Hi, thank you. I can reproduce this. Explanation and fix below.
On Fri, Aug 14, 2015 at 5:27 PM, Guillaume Devailly <gdevai...@gmail.com> wrote: > Hi, > > I was trying to run this : > http://www.aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo/ > to create a mighty cdf file for HuGene-2_0-st affymetrix array from this > bioconductor annotation package. > > When running the example code (after installing the appropriate packages) : > > library("aroma.affymetrix") > library("pd.hugene.1.0.st.v1") > pathname <- writeCdf(pd.hugene.1.0.st.v1, tags = > "pd.hugene.1.0.st.v1,HB20110111", overwrite = TRUE) > > I obtained this error: >> pathname <- writeCdf(pd.hugene.1.0.st.v1, >> tags="pd.hugene.1.0.st.v1,HB20110111", overwrite=TRUE) > Loading required namespace: pdInfoBuilder > Generating CDF file from Platform Design (PD) package... > Platform Design (PD) package: pd.hugene.1.0.st.v1 > Output path: annotationData/chipTypes/HuGene-1_0-st-v1 > Filename: HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf > Pathname to generated CDF: > annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf > Chip type: HuGene-1_0-st-v1 > Tags: pd.hugene.1.0.st.v1,HB20110111 > Chip type dimensions: 1050x1050 > Total number of cells (probes): 1102500 > Querying Platform Design database... > Units by: transcript > Names by: fsetid > Available database tables: > [1] "chrom_dict" "core_mps" "featureSet" "level_dict" "pmfeature" > [6] "table_info" "type_dict" > SQL query: > > SELECT DISTINCT > -- fid, > meta_fsetid AS probeset_id, > atom, > x, > y > FROM pmfeature > INNER JOIN core_mps USING(fsetid) > ORDER BY probeset_id, atom > > 'data.frame': 861493 obs. of 4 variables: > $ probeset_id: int 7892501 7892501 7892501 7892501 7892502 7892502 > 7892502 7892502 7892503 7892503 ... > $ atom : int 1 2 3 5 7 10 11 12 13 14 ... > $ x : int 870 28 638 888 108 411 918 958 928 495 ... > $ y : int 110 899 469 863 984 622 657 949 361 447 ... > 'data.frame': 861493 obs. of 4 variables: > $ probeset_id: int 7892501 7892501 7892501 7892501 7892502 7892502 > 7892502 7892502 7892503 7892503 ... > $ atom : int 1 2 3 5 7 10 11 12 13 14 ... > $ x : int 870 28 638 888 108 411 918 958 928 495 ... > $ y : int 110 899 469 863 984 622 657 949 361 447 ... > Number of cells (probes) in PD database: 861493 (78.14%) of 1102500 > Querying Platform Design database...done > Number of units: 33297 > Unit names: 7892501, 7892502, 7892503, ..., 8180418 > Average number of cells per units: 25.87 > List of 3 > $ 7892501:'data.frame': 4 obs. of 4 variables: > ..$ probeset_id: int [1:4] 7892501 7892501 7892501 7892501 > ..$ atom : int [1:4] 1 2 3 5 > ..$ x : int [1:4] 870 28 638 888 > ..$ y : int [1:4] 110 899 469 863 > $ 7892502:'data.frame': 4 obs. of 4 variables: > ..$ probeset_id: int [1:4] 7892502 7892502 7892502 7892502 > ..$ atom : int [1:4] 7 10 11 12 > ..$ x : int [1:4] 108 411 918 958 > ..$ y : int [1:4] 984 622 657 949 > $ 7892503:'data.frame': 4 obs. of 4 variables: > ..$ probeset_id: int [1:4] 7892503 7892503 7892503 7892503 > ..$ atom : int [1:4] 13 14 17 18 > ..$ x : int [1:4] 928 495 316 840 > ..