Thanks!

Seems working pretty well.

> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2") > cdfM <- 
> getMonocellCdf(cdf, verbose=TRUE) Retrieving monocell CDF... Monocell chip 
> type: HG-U133_Plus_2,monocell Locating monocell CDF...  Pathname:  Locating 
> monocell CDF...done Could not locate monocell CDF. Will create one for chip 
> type... Could not locate monocell CDF. Will create one for chip 
> type...doneRetrieving monocell CDF...done> print(cdfM)AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2,monocell.CDF
File size: 9.63 MB (10098009 bytes)
Chip type: HG-U133_Plus_2,monocell
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 246x245
Number of cells: 60270
Number of units: 54675
Cells per unit: 1.10
Number of QC units: 9



On Saturday, 24 January 2015 03:52:43 UTC+8, Henrik Bengtsson wrote:
>
> Solved.  Before finalize a release, would you mind making sure it 
> works on your end.  Install aroma.affymetrix 2.13.0-9001 by running 
> the following in a fresh R session: 
>
>     source('
> http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001') 
>
> Then retry with 
>
> library("aroma.affymetrix") 
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2") 
> cdfM <- getMonocellCdf(cdf, verbose=TRUE) 
> print(cdfM) 
>
> If it complains about a pre-existing *.tmp file, remove that one an retry. 
>
> As soon as you confirm it works, I'll make aroma.affymetrix 2.13.1 
> available, because this was a critical bug(*). 
>
> Thanks for the report 
>
> /Henrik 
>
> (*) DETAILS: Turns out to be due to a single stray newline. It should have 
> been 
>
>   affxparser::writeCdfUnits(...) 
>
> but it was: 
>
>   affxparser::writeCdfUnits 
>   (...) 
>
> Despite running 24 hours of regular package testing, this piece of 
> code was never tested.  I've now added an explicit test on creating 
> and re-creating monocell CDF. 
>
> On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson <h...@biostat.ucsf.edu 
> <javascript:>> wrote: 
> > I managed to reproduce this now: 
> > 
> > Error in (...) : 3 arguments passed to '(' which requires 1 
> > 20150123 08:48:49| Could not locate monocell CDF. Will create one for 
> chip type. 
> > ..done 
> > 20150123 08:48:49|Retrieving monocell CDF...done 
> >> traceback() 
> > 5: .writeCdfUnits(con = con, srcUnits, verbose = verbose2) 
> > 4: createMonocellCdf.AffymetrixCdfFile(this, ..., verbose = 
> less(verbose)) 
> > 3: createMonocellCdf(this, ..., verbose = less(verbose)) 
> > 2: getMonocellCdf.AffymetrixCdfFile(cdf, verbose = 
> Arguments$getVerbose(-8, 
> >        timestamp = TRUE)) 
> > 1: getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp = 
> TRUE)) 
> > 
> > I'll investigate and fix this asap. 
> > 
> > /Henrik 
> > 
> > 
> > On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson <h...@biostat.ucsf.edu 
> <javascript:>> wrote: 
> >> 
> >> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" <h...@biostat.ucsf.edu 
> <javascript:>> wrote: 
> >>> 
> >>> This is odd for several reasons, e.g. I'm puzzled how you ended up 
> with a 
> >>> monocell CDF previously but now it gives an error.  Let's troubleshoot 
> >>> more... 
> >>> 
> >>> What does troubleshoot() output directly after you get that error? 
> >> 
> >> I meant traceback() 
> >> 
> >>> 
> >>> Henrik 
> >>> 
> >>> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" <zqzne...@gmail.com 
> <javascript:>> wrote: 
> >>> > 
> >>> > Thanks, Henrik, 
> >>> > 
> >>> > It seems that something went wrong with the monocell cdf file by 
> >>> > troubleshooting: 
> >>> > 
> >>> > 
> >>> > > cdf 
> >>> > 
> >>> > AffymetrixCdfFile: 
> >>> > 
> >>> > Path: annotationData/chipTypes/HG-U133_Plus_2 
