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$byChipType("HG-U133_Plus_2")
cdfM <- getMonocellCdf(cdf, verbose=TRUE)
print(cdfM)
If it complains about a pre-existing *.tmp file, remove that one an retry.
As soon as you confirm it works, I'll make aroma.affymetrix 2.13.1
available, because this was a critical bug(*).
Thanks for the report
/Henrik
(*) DETAILS: Turns out to be due to a single stray newline. It should have been
affxparser::writeCdfUnits(...)
but it was:
affxparser::writeCdfUnits
(...)
Despite running 24 hours of regular package testing, this piece of
code was never tested. I've now added an explicit test on creating
and re-creating monocell CDF.
On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote:
> I managed to reproduce this now:
>
> Error in (...) : 3 arguments passed to '(' which requires 1
> 20150123 08:48:49| Could not locate monocell CDF. Will create one for chip
> type.
> ..done
> 20150123 08:48:49|Retrieving monocell CDF...done
>> traceback()
> 5: .writeCdfUnits(con = con, srcUnits, verbose = verbose2)
> 4: createMonocellCdf.AffymetrixCdfFile(this, ..., verbose = less(verbose))
> 3: createMonocellCdf(this, ..., verbose = less(verbose))
> 2: getMonocellCdf.AffymetrixCdfFile(cdf, verbose = Arguments$getVerbose(-8,
> timestamp = TRUE))
> 1: getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp = TRUE))
>
> I'll investigate and fix this asap.
>
> /Henrik
>
>
> On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson <h...@biostat.ucsf.edu>
> wrote:
>>
>> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" <h...@biostat.ucsf.edu> wrote:
>>>
>>> This is odd for several reasons, e.g. I'm puzzled how you ended up with a
>>> monocell CDF previously but now it gives an error. Let's troubleshoot
>>> more...
>>>
>>> What does troubleshoot() output directly after you get that error?
>>
>> I meant traceback()
>>
>>>
>>> Henrik
>>>
>>> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" <zqznept...@gmail.com> wrote:
>>> >
>>> > Thanks, Henrik,
>>> >
>>> > It seems that something went wrong with the monocell cdf file by
>>> > troubleshooting:
>>> >
>>> >
>>> > > cdf
>>> >
>>> > AffymetrixCdfFile:
>>> >
>>> > Path: annotationData/chipTypes/HG-U133_Plus_2
>>> >
>>> > Filename: HG-U133_Plus_2,monocell.CDF
>>> >
>>> > File size: 4.88 MB (5116945 bytes)
>>> >
>>> > Chip type: HG-U133_Plus_2,monocell
>>> >
>>> > RAM: 0.46MB
>>> >
>>> > File format: v4 (binary; XDA)
>>> >
>>> > Dimension: 182x182
>>> >
>>> > Number of cells: 33124
>>> >
>>> > Number of units: 27604
>>> >
>>> > Cells per unit: 1.20
>>> >
>>> > Number of QC units: 9
>>> >
>>> >
>>> >
>>> > So I have deleted the previous monocell cdf file in
>>> > annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
>>> >
>>> > cdf <- AffymetrixCdfFile$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
>>> >
>>> > ...
--
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