CRAN Package Check Results for Package ADAPTS

Last updated on 2021-09-21 06:48:08 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.6 6.65 89.55 96.20 OK
r-devel-linux-x86_64-debian-gcc 1.0.6 4.20 67.86 72.06 OK
r-devel-linux-x86_64-fedora-clang 1.0.6 120.50 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.6 110.53 OK
r-devel-windows-x86_64 1.0.6 8.00 97.00 105.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 1.0.6 ERROR
r-patched-linux-x86_64 1.0.6 5.20 90.77 95.97 OK
r-patched-solaris-x86 1.0.6 156.10 NOTE
r-release-linux-x86_64 1.0.6 6.27 91.31 97.58 OK
r-release-macos-arm64 1.0.6 ERROR
r-release-macos-x86_64 1.0.6 ERROR
r-release-windows-ix86+x86_64 1.0.6 13.00 132.00 145.00 NOTE
r-oldrel-macos-x86_64 1.0.6 ERROR
r-oldrel-windows-ix86+x86_64 1.0.6 12.00 89.00 101.00 NOTE

Additional issues

noSuggests

Check Details

Version: 1.0.6
Check: installed package size
Result: NOTE
     installed size is 7.6Mb
     sub-directories of 1Mb or more:
     doc 7.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-patched-solaris-x86, r-release-macos-arm64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.6
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     WARNING: installation-time patches will not be applied, could not get the patches index
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.6
Check: examples
Result: ERROR
    Running examples in 'ADAPTS-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: remakeLM22p
    > ### Title: Make an Augmented Signature Matrix
    > ### Aliases: remakeLM22p
    >
    > ### ** Examples
    >
    > #This toy example treats the LM22 deconvolution matrix as if it were all of the data
    > # For a real example, look at the vignette or comments in exprData, fullLM22, small LM22
    > library(ADAPTS)
    > fullLM22 <- ADAPTS::LM22[1:200, 1:8]
    > #Make a fake signature matrix out of 100 genes and the first 8 cell types
    > smallLM22 <- fullLM22[1:100, 1:8]
    >
    > #Make fake data representing two replicates of purified Mast.cells
    > exprData <- ADAPTS::LM22[1:200, c("Mast.cells.resting","Mast.cells.activated")]
    > colnames(exprData) <- c("Mast.cells", "Mast.cells")
    > newSig <- remakeLM22p(exprData=exprData, fullLM22=fullLM22, smallLM22=smallLM22,
    + plotToPDF=FALSE, oneCore=TRUE)
    [1] "B.cells.naive"
    [1] "B.cells.memory"
    [1] "Plasma.cells"
    [1] "T.cells.C"
    [1] "T.cells.CD4.naive"
    [1] "T.cells.CD4.memory.resting"
    [1] "T.cells.CD4.memory.activated"
    [1] "T.cells.follicular.helper"
    [1] "Mast.cells"
    Warning in gzfile(file, "wb") :
     cannot open compressed file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\ADAPTS\tmp\Rtmp6rjF06/gList.Mast.cells_T.cells.follicular.helper_T.cells.CD4.memory.activated_T.cells.CD4.memory.resting_T.cells.CD4.naive_T.cells.C_Plasma.cells_B.cells.memory_B.cells.naive.RData.RData', probable reason 'No such file or directory'
    Error in gzfile(file, "wb") : cannot open the connection
    Calls: remakeLM22p -> save -> gzfile
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.6
Check: PDF version of manual
Result: WARN
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.6
Check: PDF version of manual without hyperrefs or index
Result: ERROR
    Re-running with no redirection of stdout/stderr.
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘DeconRNASeq’
Flavors: r-release-macos-arm64, r-oldrel-macos-x86_64

Version: 1.0.6
Check: examples
Result: ERROR
    Running examples in ‘ADAPTS-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: estCellPercent.DeconRNASeq
    > ### Title: DeconRNASeq deconvolution
    > ### Aliases: estCellPercent.DeconRNASeq
    >
    > ### ** Examples
    >
    > #This toy example
    > library(ADAPTS)
    > fullLM22 <- ADAPTS::LM22[1:30, 1:4]
    > smallLM22 <- fullLM22[1:25,]
    >
    > cellEst <- estCellPercent.DeconRNASeq(refExpr=smallLM22, geneExpr=fullLM22)
    Loading required namespace: DeconRNASeq
    Failed with error: ‘there is no package called ‘DeconRNASeq’’
    estCellPercent.DeconRNASeq requires DeconRNASeq
    https://www.bioconductor.org/packages/release/bioc/html/DeconRNASeq.html
    Error in estCellPercent.DeconRNASeq(refExpr = smallLM22, geneExpr = fullLM22) :
     DeconRNASeq not installed
    Execution halted
Flavors: r-release-macos-arm64, r-oldrel-macos-x86_64

Version: 1.0.6
Check: package dependencies
Result: ERROR
    Package required but not available: ‘WGCNA’
    
    Package suggested but not available for checking: ‘DeconRNASeq’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-x86_64