function readPgf(file) does not read elements

deepstop commented 9 years ago

Hi! Using the function readPgf(file) does not read any elements and just returns the header.

This leeds to errors in other packages like pdInfoBuilder, which assume the data is read: Creating initial table for probes... Error in .Primitive(":")(dots[[1L]][[1L]], dots[[2L]][[1L]]): NA/NaN argument Please have a look at the pull request. https://github.com/HenrikBengtsson/affxparser/pull/1 Regards, G

HenrikBengtsson commented 9 years ago

Thanks for this. In order to incorporate this, I've identified the following sub tasks:

Identify/create a small example PGF file that probably will be added to the AffymetrixTestDataFiles package.
Modify readPgf() to support indices=NULL (read all), indices=integer(0) (=read nothing), indices=5 (read one), and indices=1:10 (read some).
Write unit tests for the above and add them to affxparser.
Check impact on other package, e.g. pdInfoBuilder as you mention in your Pull Request #1.

We're looking into this.

HenrikBengtsson commented 9 years ago

I can not reproduce the error, e.g.

> library(affxparser)
> pathname <- "HuGene-1_0-st-v1.r4.pgf"
> file.info(pathname)$size
[1] 55046121
> digest::digest(file=pathname)
[1] "f1b71e0f1252988e9955734602c899e0"
> data <- readPgf(pathname)
> str(data)
> str(data)
List of 14
 $ probeSequence             : chr [1:861493] "AAGCTTAGTAGACTATAAATATGAC" 
  "GCTTAGTAGACTATAAATATGACTT"  "GTAGACTATAAATATGACTTACTCA" 
  "ACTATAAATATGACTTACTCAATGA" ..
.
 $ probesetName              : chr [1:257430] "" "" "" "" ...
 $ probesetStartAtom         : int [1:257430] 1 5 9 13 17 21 25 29 33 37 ...
 $ probeId                   : int [1:861493] 116371 943979 493089 907039 103330
9 653512 690769 997409 379979 469846 ...
 $ probesetId                : int [1:257430] 7892501 7892502 7892503 7892504 78
92505 7892506 7892507 7892508 7892509 7892510 ...
 $ probesetType              : chr [1:257430] "normgene->exon" "normgene->intron"
  "normgene->intron" "normgene->intron" ...
 $ atomStartProbe            : int [1:844595] 1 2 3 4 5 6 7 8 9 10 ...
 $ header                    :List of 9
  ..$ chip_type         : chr "HuGene-1_0-st-v1"
  ..$ pgf_format_version: chr "1.0"
  ..$ lib_set_name      : chr "HuGene-1_0-st-v1"
  ..$ lib_set_version   : chr "r4"
  ..$ guid              : chr "0000050091-1228862702-0302010399-1388352192-1436570985"
  ..$ create_date       : chr "Tue Dec  9 14:45:02 PST 2008"
  ..$ header0           : chr "probeset_id\ttype"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\t
   interrogation_position\tprobe_sequence"
 $ probeGcCount              : int [1:861493] 7 7 7 6 8 10 11 8 14 11 ...
 $ atomExonPosition          : int [1:844595] 0 0 0 0 0 0 0 0 0 0 ...
 $ atomId                    : int [1:844595] 1 2 3 5 7 10 11 12 13 14 ...
 $ probeInterrogationPosition: int [1:861493] 13 13 13 13 13 13 13 13 13 13 ...
 $ probeLength               : int [1:861493] 25 25 25 25 25 25 25 25 25 25 ...
 $ probeType                 : chr [1:861493] "pm:st" "pm:st" "pm:st" "pm:st" ...
>

using:

> sessionInfo()
R version 3.1.1 Patched (2014-10-18 r66793)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.37.1

loaded via a namespace (and not attached):
[1] tools_3.1.1

It could be a problematic PGF file or an updated format. @deepstop, could you please make the PGF file causing problems available for me to download?

