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Package 27/671HostnameOS / ArchBUILDCHECKBUILD BIN
AffyTiling 1.18.0
Charles G. Danko
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/AffyTiling
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: AffyTiling
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyTiling_1.18.0.tar.gz
StartedAt: 2013-05-01 02:05:22 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 02:06:24 -0700 (Wed, 01 May 2013)
EllapsedTime: 61.6 seconds
RetCode: 0
Status:  OK 
CheckDir: AffyTiling.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AffyTiling.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AffyTiling/DESCRIPTION' ... OK
* this is package 'AffyTiling' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'AffyTiling' can be installed ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Call("rma_c_complete", ..., PACKAGE = "affy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/AffyTiling.Rcheck/00check.log'
for details.

AffyTiling.Rcheck/00install.out:

* installing *source* package 'AffyTiling' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
In file included from fusion_sdk/file/BPMAPFileData.cpp:21:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:123:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        munmap(m_lpFileMap, m_MapLen);
                        ˜˜˜˜˜˜              ^˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:300:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        m_NumberSequences = uval;
                          ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:304:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        m_SequenceItems.resize(m_NumberSequences);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:307:24: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        m_DataStartPosition = instr.tellg();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:339:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Name);
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:344:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_ProbePairs = uval;
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:344:41: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_ProbePairs = uval;
                                                           ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:346:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_HitStartPosition = uval;
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:346:47: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_HitStartPosition = uval;
                                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:350:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_NumberHits = uval;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:350:40: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                m_SequenceItems[iSeq].m_NumberHits = uval;
                                                   ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:354:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_GroupName);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:355:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_SeqVersion);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:358:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_Parameters.resize(uval);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:361:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:361:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:362:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:362:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:376:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  instr.seekg(m_SequenceItems[iSeq].m_HitStartPosition);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:378:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:378:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:382:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:382:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:383:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:423:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:425:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_pHits = NULL;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:426:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int offset = m_SequenceItems[iSeq].m_NumberHits * hitSize;
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:507:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        m_lpFileMap = mmap(NULL, m_MapLen, PROT_READ, MAP_SHARED, fileno(m_fp), 0);
                      ˜˜˜˜       ^˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:525:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_bMapped = true;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:526:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_lpData = m_lpData + m_SequenceItems[iSeq].m_HitStartPosition;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:526:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_lpData = m_lpData + m_SequenceItems[iSeq].m_HitStartPosition;
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:370:16: warning: unused variable 'probeIn' [-Wunused-variable]
        unsigned char probeIn[PROBE_STORAGE_BUFFER_LENGTH]="";
                      ^
fusion_sdk/file/BPMAPFileData.cpp:371:7: warning: unused variable 'probeOut' [-Wunused-variable]
        char probeOut[probeBufSize]="";
             ^
fusion_sdk/file/BPMAPFileData.cpp:383:48: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                  m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
                                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:503:17: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                m_MapLen = st.st_size;
                         ˜ ˜˜˜^˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:538:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        seq.MakeShallowCopy(m_SequenceItems[index]);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:584:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          hit = (*m_pHits)[index];
                ˜          ^˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:639:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          return m_Parameters[index];
                 ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
39 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
In file included from fusion_sdk/file/BPMAPFileWriter.cpp:21:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:216:55: warning: implicit conversion loses integer precision: 'unsigned int' to 'char' [-Wconversion]
        packedSequence[i] = ((packedSequence[i] << 2) | base);
                          ˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:216:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        packedSequence[i] = ((packedSequence[i] << 2) | base);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜  ˜
fusion_sdk/file/BPMAPFileWriter.cpp:222:45: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
