Many, many thanks, Henrik! Well done!
On Saturday, 24 January 2015 08:17:30 UTC+8, Henrik Bengtsson wrote:
>
> Great. I've now made aroma.affymetrix 2.13.1 available, which is
> installed the usual way:
>
> source('http://callr.org/install#aroma.affymetrix";)
>
> Anyone who reads this should update this way.
>
> /Henrik
>
> On Fri, Jan 23, 2015 at 2:57 PM, Qingzhou Zhang <zqzne...@gmail.com
> <javascript:>> wrote:
> > Thanks!
> >
> > Seems working pretty well.
> >
> >> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
> >> cdfM <- getMonocellCdf(cdf, verbose=TRUE)
> > Retrieving monocell CDF...
> > Monocell chip type: HG-U133_Plus_2,monocell
> > Locating monocell CDF...
> > Pathname:
> > Locating monocell CDF...done
> > Could not locate monocell CDF. Will create one for chip type...
> > Could not locate monocell CDF. Will create one for chip type...done
> > Retrieving monocell CDF...done
> >> print(cdfM)
> > AffymetrixCdfFile:
> > Path: annotationData/chipTypes/HG-U133_Plus_2
> > Filename: HG-U133_Plus_2,monocell.CDF
> > File size: 9.63 MB (10098009 bytes)
> > Chip type: HG-U133_Plus_2,monocell
> > RAM: 0.00MB
> > File format: v4 (binary; XDA)
> > Dimension: 246x245
> > Number of cells: 60270
> > Number of units: 54675
> > Cells per unit: 1.10
> > Number of QC units: 9
> >
> >
> >
> > On Saturday, 24 January 2015 03:52:43 UTC+8, Henrik Bengtsson wrote:
> >>
> >> Solved. Before finalize a release, would you mind making sure it
> >> works on your end. Install aroma.affymetrix 2.13.0-9001 by running
> >> the following in a fresh R session:
> >>
> >>
> >> source('
> http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001')
> >>
> >> Then retry with
> >>
> >> library("aroma.affymetrix")
> >> cdf <- AffymetrixCdfFile$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>
> >> 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" <zqzne...@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
> >> >>> >
> >> >>> > ...
> >
> > --
> > --
> > 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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> <javascript:>
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> >
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