HenrikBengtsson commented 9 years ago

Ok, looking at the actual C++ source code (first time; was written by contributors) I agree that there is/could be something odd about indices=NULL. I puzzled that it works for me. Still, please share the PGF for which you experience problems and I'll take it from there.

deepstop commented 9 years ago

Maybe its mac OS 10.10 (yosemite) related? i run some checks:

on my (Linux 3.16.5-gentoo) box its fine / affxparser 1.36:

> library(affxparser)
> pathname <- "DroGene-1_0-st.pgf"
> file.info(pathname)$size
[1] 51351648
> digest::digest(file=pathname)
[1] "356a211ec59140898d64e0b188aa8e50"
> data <- readPgf(pathname)
> str(data)
List of 14
 $ probeSequence             : chr [1:818474] "TCTGCCCGATTGCTCATGAACGTAG" "GTAATAACAGAGTCACGTCAACAGT" "AGTCACGTCAACAGTCAACGTCAAG" "TCGAAGACGACATGCCTAGAAGGAT" ...
 $ probesetName              : chr [1:176275] "18130641" "18130642" "18130643" "18130644" ...
 $ probesetStartAtom         : int [1:176275] 1 4 9 12 15 18 21 24 27 30 ...
 $ probeId                   : int [1:818474] 827673 1028834 1216853 835540 954337 1342563 984600 1272219 140936 1042131 ...
 $ probesetId                : int [1:176275] 18130641 18130642 18130643 18130644 18130645 18130646 18130647 18130648 18130649 18130651 ...
 $ probesetType              : chr [1:176275] "main" "main" "main" "main" ...
 $ atomStartProbe            : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ header                    :List of 15
  ..$ chip_type         : chr "DroGene-1_0-st"
  ..$ lib_set_name      : chr "DroGene-1_0-st"
  ..$ lib_set_version   : chr "r4"
  ..$ create_date       : chr "Mon Oct 15 16:34:36 PDT 2012"
  ..$ guid              : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33"
  ..$ pgf_format_version: chr "1.0"
  ..$ num-cols          : chr "1190"
  ..$ num-rows          : chr "1190"
  ..$ probesets         : chr "176275"
  ..$ datalines         : chr "1813223"
  ..$ sequential        : chr "1"
  ..$ order             : chr "row_major"
  ..$ header0           : chr "probeset_id\ttype\tprobeset_name"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\tinterrogation_position\tprobe_sequence"
 $ probeGcCount              : int [1:818474] 13 10 12 12 10 13 15 12 12 12 ...
 $ atomExonPosition          : int [1:818474] 6322120 6322120 6322120 6322120 6322120 6322120 6322120 6322120 6322120 6322120 ...
 $ atomId                    : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ probeInterrogationPosition: int [1:818474] 13 13 13 13 13 13 13 13 13 13 ...
 $ probeLength               : int [1:818474] 25 25 25 25 25 25 25 25 25 25 ...
 $ probeType                 : chr [1:818474] "pm:st" "pm:st" "pm:st" "pm:st" ...
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.36.0

loaded via a namespace (and not attached):
[1] digest_0.6.4

on my (Linux 3.16.5-gentoo) - even after upgrading (bioconductor 2.14 to 3.0) and affxparser (1.36 to 1.38) its fine:

