Last updated on 2025-02-24 19:50:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.6 | 12.38 | 128.08 | 140.46 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.0.6 | 9.30 | 93.93 | 103.23 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.0.6 | 220.07 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.6 | 227.82 | ERROR | |||
| r-devel-macos-arm64 | 0.0.6 | 68.00 | OK | |||
| r-devel-macos-x86_64 | 0.0.6 | 122.00 | OK | |||
| r-devel-windows-x86_64 | 0.0.6 | 14.00 | 175.00 | 189.00 | OK | |
| r-patched-linux-x86_64 | 0.0.6 | 11.97 | 118.69 | 130.66 | OK | |
| r-release-linux-x86_64 | 0.0.6 | 12.68 | 119.88 | 132.56 | OK | |
| r-release-macos-arm64 | 0.0.6 | 66.00 | OK | |||
| r-release-macos-x86_64 | 0.0.6 | 102.00 | OK | |||
| r-release-windows-x86_64 | 0.0.6 | 14.00 | 163.00 | 177.00 | OK | |
| r-oldrel-macos-arm64 | 0.0.6 | 77.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.0.6 | 114.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.0.6 | 16.00 | 179.00 | 195.00 | OK |
Version: 0.0.6
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 regexpr(as.character(pattern), text, ignore.case, perl, fixed, :
NA in coercion to Rboolean
Calls: generatingCDSaaFile ... popTemporaryFile -> popTemporaryFile.default -> regexpr
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’ [11s/12s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> BiocGenerics:::testPackage("geno2proteo")
Timing stopped at: 2.408 0.137 2.838
Error in regexpr(as.character(pattern), text, ignore.case, perl, fixed, :
NA in coercion to Rboolean
Timing stopped at: 0.068 0.001 0.07
Error in getWritablePathname.Arguments(static, ...) :
File already exists: /tmp/RtmpgOW3Gv/working_dir/RtmpUjabuL/Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.tmp
RUNIT TEST PROTOCOL -- Mon Feb 24 15:11:03 2025
***********************************************
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 regexpr(as.character(pattern), text, ignore.case, perl, fixed, :
NA in coercion to Rboolean
ERROR in test_genomicLocsToWholeDNASequence: Error in getWritablePathname.Arguments(static, ...) :
File already exists: /tmp/RtmpgOW3Gv/working_dir/RtmpUjabuL/Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.tmp
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-linux-x86_64-fedora-clang
Version: 0.0.6
Check: re-building of vignette outputs
Result: ERROR
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 regexpr(as.character(pattern), text, ignore.case, perl, fixed, :
NA in coercion to Rboolean
--- failed re-building ‘geno2proteoIntroduction.Rnw’
SUMMARY: processing the following file failed:
‘geno2proteoIntroduction.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.6
Check: tests
Result: ERROR
Running ‘runTests.R’ [11s/30s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
> BiocGenerics:::testPackage("geno2proteo")
Timing stopped at: 2.419 0.117 7.239
Error in regexpr(as.character(pattern), text, ignore.case, perl, fixed, :
NA in coercion to Rboolean
Timing stopped at: 0.078 0.001 0.242
Error in getWritablePathname.Arguments(static, ...) :
File already exists: /tmp/RtmpbXeqXI/working_dir/RtmpX6JW6V/Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.tmp
RUNIT TEST PROTOCOL -- Mon Feb 24 14:10:00 2025
***********************************************
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 regexpr(as.character(pattern), text, ignore.case, perl, fixed, :
NA in coercion to Rboolean
ERROR in test_genomicLocsToWholeDNASequence: Error in getWritablePathname.Arguments(static, ...) :
File already exists: /tmp/RtmpbXeqXI/working_dir/RtmpX6JW6V/Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.tmp
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-linux-x86_64-fedora-gcc