$ y : int [1:4] 361 447 686 698 > Error in affxparser::writeCdf(...) : > unused argument (pathname = > "annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf") > > > I am a simple R user and not an advanced package-maker wizard, so what I > will say next is likely to be absurd, but: > > 1) AffyGenePDInfo.writeCdf.R source code: > setMethodS3("writeCdf", "AffyGenePDInfo", function(this, tags=c("*"), > unitsBy=c("transcript", "exon"), namesBy=c("fsetid", "id"), path=NULL, > overwrite=FALSE, verbose=TRUE, ...) { > [...] > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Writing CDF file > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > pathname <- .writeCdf(ffs, pathname=pathname, overwrite=overwrite, > verbose=less(verbose)); > [...] > } > > setMethodS3("writeCdf", "PDInfoList", function(ffs, pathname, > overwrite=FALSE, ..., verbose=TRUE) { > [...] > pathnameT <- pushTemporaryFile(pathname, verbose=verbose); > > .writeCdf(pathnameT, cdfheader=cdfHeader, cdf=cdfList, > cdfqc=NULL, verbose=verbose, overwrite=overwrite); > [...] > } > I am totaly confused by what is this .writeCdf function. Is it the writeCdf > function from affxparser package? > > 2) affxparser::writeCdf first parameter is fname and not pathname. Hence the > error? > writeCdf(fname, cdfheader, cdf, cdfqc, overwrite=FALSE, verbose=0) You did a pretty good job nailing this one down. The .writeCdf() is a light-weight wrapper for calling affxparser::writeCdf() with the feature of loading and the affxparser package. It's a trick to please R CMD check and CRAN. The problem you're experiencing is because there is a typo in writeCdf() for class AffyGenePDInfo; It should call writeCdf() (without the period) such that writeCdf() for PDInfoList is called which in turn calls .writeCdf() which calls affxparser::writeCdf(). This bug was introduce in January 2015, cf. https://github.com/HenrikBengtsson/aroma.affymetrix/blame/master/R/AffyGenePDInfo.writeCdf.R#L295 I've fixed this in the develop branch, which you can install as: source("http://callr.org/install#HenrikBengtsson/aroma.affymetrix@develop";) This should install aroma.affymetrix 2.13.2-9000 ("-9000" indicates develop version). Thank you Henrik > > 3) aroma is loading affxparser itself, and is masking the writeCdf function: > Loading required package: affxparser > > Attaching package: âaffxparserâ > > The following object is masked from âpackage:aroma.affymetrixâ: > > writeCdf > > and the annotation package: > Attaching package: âoligoâ > > The following object is masked _by_ package:aroma.affymetrix: > > writeCdf > > > Reversing the order of package loading did not solved the issue. > I am having the same issue when generating the cdf for the HuGene-2_0-st > array. > > Thanks, > > Guillaume > >> sessionInfo() > R version 3.2.0 (2015-04-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > Running under: Scientific Linux release 6.5 (Carbon) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] pd.hugene.1.0.st.v1_3.14.1 Biobase_2.28.0 > [3] oligoClasses_1.30.0 RSQLite_1.0.0 > [5] DBI_0.3.1 Biostrings_2.36.3 > [7] XVector_0.8.0 IRanges_2.2.5 > [9] S4Vectors_0.6.2 BiocGenerics_0.14.0 > [11] aroma.light_2.4.0 aroma.affymetrix_2.13.2 > [13] aroma.core_2.13.1 R.devices_2.13.0 > [15] R.filesets_2.8.0 R.utils_2.1.0 > [17] R.oo_1.19.0 oligo_1.32.0 > [19] affxparser_1.40.0 R.methodsS3_1.7.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.18.4 pdInfoBuilder_1.32.1 GenomeInfoDb_1.4.1 > [4] base64enc_0.1-3 iterators_1.0.7 tools_3.2.0 > [7] zlibbioc_1.14.0 digest_0.6.8 aroma.apd_0.6.0 > [10] bit_1.1-12 preprocessCore_1.30.0 R.cache_0.10.0 > [13] ff_2.2-13 foreach_1.4.2 R.rsp_0.20.0 > [16] PSCBS_0.44.0 DNAcopy_1.42.0 codetools_0.2-14 > [19] matrixStats_0.14.2 GenomicRanges_1.20.5 splines_3.2.0 > [22] R.huge_0.9.0 Cairo_1.5-8 affyio_1.36.0 > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