> library(affxparser)
> pathname <- "DroGene-1_0-st.pgf"
> file.info(pathname)$size
[1] 51351648
> digest::digest(file=pathname)
[1] "356a211ec59140898d64e0b188aa8e50"
> data <- readPgf(pathname)
> str(data)
List of 14
 $ probeSequence             : chr [1:818474] "TCTGCCCGATTGCTCATGAACGTAG" "GTAATAACAGAGTCACGTCAACAGT" "AGTCACGTCAACAGTCAACGTCAAG" "TCGAAGACGACATGCCTAGAAGGAT" ...
 $ probesetName              : chr [1:176275] "18130641" "18130642" "18130643" "18130644" ...
 $ probesetStartAtom         : int [1:176275] 1 4 9 12 15 18 21 24 27 30 ...
 $ probeId                   : int [1:818474] 827673 1028834 1216853 835540 954337 1342563 984600 1272219 140936 1042131 ...
 $ probesetId                : int [1:176275] 18130641 18130642 18130643 18130644 18130645 18130646 18130647 18130648 18130649 18130651 ...
 $ probesetType              : chr [1:176275] "main" "main" "main" "main" ...
 $ atomStartProbe            : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ header                    :List of 15
  ..$ chip_type         : chr "DroGene-1_0-st"
  ..$ lib_set_name      : chr "DroGene-1_0-st"
  ..$ lib_set_version   : chr "r4"
  ..$ create_date       : chr "Mon Oct 15 16:34:36 PDT 2012"
  ..$ guid              : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33"
  ..$ pgf_format_version: chr "1.0"
  ..$ num-cols          : chr "1190"
  ..$ num-rows          : chr "1190"
  ..$ probesets         : chr "176275"
  ..$ datalines         : chr "1813223"
  ..$ sequential        : chr "1"
  ..$ order             : chr "row_major"
  ..$ header0           : chr "probeset_id\ttype\tprobeset_name"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\tinterrogation_position\tprobe_sequence"
 $ probeGcCount              : int [1:818474] 13 10 12 12 10 13 15 12 12 12 ...
 $ atomExonPosition          : int [1:818474] 0 0 0 0 0 0 0 0 0 0 ...
 $ atomId                    : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ probeInterrogationPosition: int [1:818474] 13 13 13 13 13 13 13 13 13 13 ...
 $ probeLength               : int [1:818474] 25 25 25 25 25 25 25 25 25 25 ...
 $ probeType                 : chr [1:818474] "pm:st" "pm:st" "pm:st" "pm:st" ...
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.38.0

loaded via a namespace (and not attached):
[1] digest_0.6.4

BUT on my mac (without the patch) / affxparser 1.38:

> library(affxparser)
> pathname <- "DroGene-1_0-st.pgf"
> file.info(pathname)$size
[1] 51351648
> digest::digest(file=pathname)
[1] "356a211ec59140898d64e0b188aa8e50"
> data <- readPgf(pathname)
> str(data)
List of 14
 $ probeSequence             : chr(0)
 $ probesetName              : chr(0)
 $ probesetStartAtom         : int(0)
 $ probeId                   : int(0)
 $ probesetId                : int(0)
 $ probesetType              : chr(0)
 $ atomStartProbe            : int(0)
 $ header                    :List of 15
  ..$ chip_type         : chr "DroGene-1_0-st"
  ..$ lib_set_name      : chr "DroGene-1_0-st"
  ..$ lib_set_version   : chr "r4"
  ..$ create_date       : chr "Mon Oct 15 16:34:36 PDT 2012"
  ..$ guid              : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33"
  ..$ pgf_format_version: chr "1.0"
  ..$ num-cols          : chr "1190"
  ..$ num-rows          : chr "1190"
  ..$ probesets         : chr "176275"
  ..$ datalines         : chr "1813223"
  ..$ sequential        : chr "1"
  ..$ order             : chr "row_major"
  ..$ header0           : chr "probeset_id\ttype\tprobeset_name"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\tinterrogation_position\tprobe_sequence"
 $ probeGcCount              : int(0)
 $ atomExonPosition          : int(0)
 $ atomId                    : int(0)
 $ probeInterrogationPosition: int(0)
 $ probeLength               : int(0)
 $ probeType                 : chr(0)
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin14.0.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.38.0

loaded via a namespace (and not attached):
[1] digest_0.6.4

on my mac (with the patch) / affxparser 1.38 patched:

