CRAN Package Check Results for Package geno2proteo

Last updated on 2021-11-30 20:49:17 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.3 15.01 144.86 159.87 OK
r-devel-linux-x86_64-debian-gcc 0.0.3 12.59 112.39 124.98 OK
r-devel-linux-x86_64-fedora-clang 0.0.3 206.40 OK
r-devel-linux-x86_64-fedora-gcc 0.0.3 194.12 OK
r-devel-windows-x86_64-new-UL 0.0.3 24.00 614.00 638.00 ERROR
r-devel-windows-x86_64-new-TK 0.0.3 ERROR
r-devel-windows-x86_64-old 0.0.3 21.00 156.00 177.00 OK
r-patched-linux-x86_64 0.0.3 13.67 140.95 154.62 OK
r-patched-solaris-x86 0.0.3 276.70 OK
r-release-linux-x86_64 0.0.3 14.02 144.42 158.44 OK
r-release-macos-arm64 0.0.3 OK
r-release-macos-x86_64 0.0.3 OK
r-release-windows-ix86+x86_64 0.0.3 31.00 167.00 198.00 OK
r-oldrel-macos-x86_64 0.0.3 OK
r-oldrel-windows-ix86+x86_64 0.0.3 25.00 213.00 238.00 OK

Check Details

Version: 0.0.3
Check: examples
Result: ERROR
    Running examples in 'geno2proteo-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: generatingCDSaaFile
    > ### Title: Generating a file containing the DNA and AA sequences of all the
    > ### protein coding regions (CDSs) in a genome
    > ### Aliases: generatingCDSaaFile
    >
    > ### ** Examples
    >
    > # the data folder in this package
    > dataFolder = system.file("extdata", package="geno2proteo")
    >
    > geneticCodeFile_line = file.path(dataFolder,
    + "geneticCode_standardTable_lines.txt")
    > gtfFile = file.path(dataFolder,
    + "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
    > DNAfastaFile = file.path(dataFolder,
    + "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
    >
    > outputFolder = tempdir(); # using the current folder as output folder
    > # calling the function.
    > generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line,
    + gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
    Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
    Calls: generatingCDSaaFile -> read.table -> scan
    Execution halted
Flavors: r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK

Version: 0.0.3
Check: tests
Result: ERROR
     Running 'runTests.R' [157s]
    Running the tests in 'tests/runTests.R' failed.
    Complete output:
     > BiocGenerics:::testPackage("geno2proteo")
     Timing stopped at: 37.52 106.8 149.8
     Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
     Timing stopped at: 0.11 0.03 0.42
     Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 13 elements
    
    
     RUNIT TEST PROTOCOL -- Fri Nov 26 04:35:04 2021
     ***********************************************
     Number of test functions: 6
     Number of errors: 2
     Number of failures: 0
    
    
     1 Test Suite :
     geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
     ERROR in test_generatingCDSaaFile: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
     ERROR in test_genomicLocsToWholeDNASequence: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 13 elements
    
     Test files with failing tests
    
     test_functionsInGeno2proteo.R
     test_generatingCDSaaFile
     test_genomicLocsToWholeDNASequence
    
    
     Error in BiocGenerics:::testPackage("geno2proteo") :
     unit tests failed for package geno2proteo
     Execution halted
Flavor: r-devel-windows-x86_64-new-UL

Version: 0.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'geno2proteoIntroduction.Rnw' using Sweave
    
    Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
     chunk 3 (label = example_generatingCDSaaFile)
    Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
    
    --- failed re-building 'geno2proteoIntroduction.Rnw'
    
    SUMMARY: processing the following file failed:
     'geno2proteoIntroduction.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-new-UL

Version: 0.0.3
Check: tests
Result: ERROR
     Running 'runTests.R'
    Running the tests in 'tests/runTests.R' failed.
    Complete output:
     > BiocGenerics:::testPackage("geno2proteo")
     Timing stopped at: 1.51 0.11 3.06
     Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
     Timing stopped at: 0.13 0.02 0.28
     Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 13 elements
    
    
     RUNIT TEST PROTOCOL -- Mon Nov 29 05:39:14 2021
     ***********************************************
     Number of test functions: 6
     Number of errors: 2
     Number of failures: 0
    
    
     1 Test Suite :
     geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
     ERROR in test_generatingCDSaaFile: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
     ERROR in test_genomicLocsToWholeDNASequence: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 13 elements
    
     Test files with failing tests
    
     test_functionsInGeno2proteo.R
     test_generatingCDSaaFile
     test_genomicLocsToWholeDNASequence
    
    
     Error in BiocGenerics:::testPackage("geno2proteo") :
     unit tests failed for package geno2proteo
     Execution halted
Flavor: r-devel-windows-x86_64-new-TK

Version: 0.0.3
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in 'geno2proteoIntroduction.Rnw'
    
    > options(width = 72)
    
    > library(geno2proteo)
    
    > dataFolder = system.file("extdata", package = "geno2proteo")
    
    > geneticCodeFile = file.path(dataFolder, "geneticCode_standardTable_lines.txt")
    
    > gtfFile_chr16 = file.path(dataFolder, "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
    
    > DNAfastaFile_chr16 = file.path(dataFolder, "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
    
    > tmpFolder = tempdir()
    
    > generatingCDSaaFile(geneticCodeFile_line = geneticCodeFile,
    + gtfFile = gtfFile_chr16, DNAfastaFile = DNAfastaFile_chr16,
    + outputFolder = .... [TRUNCATED]
    
     When sourcing 'geno2proteoIntroduction.R':
    Error: line 2 did not have 7 elements
    Execution halted
    
     'geno2proteoIntroduction.Rnw'... failed
Flavor: r-devel-windows-x86_64-new-TK

Version: 0.0.3
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
    --- re-building 'geno2proteoIntroduction.Rnw' using Sweave
    
    Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
     chunk 3 (label = example_generatingCDSaaFile)
    Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
    
    --- failed re-building 'geno2proteoIntroduction.Rnw'
    
    SUMMARY: processing the following file failed:
     'geno2proteoIntroduction.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-new-TK