
+   x <- NormalizeData(x)
+   x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 1000)
+   x <- ScaleData(x,features = VariableFeatures(x))
+   x <- RunPCA(x, features = VariableFeatures(object = x))
+   x <- FindNeighbors(x, dims = seq(10))
+   x <- FindClusters(x, resolution = 0.1)
+ })
+ # Calculate the similarity between the two datasets:
+ similarity.table <- clusterFoldSimilarity(sceList=singlecell.object.list, topN=1)
+ head(similarity.table)
+ }
Loading required namespace: Seurat
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
Loading required namespace: SingleCellExperiment
Loading required namespace: scRNAseq
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
downloading 1 resources
retrieving 1 resource
loading from cache
require("ensembldb")
Warning: Unable to map 2692 of 24341 requested IDs.
Error in CreateSeuratObject(counts = counts(mouse.brain.romanov), meta.data = as.data.frame(colData(mouse.brain.romanov))) : 
  could not find function "CreateSeuratObject"
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 ... [4s/4s] OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2900/0dba564e6a476c253de74a541a071e5d559dd81f/ClusterFoldSimilarity.Rcheck/00check.log’
for details.





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 BiocCheck('ClusterFoldSimilarity_0.99.4.tar.gz')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ClusterFoldSimilarity
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpTPxbPC/file86631747068a/ClusterFoldSimilarity
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpTPxbPC/file86631bc44232
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2900/0dba564e6a476c253de74a541a071e5d559dd81f/ClusterFoldSimilarity.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      RNASeq
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import graphics, stats, utils in DESCRIPTION as well as
      NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClusterFoldSimilarity...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in vignettes/ClusterFoldSimilarity.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 249 lines (24%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 227 lines
      (22%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 12 NOTES

See the ClusterFoldSimilarity.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ClusterFoldSimilarity_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package ‘ClusterFoldSimilarity’ ...
** using staged installation
** R
** 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 (ClusterFoldSimilarity)