> library(affxparser, lib.loc="/var/testlibs/")
> pathname <- "DroGene-1_0-st.pgf"
> file.info(pathname)$size
[1] 51351648
> data <- readPgf(pathname)
> str(data)
List of 14
 $ probeSequence             : chr [1:818474] "TCTGCCCGATTGCTCATGAACGTAG" "GTAATAACAGAGTCACGTCAACAGT" "AGTCACGTCAACAGTCAACGTCAAG" "TCGAAGACGACATGCCTAGAAGGAT" ...
 $ probesetName              : chr [1:176275] "18130641" "18130642" "18130643" "18130644" ...
 $ probesetStartAtom         : int [1:176275] 1 4 9 12 15 18 21 24 27 30 ...
 $ probeId                   : int [1:818474] 827673 1028834 1216853 835540 954337 1342563 984600 1272219 140936 1042131 ...
 $ probesetId                : int [1:176275] 18130641 18130642 18130643 18130644 18130645 18130646 18130647 18130648 18130649 18130651 ...
 $ probesetType              : chr [1:176275] "main" "main" "main" "main" ...
 $ atomStartProbe            : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ header                    :List of 15
  ..$ chip_type         : chr "DroGene-1_0-st"
  ..$ lib_set_name      : chr "DroGene-1_0-st"
  ..$ lib_set_version   : chr "r4"
  ..$ create_date       : chr "Mon Oct 15 16:34:36 PDT 2012"
  ..$ guid              : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33"
  ..$ pgf_format_version: chr "1.0"
  ..$ num-cols          : chr "1190"
  ..$ num-rows          : chr "1190"
  ..$ probesets         : chr "176275"
  ..$ datalines         : chr "1813223"
  ..$ sequential        : chr "1"
  ..$ order             : chr "row_major"
  ..$ header0           : chr "probeset_id\ttype\tprobeset_name"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\tinterrogation_position\tprobe_sequence"
 $ probeGcCount              : int [1:818474] 13 10 12 12 10 13 15 12 12 12 ...
 $ atomExonPosition          : int [1:818474] 0 0 0 0 0 0 0 0 0 0 ...
 $ atomId                    : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ probeInterrogationPosition: int [1:818474] 13 13 13 13 13 13 13 13 13 13 ...
 $ probeLength               : int [1:818474] 25 25 25 25 25 25 25 25 25 25 ...
 $ probeType                 : chr [1:818474] "pm:st" "pm:st" "pm:st" "pm:st" ...
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin14.0.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.38.0

deepstop commented 9 years ago

thanks for looking into this, i'll send you the DroGene-1_0-st.pgf by mail.

HenrikBengtsson commented 9 years ago

Another negative example on OSX:

When I run on R version 3.1.1 Patched (2014-08-04 r66309) [x86_64-apple-darwin10.8.0 (64-bit)] when using affxparser 1.36.0 (sic!) the following works:

library("affxparser")
pgf <- "annotationData/chipTypes/DroGene-1_0-st-v1/DroGene-1_0-st.pgf"
data <- readPgf(pgf)
stopifnot(length(data$probesetName) == 176275)

HenrikBengtsson commented 9 years ago

@deepstop, on your OSX machine, which seems to be the only place where you have this problem, are you installing from source or from (Bioc's OSX) binaries? I'd like to narrow down the cause behind these discrepancies before applying any patches.

EDIT: To clarify, it could either be (i) an OSX 10.10 issue (there seems to be various reports on that version not playing well with R) or (ii) an issue with your build.

UPDATE: To clarify, it could be:

an issue with OSX 10.10 (there seems to be various reports on that version not playing well with R)
an issue that started already with OSX 10.9,
or (ii) an issue with your build.

deepstop commented 9 years ago

I am installing from source.... ...and just noticed the warnings:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> biocLite("affxparser")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Installing package(s) 'affxparser'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/affxparser_1.38.0.tar.gz'
Content type 'application/x-gzip' length 804858 bytes (785 Kb)
opened URL
==================================================
downloaded 785 Kb

