Last updated on 2025-04-03 09:56:46 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| DBCVindex | 15 | ||
| geneExpressionFromGEO | 5 | 1 | 9 |
| SaturnCoefficient | 15 |
Current CRAN status: OK: 15
Current CRAN status: ERROR: 5, NOTE: 1, OK: 9
Version: 0.9
Check: examples
Result: ERROR
Running examples in ‘geneExpressionFromGEO-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGeneExpressionFromGEO
> ### Title: Function that reads in the GEO code of a dataset, and returns
> ### the gene expression dataframe.
> ### Aliases: getGeneExpressionFromGEO
>
> ### ** Examples
>
> geneExpressionDF1 <- getGeneExpressionFromGEO("GSE3268", FALSE, FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3268
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 0 file(s)
NA
HTTP 404 Not Found.File stored at:
/tmp/Rtmp6kGPft/NA
Error in downloadFile(url, destfile = destfile, mode = "wb") :
Failed to download /tmp/Rtmp6kGPft/NA!
Calls: getGeneExpressionFromGEO ... <Anonymous> -> getAndParseGSEMatrices -> downloadFile
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘BiocManager’ ‘R.utils’ ‘markdown’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9
Check: examples
Result: ERROR
Running examples in ‘geneExpressionFromGEO-Ex.R’ failed
The error most likely occurred in:
> ### Name: getGeneExpressionFromGEO
> ### Title: Function that reads in the GEO code of a dataset, and returns
> ### the gene expression dataframe.
> ### Aliases: getGeneExpressionFromGEO
>
> ### ** Examples
>
> geneExpressionDF1 <- getGeneExpressionFromGEO("GSE3268", FALSE, FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3268
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 1 file(s)
GSE3268_series_matrix.txt.gz
HTTP 403 Forbidden.File stored at:
/tmp/RtmpqGsEBA/working_dir/RtmpFQBlyk/GSE3268_series_matrix.txt.gz
Error in downloadFile(url, destfile = destfile, mode = "wb") :
Failed to download /tmp/RtmpqGsEBA/working_dir/RtmpFQBlyk/GSE3268_series_matrix.txt.gz!
Calls: getGeneExpressionFromGEO ... <Anonymous> -> getAndParseGSEMatrices -> downloadFile
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.9
Check: examples
Result: ERROR
Running examples in ‘geneExpressionFromGEO-Ex.R’ failed
The error most likely occurred in:
> ### Name: getGeneExpressionFromGEO
> ### Title: Function that reads in the GEO code of a dataset, and returns
> ### the gene expression dataframe.
> ### Aliases: getGeneExpressionFromGEO
>
> ### ** Examples
>
> geneExpressionDF1 <- getGeneExpressionFromGEO("GSE3268", FALSE, FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3268
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error in open.connection(x, "rb") : cannot open the connection
Calls: getGeneExpressionFromGEO ... getAndParseGSEMatrices -> getDirListing -> <Anonymous> -> read_html.default
Execution halted
Flavor: r-devel-macos-arm64
Version: 0.9
Check: examples
Result: ERROR
Running examples in 'geneExpressionFromGEO-Ex.R' failed
The error most likely occurred in:
> ### Name: getGeneExpressionFromGEO
> ### Title: Function that reads in the GEO code of a dataset, and returns
> ### the gene expression dataframe.
> ### Aliases: getGeneExpressionFromGEO
>
> ### ** Examples
>
> geneExpressionDF1 <- getGeneExpressionFromGEO("GSE3268", FALSE, FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3268
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 0 file(s)
NA
HTTP 404 Not Found.File stored at:
D:\temp\2025_04_01_01_50_00_15887\RtmpEVARyT/NA
Error in downloadFile(url, destfile = destfile, mode = "wb") :
Failed to download D:\temp\2025_04_01_01_50_00_15887\RtmpEVARyT/NA!
Calls: getGeneExpressionFromGEO ... <Anonymous> -> getAndParseGSEMatrices -> downloadFile
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.9
Check: package dependencies
Result: ERROR
Package required but not available: ‘GEOquery’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-arm64
Current CRAN status: OK: 15