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. > > > > > > 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-af...@googlegroups.com > <javascript:> > > 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-affymetr...@googlegroups.com <javascript:>. > > 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.