* installing *source* package ‘affxparser’ ...
** libs
rm -f fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/calvin_files/data/src/CDFData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o
fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:109:15: warning:
      comparison of unsigned expression < 0 is always false
      [-Wtautological-compare]
        if (groupIdx < 0 || groupIdx >= groupCnt)
            ~~~~~~~~ ^ ~
1 warning generated.
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk/calvin_files/data/src/CELData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPData.cpp -o fusion_sdk/calvin_files/data/src/CHPData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp -o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPTilingData.cpp -o fusion_sdk/calvin_files/data/src/CHPTilingData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/ColumnInfo.cpp -o fusion_sdk/calvin_files/data/src/ColumnInfo.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_sdk/calvin_files/data/src/DataGroup.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fusion_sdk/calvin_files/data/src/DataGroupHeader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk/calvin_files/data/src/DataSet.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusion_sdk/calvin_files/data/src/DataSetHeader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_sdk/calvin_files/data/src/FileHeader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion_sdk/calvin_files/data/src/GenericData.o
fusion_sdk/calvin_files/data/src/GenericData.cpp:388:18: warning: comparison of
      unsigned expression >= 0 is always true [-Wtautological-compare]
                if (dataSetIdx >= 0 && (int32_t)dataSetIdx < dch->GetDat...
                    ~~~~~~~~~~ ^  ~
1 warning generated.
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CelFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/utils/src/DateTime.cpp -o fusion_sdk/calvin_files/utils/src/DateTime.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/utils/src/StringUtils.cpp -o fusion_sdk/calvin_files/utils/src/StringUtils.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/CHPFileData.cpp -o fusion_sdk/file/CHPFileData.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/TsvFile/ClfFile.cpp -o fusion_sdk/file/TsvFile/ClfFile.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/TsvFile/PgfFile.cpp -o fusion_sdk/file/TsvFile/PgfFile.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/file/TsvFile/TsvFile.cpp -o fusion_sdk/file/TsvFile/TsvFile.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/AffxByteArray.cpp -o fusion_sdk/util/AffxByteArray.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/AffxConv.cpp -o fusion_sdk/util/AffxConv.o
fusion_sdk/util/AffxConv.cpp:124:8: warning: self-comparison always evaluates to
      false [-Wtautological-compare]
        if (i != i) {return "nan";}
              ^
1 warning generated.
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/MsgStream.cpp -o fusion_sdk/util/MsgStream.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/Util.cpp -o fusion_sdk/util/Util.o
fusion_sdk/util/Util.cpp:788:7: warning: expression result unused
      [-Wunused-value]
      *wStart++;
      ^~~~~~~~~
fusion_sdk/util/Util.cpp:856:10: warning: 'finite' is deprecated: first
      deprecated in OS X 10.9 [-Wdeprecated-declarations]
  isOk = finite(x);
         ^
/usr/include/math.h:718:12: note: 'finite' has been explicitly marked deprecated
      here
extern int finite(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __M...
           ^
2 warnings generated.
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/Err.cpp -o fusion_sdk/util/Err.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/Fs.cpp -o fusion_sdk/util/Fs.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/Verbose.cpp -o fusion_sdk/util/Verbose.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/RowFile.cpp -o fusion_sdk/util/RowFile.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/TableFile.cpp -o fusion_sdk/util/TableFile.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c fusion_sdk/util/Convert.cpp -o fusion_sdk/util/Convert.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o
R_affx_cdf_parser.cpp:169:31: warning: expression result unused [-Wunused-value]
        for(int i = 0; i++; i < length(unitIndices)) {
                            ~ ^ ~~~~~~~~~~~~~~~~~~~
R_affx_cdf_parser.cpp:619:31: warning: expression result unused [-Wunused-value]
        for(int i = 0; i++; i < length(unitIndices)) {
                            ~ ^ ~~~~~~~~~~~~~~~~~~~
2 warnings generated.
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o
/usr/bin/clang++ -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++  -O0 -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o
/usr/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/lib -Wl,-headerpad_max_install_names -arch x86_64 -o affxparser.so fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/affxparser/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affxparser)

HenrikBengtsson commented 9 years ago

Before troubleshooting your setup/building from source, can't you install BioC binaries instead? Have you forced the settings to install from source? Because I would expect biocLite("affxparser") to install from binaries by default.

deepstop commented 9 years ago

I didnt change any default and the default seems to be source:

> getOption("pkgType")
[1] "source"

when uninstalling the source version and forcing the binary with:

>biocLite("affxparser",type="mac.binary")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Installing package(s) 'affxparser'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/affxparser_1.38.0.tgz'
Content type 'application/x-gzip' length 1530349 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

The downloaded binary packages are in
    /tmp/Rtmp3aXURl/downloaded_packages

it looks fine!

