CRAN Package Check Results for Package geno2proteo

Last updated on 2021-04-15 06:47:44 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.3 12.93 149.45 162.38 OK
r-devel-linux-x86_64-debian-gcc 0.0.3 11.40 113.75 125.15 OK
r-devel-linux-x86_64-fedora-clang 0.0.3 213.96 OK
r-devel-linux-x86_64-fedora-gcc 0.0.3 194.35 OK
r-devel-windows-ix86+x86_64 0.0.3 31.00 205.00 236.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.0.3 ERROR
r-patched-linux-x86_64 0.0.3 12.88 139.31 152.19 OK
r-patched-solaris-x86 0.0.3 270.50 ERROR
r-release-linux-x86_64 0.0.3 13.07 141.36 154.43 OK
r-release-macos-x86_64 0.0.3 OK
r-release-windows-ix86+x86_64 0.0.3 27.00 223.00 250.00 OK
r-oldrel-macos-x86_64 0.0.3 ERROR
r-oldrel-windows-ix86+x86_64 0.0.3 28.00 146.00 174.00 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
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.0.3
Check: tests
Result: ERROR
     Running 'runTests.R'
    Running the tests in 'tests/runTests.R' failed.
    Last 13 lines of output:
     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-gcc10-UCRT

Version: 0.0.3
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in 'geno2proteoIntroduction.Rnw'
     ...
    
    > 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-gcc10-UCRT

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-gcc10-UCRT

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)
    ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
    ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
    Warning in file(file, "rt") :
     cannot open file '/tmp/RtmpBraqrn/working_dir/Rtmp9TaO6G/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_AAseq.txt': No such file or directory
    Error in file(file, "rt") : cannot open the connection
    Calls: generatingCDSaaFile -> read.table -> file
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.0.3
Check: tests
Result: ERROR
     Running ‘runTests.R’ [15s/17s]
    Running the tests in ‘tests/runTests.R’ failed.
    Complete output:
     > BiocGenerics:::testPackage("geno2proteo")
     ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
     ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
     Timing stopped at: 2.78 0.366 3.642
     Error in file(file, "rt") : cannot open the connection
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '/tmp/RtmpBraqrn/working_dir/RtmplLaq4H/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_AAseq.txt': No such file or directory
     ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
     Timing stopped at: 0.183 0.033 0.222
     Error in file(file, "rt") : cannot open the connection
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '/tmp/RtmpBraqrn/working_dir/RtmplLaq4H/inputFile_loci_genomicLoc_DNAseq.txt': No such file or directory
    
    
     RUNIT TEST PROTOCOL -- Mon Apr 12 20:46:19 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 file(file, "rt") : cannot open the connection
     ERROR in test_genomicLocsToWholeDNASequence: Error in file(file, "rt") : cannot open the connection
    
     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-patched-solaris-x86

Version: 0.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘geno2proteoIntroduction.Rnw’ using Sweave
    ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
    ld.so.1: perl: fatal: relocation error: file /usr/local/bin/perl: symbol PL_perl_destruct_level: referenced symbol not found
    Warning in file(file, "rt") :
     cannot open file '/tmp/RtmpBraqrn/working_dir/RtmpMXaqLK/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_AAseq.txt': No such file or directory
    
    Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
     chunk 3 (label = example_generatingCDSaaFile)
    Error in file(file, "rt") : cannot open the connection
    
    --- failed re-building ‘geno2proteoIntroduction.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘geno2proteoIntroduction.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.0.3
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-oldrel-macos-x86_64