Last updated on 2021-11-29 23:50:39 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 | 11.79 | 113.49 | 125.28 | 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 | 12.82 | 141.35 | 154.17 | 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 |
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