data <- readPgf(pathname)
> str(data)
List of 14
 $ probeSequence             : chr [1:818474] "TCTGCCCGATTGCTCATGAACGTAG" "GTAATAACAGAGTCACGTCAACAGT" "AGTCACGTCAACAGTCAACGTCAAG" "TCGAAGACGACATGCCTAGAAGGAT" ...
 $ probesetName              : chr [1:176275] "18130641" "18130642" "18130643" "18130644" ...
 $ probesetStartAtom         : int [1:176275] 1 4 9 12 15 18 21 24 27 30 ...
 $ probeId                   : int [1:818474] 827673 1028834 1216853 835540 954337 1342563 984600 1272219 140936 1042131 ...
 $ probesetId                : int [1:176275] 18130641 18130642 18130643 18130644 18130645 18130646 18130647 18130648 18130649 18130651 ...
 $ probesetType              : chr [1:176275] "main" "main" "main" "main" ...
 $ atomStartProbe            : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ header                    :List of 15
  ..$ chip_type         : chr "DroGene-1_0-st"
  ..$ lib_set_name      : chr "DroGene-1_0-st"
  ..$ lib_set_version   : chr "r4"
  ..$ create_date       : chr "Mon Oct 15 16:34:36 PDT 2012"
  ..$ guid              : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33"
  ..$ pgf_format_version: chr "1.0"
  ..$ num-cols          : chr "1190"
  ..$ num-rows          : chr "1190"
  ..$ probesets         : chr "176275"
  ..$ datalines         : chr "1813223"
  ..$ sequential        : chr "1"
  ..$ order             : chr "row_major"
  ..$ header0           : chr "probeset_id\ttype\tprobeset_name"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\tinterrogation_position\tprobe_sequence"
 $ probeGcCount              : int [1:818474] 13 10 12 12 10 13 15 12 12 12 ...
 $ atomExonPosition          : int [1:818474] 682181688 682181688 682181688 682181688 682181688 682181688 682181688 682181688 682181688 682181688 ...
 $ atomId                    : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ probeInterrogationPosition: int [1:818474] 13 13 13 13 13 13 13 13 13 13 ...
 $ probeLength               : int [1:818474] 25 25 25 25 25 25 25 25 25 25 ...
 $ probeType                 : chr [1:818474] "pm:st" "pm:st" "pm:st" "pm:st" ...
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin14.0.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.38.0

So it seems to appear if you compile from source on os 10.10 (xcode 6.1).

HenrikBengtsson commented 9 years ago

Great, now we're narrowing down the problem. Next, could you try (cf. ?options):

biocLite("affxparser", type="mac.binary.mavericks")

(don't forget to do this in a fresh R session). That should install the OSX Mavericks builds done by Bioconductor. If the problems gets back, then we can be pretty certain that this is an OSX (>= 10.9) issue and we should be able to reproduce it on the Bioc Mavericks test servers.

On Mon, Oct 27, 2014 at 12:07 PM, deepstop notifications@github.com wrote:

I didnt change any default and the default seems to be source:

getOption("pkgType") [1] "source"

when uninstalling the source version and forcing the binary with:

biocLite("affxparser",type="mac.binary") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1. Installing package(s) 'affxparser' trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/affxparser_1.38.0.tgz' Content type 'application/x-gzip' length 1530349 bytes (1.5 Mb)

opened URL

downloaded 1.5 Mb

The downloaded binary packages are in /tmp/Rtmp3aXURl/downloaded_packages

it looks fine!

data <- readPgf(pathname)