> >>> > 
> >>> > Filename: HG-U133_Plus_2,monocell.CDF 
> >>> > 
> >>> > File size: 4.88 MB (5116945 bytes) 
> >>> > 
> >>> > Chip type: HG-U133_Plus_2,monocell 
> >>> > 
> >>> > RAM: 0.46MB 
> >>> > 
> >>> > File format: v4 (binary; XDA) 
> >>> > 
> >>> > Dimension: 182x182 
> >>> > 
> >>> > Number of cells: 33124 
> >>> > 
> >>> > Number of units: 27604 
> >>> > 
> >>> > Cells per unit: 1.20 
> >>> > 
> >>> > Number of QC units: 9 
> >>> > 
> >>> > 
> >>> > 
> >>> > So I have deleted the previous monocell cdf file in 
> >>> > annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the 
> following: 
> >>> > 
> >>> > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2") 
> >>> > 
> >>> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, 
> timestamp 
> >>> > = TRUE)) 
> >>> > 
> >>> > 
> >>> > 
> >>> > However, the above process also failed, here is the output: 
> >>> > 
> >>> > > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, 
> >>> > > timestamp = TRUE)) 
> >>> > 
> >>> > 20150123 21:47:53|Retrieving monocell CDF... 
> >>> > 
> >>> > 20150123 21:47:53| Monocell chip type: HG-U133_Plus_2,monocell 
> >>> > 
> >>> > 20150123 21:47:53| Locating monocell CDF... 
> >>> > 
> >>> > 20150123 21:47:53|  Pathname: 
> >>> > 
> >>> > 20150123 21:47:53| Locating monocell CDF...done 
> >>> > 
> >>> > 20150123 21:47:53| Could not locate monocell CDF. Will create one 
> for 
> >>> > chip type... 
> >>> > 
> >>> > 20150123 21:47:53|  Creating monocell CDF... 
> >>> > 
> >>> > 20150123 21:47:53|   Chip type: HG-U133_Plus_2 
> >>> > 
> >>> > 20150123 21:47:53|   Validate (main) CDF... 
> >>> > 
> >>> > 20150123 21:47:54|   Validate (main) CDF...done 
> >>> > 
> >>> > 20150123 21:47:55|   Adding temporary suffix from file... 
> >>> > 
> >>> > 20150123 21:47:55|    Pathname: 
> >>> > annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF 
> >>> > 
> >>> > 20150123 21:47:55|    Suffix: .tmp 
> >>> > 
> >>> > 20150123 21:47:55|    Rename existing file?: FALSE 
> >>> > 
> >>> > 20150123 21:47:55|    Temporary pathname: 
> >>> > 
> annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF.tmp 
> >>> > 
> >>> > 20150123 21:47:55|   Adding temporary suffix from file...done 
> >>> > 
> >>> > 20150123 21:47:55|   Number of cells per group field: 1 
> >>> > 
> >>> > 20150123 21:47:55|   Reading CDF group names... 
> >>> > 
> >>> > 20150123 21:47:55|   Reading CDF group names...done 
> >>> > 
> >>> >              used (Mb) gc trigger (Mb) max used (Mb) 
> >>> > 
> >>> >    Ncells  603933 32.3     899071 48.1   741108 39.6 
> >>> > 
> >>> >    Vcells 1027587  7.9    1757946 13.5  1424724 10.9 
> >>> > 
> >>> >             used (Mb) gc trigger (Mb) max used (Mb) 
> >>> > 
> >>> >    Ncells 549349 29.4     899071 48.1   899071 48.1 
> >>> > 
> >>> >    Vcells 945722  7.3    1757946 13.5  1424724 10.9 
> >>> > 
> >>> > 20150123 21:47:56|   Number of cells per unit: 
> >>> > 
> >>> >       Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
> >>> > 
> >>> >          1       1       1       1       1       1 
> >>> > 
> >>> > 20150123 21:47:56|   Reading CDF QC units... 
> >>> > 
> >>> > 20150123 21:47:56|   Reading CDF QC units...done 
> >>> > 
> >>> > 20150123 21:47:56|   Number of QC cells: 5385 in 9 QC units (0.1MB) 
> >>> > 
> >>> > 20150123 21:47:56|   Total number of cells: 60060 
> >>> > 
> >>> > 20150123 21:47:56|   Best array dimension: 246x245 (=60270 cells, 
> i.e. 
> >>> > 210 left-over cells) 
> >>> > 
> >>> > 20150123 21:47:56|   Creating CDF header with source CDF as 
> template... 
> >>> > 
> >>> > 20150123 21:47:56|    Setting up header... 
> >>> > 
> >>> > 20150123 21:47:56|     Reading CDF header... 