      packedSequence[i] = packedSequence[i] << 2*(4-k);
                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:297:21: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
  hit.ProbeLength = (int)sequence.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:622:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
            WriteUInt32_N(of, (*i).m_ProbePairsValue);// 2.3
            ˜˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:661:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
            WriteUInt32_N(of, (*i).m_HitStartPosition);   // 2.4 fixup
            ˜˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:638:32: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
            (*i).m_HitStartPosition = of.tellp();
                                    ˜ ^˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
In file included from fusion_sdk/file/FileIO.cpp:38:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/file/FileIO.cpp:39:
fusion_sdk/util/Convert.h:63:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/file/FileIO.cpp:40:
fusion_sdk/util/Err.h:91:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int size = getParam().m_ErrHandlers.size();
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Err.h:114:26: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int count = getParam().m_ErrHandlers.size();
                 ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:265:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(line,0,len);
        ˜˜˜˜˜˜        ^˜˜
fusion_sdk/file/FileIO.cpp:297:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
  return MmGetUInt32_I((uint32_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:302:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
  return MmGetUInt16_I((uint16_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:307:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
  return MmGetUInt32_N((uint32_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:312:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
  return MmGetUInt16_N((uint16_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:317:10: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
  return MmGetUInt8((uint8_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
In file included from fusion_sdk/file/FileWriter.cpp:37:
In file included from fusion_sdk/file/FileWriter.h:29:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileWriter.cpp:174:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        WriteFixedString(outstr, str, len);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜              ^˜˜
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_parseBPMAP.cpp -o R_affx_parseBPMAP.o
R_affx_parseBPMAP.cpp:276:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        TMPStart = seqHit.getStartPosition();
                                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_parseBPMAP.cpp:291:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        bd[NPROBES].pmx = seqHit.PMX;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_parseBPMAP.cpp:292:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        bd[NPROBES].pmy = seqHit.PMY;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_parseBPMAP.cpp:293:44: warning: format string contains '\0' within the string body [-Wformat]
                        snprintf(bd[NPROBES].chr, sizeCHR+1, "%s\0", (char*)seq.FullName().c_str());
                                                             ˜˜˜^˜˜
R_affx_parseBPMAP.cpp:295:50: warning: format string contains '\0' within the string body [-Wformat]
                                snprintf(bd[NPROBES].sequence, sizeSEQ+1, "%s\0", seqHit.PMProbe.c_str());
                                                                          ˜˜˜^˜˜
R_affx_parseBPMAP.cpp:367:23: warning: format string contains '\0' within the string body [-Wformat]
                        sprintf(TMP, "%s-%i\0", bd[i].chr, bd[i].start);
                                     ˜˜˜˜˜˜^˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp:10:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o AffyTiling.so fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_parseBPMAP.o AnnotateProbes.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -f fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_parseBPMAP.o AnnotateProbes.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
In file included from fusion_sdk/file/BPMAPFileData.cpp:21:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:123:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        munmap(m_lpFileMap, m_MapLen);
                        ˜˜˜˜˜˜              ^˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:300:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        m_NumberSequences = uval;
                          ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:304:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        m_SequenceItems.resize(m_NumberSequences);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:307:24: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        m_DataStartPosition = instr.tellg();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:339:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Name);
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:344:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_ProbePairs = uval;
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:344:41: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_ProbePairs = uval;
                                                           ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:346:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_HitStartPosition = uval;
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:346:47: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_HitStartPosition = uval;
                                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:350:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_NumberHits = uval;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:350:40: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                m_SequenceItems[iSeq].m_NumberHits = uval;
                                                   ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:354:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_GroupName);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:355:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_SeqVersion);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:358:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_Parameters.resize(uval);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:361:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:361:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:362:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:362:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:376:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  instr.seekg(m_SequenceItems[iSeq].m_HitStartPosition);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:378:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:378:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:382:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:382:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:383:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:423:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:425:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_pHits = NULL;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:426:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int offset = m_SequenceItems[iSeq].m_NumberHits * hitSize;