str(data) List of 14 $ probeSequence : chr [1:818474] "TCTGCCCGATTGCTCATGAACGTAG" "GTAATAACAGAGTCACGTCAACAGT" "AGTCACGTCAACAGTCAACGTCAAG" "TCGAAGACGACATGCCTAGAAGGAT" ... $ probesetName : chr [1:176275] "18130641" "18130642" "18130643" "18130644" ... $ probesetStartAtom : int [1:176275] 1 4 9 12 15 18 21 24 27 30 ... $ probeId : int [1:818474] 827673 1028834 1216853 835540 954337 1342563 984600 1272219 140936 1042131 ... $ probesetId : int [1:176275] 18130641 18130642 18130643 18130644 18130645 18130646 18130647 18130648 18130649 18130651 ... $ probesetType : chr [1:176275] "main" "main" "main" "main" ... $ atomStartProbe : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ... $ header :List of 15 ..$ chip_type : chr "DroGene-1_0-st" ..$ lib_set_name : chr "DroGene-1_0-st" ..$ lib_set_version : chr "r4" ..$ create_date : chr "Mon Oct 15 16:34:36 PDT 2012" ..$ guid : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33" ..$ pgf_format_version: chr "1.0" ..$ num-cols : chr "1190" ..$ num-rows : chr "1190" ..$ probesets : chr "176275" ..$ datalines : chr "1813223" ..$ sequential : chr "1" ..$ order : chr "row_major" ..$ header0 : chr "probeset_id\ttype\tprobeset_name" ..$ header1 : chr "\tatom_id" ..$ header2 : chr "\t\tprobe_id\ttype\tgc_count\tprobelength\tinterrogation position\tprobe_sequence" $ probeGcCount : int [1:818474] 13 10 12 12 10 13 15 12 12 12 ... $ atomExonPosition : int [1:818474] 682181688 682181688 682181688 682181688 682181688 682181688 682181688 682181688 682181688 682181688 ... $ atomId : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ... $ probeInterrogationPosition: int [1:818474] 13 13 13 13 13 13 13 13 13 13 ... $ probeLength : int [1:818474] 25 25 25 25 25 25 25 25 25 25 ... $ probeType : chr [1:818474] "pm:st" "pm:st" "pm:st" "pm:st" ... sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin14.0.0 (64-bit)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] affxparser_1.38.0

So it seems to appear if you compile from source on os 10.10 (xcode 6.1).

— Reply to this email directly or view it on GitHub https://github.com/HenrikBengtsson/affxparser/issues/2#issuecomment-60651164 .

deepstop commented 9 years ago

Nope, seems to be an OSX (>=10.10), xcode 6.1 problem. uninstalling and than installing the mavericks binary version...

> biocLite("affxparser", type="mac.binary.mavericks")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Installing package(s) 'affxparser'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/affxparser_1.38.0.tgz'
Content type 'application/x-gzip' length 1363980 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

The downloaded binary packages are in
    /tmp/RtmpYDJisX/downloaded_packages

also works (using a fresh session):

> str(data)
List of 14
 $ probeSequence             : chr [1:818474] "TCTGCCCGATTGCTCATGAACGTAG" "GTAATAACAGAGTCACGTCAACAGT" "AGTCACGTCAACAGTCAACGTCAAG" "TCGAAGACGACATGCCTAGAAGGAT" ...
 $ probesetName              : chr [1:176275] "18130641" "18130642" "18130643" "18130644" ...
 $ probesetStartAtom         : int [1:176275] 1 4 9 12 15 18 21 24 27 30 ...
 $ probeId                   : int [1:818474] 827673 1028834 1216853 835540 954337 1342563 984600 1272219 140936 1042131 ...
 $ probesetId                : int [1:176275] 18130641 18130642 18130643 18130644 18130645 18130646 18130647 18130648 18130649 18130651 ...
 $ probesetType              : chr [1:176275] "main" "main" "main" "main" ...
 $ atomStartProbe            : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ header                    :List of 15
  ..$ chip_type         : chr "DroGene-1_0-st"
  ..$ lib_set_name      : chr "DroGene-1_0-st"
  ..$ lib_set_version   : chr "r4"
  ..$ create_date       : chr "Mon Oct 15 16:34:36 PDT 2012"
  ..$ guid              : chr "28ac67b4-62f6-4028-dde0-5596fa61cd33"
  ..$ pgf_format_version: chr "1.0"
  ..$ num-cols          : chr "1190"
  ..$ num-rows          : chr "1190"
  ..$ probesets         : chr "176275"
  ..$ datalines         : chr "1813223"
  ..$ sequential        : chr "1"
  ..$ order             : chr "row_major"
  ..$ header0           : chr "probeset_id\ttype\tprobeset_name"
  ..$ header1           : chr "\tatom_id"
  ..$ header2           : chr "\t\tprobe_id\ttype\tgc_count\tprobe_length\tinterrogation_position\tprobe_sequence"
 $ probeGcCount              : int [1:818474] 13 10 12 12 10 13 15 12 12 12 ...
 $ atomExonPosition          : int [1:818474] 0 0 0 0 0 0 0 0 0 0 ...
 $ atomId                    : int [1:818474] 1 2 3 4 5 6 7 8 9 10 ...
 $ probeInterrogationPosition: int [1:818474] 13 13 13 13 13 13 13 13 13 13 ...
 $ probeLength               : int [1:818474] 25 25 25 25 25 25 25 25 25 25 ...
 $ probeType                 : chr [1:818474] "pm:st" "pm:st" "pm:st" "pm:st" ...

