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HenrikBengtsson / aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
https://cran.r-project.org/package=aroma.affymetrix
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affyio::read.celfile.header() requires methods package to be attached? #26

Closed HenrikBengtsson closed 7 years ago

HenrikBengtsson commented 7 years ago

Issue

It looks like affyio::read.celfile.header() produce an error if the methods package is not attached.

Example

> detach("package:methods")
> source("testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractAffyBatch.R", echo = TRUE)

> library("aroma.affymetrix");
[...]
aroma.affymetrix v3.0.0-9000 (2016-09-04) successfully loaded. See ?aroma.affymetrix for help.

> verbose <- Arguments$getVerbose(-8, timestamp=TRUE);

> dataSet <- "GSE9890";

> chipType <- "HG-U133_Plus_2";

> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);

> print(csR);
AffymetrixCelSet:
Name: GSE9890
Tags: 
Path: rawData/GSE9890/HG-U133_Plus_2
Platform: Affymetrix
Chip type: HG-U133_Plus_2
Number of arrays: 10
Names: GSM249671, GSM249672, GSM249673, ..., GSM249680 [10]
Time period: 2006-12-12 15:27:01 -- 2007-06-28 10:55:52
Total file size: 129.36MB

> ab <- extractAffyBatch(csR, verbose=verbose);
Loading required namespace: affy
Loading required package: hgu133plus2cdf

20170312 19:55:14|Creating AffyBatch from 10 CEL files...
20170312 19:55:14| Filenames: rawData/GSE9890/HG-U133_Plus_2/GSM249671.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249672.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249673.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249674.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249675.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249676.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249677.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249678.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249679.CEL, rawData/GSE9890/HG-U133_Plus_2/GSM249680.CEL
20170312 19:55:15| Sample names: GSM249671, GSM249672, GSM249673, GSM249674, GSM249675, GSM249676, GSM249677, GSM249678, GSM249679, GSM249680
1 reading rawData/GSE9890/HG-U133_Plus_2/GSM249671.CEL ...Error in read.celfile.header(filenames[i], info = "full") : 
  could not find function "is"
20170312 19:55:15|Creating AffyBatch from 10 CEL files...done
> traceback()
12: read.celfile.header(filenames[i], info = "full")
11: FUN(X[[i]], ...)
10: lapply(X = X, FUN = FUN, ...)
9: sapply(seq_len(length(filenames)), function(i) {
       sdate <- read.celfile.header(filenames[i], info = "full")[["ScanDate"]]
       if (is.null(sdate) || length(sdate) == 0) 
           NA_character_
       else sdate
   })
8: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, 
       description = l$description, notes = notes, compress = compress, 
       rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, 
       verbose = verbose, sd = sd, cdfname = cdfname)
7: ReadAffy(filenames = filenames, sampleNames = sampleNames, ..., 
       verbose = as.logical(verbose))
6: extractAffyBatch.AffymetrixCelSet(csR, verbose = verbose)
5: extractAffyBatch(csR, verbose = verbose) at 81.doRMA,extractAffyBatch.R#9
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractAffyBatch.R", 
       echo = TRUE)

Session info

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     

other attached packages:
 [1] hgu133plus2cdf_2.18.0       aroma.light_3.4.0          
 [3] aroma.affymetrix_3.0.0-9000 affxparser_1.46.0          
 [5] aroma.core_3.0.0-9000       R.devices_2.15.1           
 [7] R.filesets_2.11.0           R.utils_2.5.0              
 [9] R.oo_1.21.0                 R.methodsS3_1.7.1          
[11] R.archive_0.3.0            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9           AnnotationDbi_1.36.2  DNAcopy_1.48.0       
 [4] IRanges_2.8.1         BiocGenerics_0.20.0   zlibbioc_1.20.0      
 [7] aroma.apd_0.6.0       R.cache_0.12.0        globals_0.9.0-9000   
[10] tools_3.3.3           parallel_3.3.3        Biobase_2.34.0       
[13] R.huge_0.9.0          DBI_0.6               affy_1.52.0          
[16] PSCBS_0.62.0          matrixStats_0.51.0    digest_0.6.12        
[19] preprocessCore_1.36.0 affyio_1.44.0         R.rsp_0.40.0         
[22] S4Vectors_0.12.1      base64enc_0.1-4       codetools_0.2-15     
[25] memoise_1.0.0         RSQLite_1.1-2         BiocInstaller_1.24.0 
[28] methods_3.3.3         stats4_3.3.3          future_1.3.0-9000    
[31] listenv_0.6.0         Cairo_1.5-9
HenrikBengtsson commented 7 years ago

Seems to have been an issue when upgrading from R 3.3.2 to R 3.3.3.