> >>> > 
> >>> > 20150123 21:47:56|     Reading CDF header...done 
> >>> > 
> >>> > 20150123 21:47:56|     Reading CDF unit names... 
> >>> > 
> >>> > 20150123 21:47:56|     Reading CDF unit names...done 
> >>> > 
> >>> > 20150123 21:47:56|    Setting up header...done 
> >>> > 
> >>> > 20150123 21:47:56|    Writing... 
> >>> > 
> >>> > 20150123 21:47:56|     destHeader: 
> >>> > 
> >>> >      List of 12 
> >>> > 
> >>> >       $ ncols      : int 245 
> >>> > 
> >>> >       $ nrows      : int 246 
> >>> > 
> >>> >       $ nunits     : int 54675 
> >>> > 
> >>> >       $ nqcunits   : int 9 
> >>> > 
> >>> >       $ refseq     : chr "" 
> >>> > 
> >>> >       $ chiptype   : chr "HG-U133_Plus_2" 
> >>> > 
> >>> >       $ filename   : chr 
> >>> > "annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf" 
> >>> > 
> >>> >       $ rows       : int 1164 
> >>> > 
> >>> >       $ cols       : int 1164 
> >>> > 
> >>> >       $ probesets  : int 54675 
> >>> > 
> >>> >       $ qcprobesets: int 9 
> >>> > 
> >>> >       $ reference  : chr "" 
> >>> > 
> >>> > 20150123 21:47:56|     unitNames: 
> >>> > 
> >>> >       chr [1:54675] "AFFX-BioB-5_at" "AFFX-BioB-M_at" 
> "AFFX-BioB-3_at" 
> >>> > "AFFX-BioC-5_at" ... 
> >>> > 
> >>> > 20150123 21:47:56|     qcUnitLengths: 
> >>> > 
> >>> >       num [1:9] 15966 174 230 1658 69 ... 
> >>> > 
> >>> > 20150123 21:47:56|     unitLengths: 
> >>> > 
> >>> >       num [1:54675] 116 116 116 116 116 116 116 116 116 116 ... 
> >>> > 
> >>> >                used (Mb) gc trigger (Mb) max used (Mb) 
> >>> > 
> >>> >      Ncells  561416 30.0     984024 52.6   899071 48.1 
> >>> > 
> >>> >      Vcells 1120064  8.6    1925843 14.7  1515846 11.6 
> >>> > 
> >>> >                used (Mb) gc trigger (Mb) max used (Mb) 
> >>> > 
> >>> >      Ncells  562232 30.1     984024 52.6   899071 48.1 
> >>> > 
> >>> >      Vcells 1010995  7.8    5484388 41.9  6516658 49.8 
> >>> > 
> >>> > 20150123 21:47:57|    Writing...done 
> >>> > 
> >>> > 20150123 21:47:57|   Creating CDF header with source CDF as 
> >>> > template...done 
> >>> > 
> >>> > 20150123 21:47:57|   Writing QC units... 
> >>> > 
> >>> > 20150123 21:47:57|    Rearranging QC unit cell indices... 
> >>> > 
> >>> > 20150123 21:47:57|     Units: 20150123 21:47:57| 
> >>> > 
> >>> > 20150123 21:47:57|    Rearranging QC unit cell indices...done 
> >>> > 
> >>> >              used (Mb) gc trigger (Mb) max used (Mb) 
> >>> > 
> >>> >     Ncells 562529 30.1     984024 52.6   984024 52.6 
> >>> > 
> >>> >     Vcells 994748  7.6    3510008 26.8  6516658 49.8 
> >>> > 
> >>> > 20150123 21:47:57|   Writing QC units...done 
> >>> > 
> >>> > 20150123 21:47:57|   Number of units: 54675 
> >>> > 
> >>> > 20150123 21:47:57|   Argument 'ram': 1.000000 
> >>> > 
> >>> > 20150123 21:47:57|   Average unit length: 116.000000 bytes 
> >>> > 
> >>> > 20150123 21:47:57|   Number of chunks: 2 (34482 units/chunk) 
> >>> > 
> >>> > 20150123 21:47:57|   Reading, extracting, and writing units... 
> >>> > 
> >>> > 20150123 21:47:57|    Chunk #1 of 2 (34482 units) 
> >>> > 
> >>> > 20150123 21:47:57|    Reading CDF list structure... 
> >>> > 
> >>> > 20150123 21:47:59|    Reading CDF list structure...done 
> >>> > 
> >>> >  => RAM: 132MB 
> >>> > 
> >>> > Error in (...) : 3 arguments passed to '(' which requires 1 
> >>> > 
> >>> > 20150123 21:48:01| Could not locate monocell CDF. Will create one 
> for 
> >>> > chip type...done 
> >>> > 
> >>> > 20150123 21:48:01|Retrieving monocell CDF...done 
> >>> > 
> >>> > ... 
>

-- 
-- 
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.


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