HenrikBengtsson commented 9 years ago

I agree, it looks like it is an issue that shows itself on OSX 10.10 (Yosemite). I've pushed affxparser 1.39.1 to Bioc devel with unit tests on readPgf() to confirm that the error does not appear on the BioC Mavericks machine and it does not, cf. http://master.bioconductor.org/checkResults/devel/bioc-LATEST/affxparser/

Also, the BioC Mavericks machine show the same build warnings as you get, e.g.

fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:109:15: 
warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if (groupIdx < 0 || groupIdx >= groupCnt)

Those concern me too and may be related and they should also be corrected.

All of this will take a while, but I hope I can get back to you to run some tests for us. Thanks.

HenrikBengtsson commented 9 years ago

I can now reproduce this issue of readPgf(..., indices=NULL) not reading any probesets:

 ERROR
Running the tests in ‘tests/readPgf.R’ failed.
Last 13 lines of output:
  +     message(sprintf("Testing readPgf() with '%s' indices...done", name))
  +   } # for (ii ...)
  + } # if (require("AffymetrixDataTestFiles"))
  Loading required package: AffymetrixDataTestFiles
  List of 6
   $ probeSequence    : chr(0) 
   $ probesetName     : chr(0) 
   $ probesetStartAtom: int(0) 
   $ probeId          : int(0) 
   $ probesetId       : int(0) 
   $ probesetType     : chr(0) 
  Error: length(data$probesetName) == Jall is not TRUE
  Execution halted

on the _BioC Mac OS X Mavericks (10.9.5) / x8664 test server, cf. http://master.bioconductor.org/checkResults/devel/bioc-LATEST/affxparser/morelia-checksrc.html

HenrikBengtsson commented 9 years ago

Another progress report: I can now reproduce this issue on all platforms; the package test for readPgf(..., indices=NULL) now gives this erroneous/empty output everywhere, cf. http://master.bioconductor.org/checkResults/devel/bioc-LATEST/affxparser/.

There was what looks like a very-old bug on top of another bug (circa 2008) in the code that caused readPgf(..., indices=NULL) to work although it shouldn't have. The native code tested the length of argument 'indices' using LENGTH(indices), which I've confirmed gives random garbage on most platforms. The reason is that the LENGTH macro tries to access some element that are only available in vectors not NULL objects. Since its an unsigned integer, the random value returned was often a large-enough number such that the following conditional test/break never occurred:

if (nProbesets >= LENGTH(indices)) {
            break;
}

which meant it actually read all probesets. However, as code is written this was actually never intended, or at least, should never have worked as such. Interestingly, on all/some(?) Mac OS X Mavericks / Yosemite setups, LENGTH(indices) always return 0.

I've updated the code to use length(indices) and now it properly returns 0, which causes the parser to stop immediately returning zero probesets as expected from the current code.

Finally, I'm ready to attack the actual bug and your Pull Request #1.

deepstop commented 9 years ago

I merged the changes from pull request 1, added some comments and re added them against master: https://github.com/HenrikBengtsson/affxparser/pull/7 (by using as.integer(0) as index only the header gets returned)

HenrikBengtsson commented 9 years ago

@deepstop, thank you for all your help on this. I did most of the fixes a few weeks ago, but it's only a few days ago I had time to thoroughly think it through and test it. So...

readPgf(...indices=NULL) now reads all elements. affxparser 1.39.3 is available via BioC devel, cf.

http://master.bioconductor.org/packages/3.1/bioc/html/affxparser.html

In order to avoid surprises, I've set readPgf(..., indices=integer(0)) to give an informative error message for now, just like many other affxparser functions now do. This will eventually be transitioned to be supported. See Issue #3.

HenrikBengtsson / affxparser

function readPgf(file) does not read elements #2

opened URL