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:507:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        m_lpFileMap = mmap(NULL, m_MapLen, PROT_READ, MAP_SHARED, fileno(m_fp), 0);
                      ˜˜˜˜       ^˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:525:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_bMapped = true;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:526:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_lpData = m_lpData + m_SequenceItems[iSeq].m_HitStartPosition;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:526:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_lpData = m_lpData + m_SequenceItems[iSeq].m_HitStartPosition;
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:370:16: warning: unused variable 'probeIn' [-Wunused-variable]
        unsigned char probeIn[PROBE_STORAGE_BUFFER_LENGTH]="";
                      ^
fusion_sdk/file/BPMAPFileData.cpp:371:7: warning: unused variable 'probeOut' [-Wunused-variable]
        char probeOut[probeBufSize]="";
             ^
fusion_sdk/file/BPMAPFileData.cpp:383:48: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                  m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
                                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:503:17: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                m_MapLen = st.st_size;
                         ˜ ˜˜˜^˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:538:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        seq.MakeShallowCopy(m_SequenceItems[index]);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:584:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          hit = (*m_pHits)[index];
                ˜          ^˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:639:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          return m_Parameters[index];
                 ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
39 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
In file included from fusion_sdk/file/BPMAPFileWriter.cpp:21:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:216:55: warning: implicit conversion loses integer precision: 'unsigned int' to 'char' [-Wconversion]
        packedSequence[i] = ((packedSequence[i] << 2) | base);
                          ˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:216:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        packedSequence[i] = ((packedSequence[i] << 2) | base);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜  ˜
fusion_sdk/file/BPMAPFileWriter.cpp:222:45: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
      packedSequence[i] = packedSequence[i] << 2*(4-k);
                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:297:21: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
  hit.ProbeLength = (int)sequence.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:622:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
            WriteUInt32_N(of, (*i).m_ProbePairsValue);// 2.3
            ˜˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:661:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
            WriteUInt32_N(of, (*i).m_HitStartPosition);   // 2.4 fixup
            ˜˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:638:32: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
            (*i).m_HitStartPosition = of.tellp();
                                    ˜ ^˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
In file included from fusion_sdk/file/FileIO.cpp:38:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/file/FileIO.cpp:39:
fusion_sdk/util/Convert.h:63:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/file/FileIO.cpp:40:
fusion_sdk/util/Err.h:91:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int size = getParam().m_ErrHandlers.size();
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Err.h:114:26: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int count = getParam().m_ErrHandlers.size();
                 ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:265:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(line,0,len);
        ˜˜˜˜˜˜        ^˜˜
fusion_sdk/file/FileIO.cpp:297:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
  return MmGetUInt32_I((uint32_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:302:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
  return MmGetUInt16_I((uint16_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:307:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
  return MmGetUInt32_N((uint32_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:312:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
  return MmGetUInt16_N((uint16_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:317:10: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
  return MmGetUInt8((uint8_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
In file included from fusion_sdk/file/FileWriter.cpp:37:
In file included from fusion_sdk/file/FileWriter.h:29:
fusion_sdk/file/FileIO.h:65:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileWriter.cpp:174:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        WriteFixedString(outstr, str, len);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜              ^˜˜
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_parseBPMAP.cpp -o R_affx_parseBPMAP.o
R_affx_parseBPMAP.cpp:276:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        TMPStart = seqHit.getStartPosition();
                                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_parseBPMAP.cpp:291:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        bd[NPROBES].pmx = seqHit.PMX;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_parseBPMAP.cpp:292:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        bd[NPROBES].pmy = seqHit.PMY;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_parseBPMAP.cpp:293:44: warning: format string contains '\0' within the string body [-Wformat]
                        snprintf(bd[NPROBES].chr, sizeCHR+1, "%s\0", (char*)seq.FullName().c_str());
                                                             ˜˜˜^˜˜
R_affx_parseBPMAP.cpp:295:50: warning: format string contains '\0' within the string body [-Wformat]
                                snprintf(bd[NPROBES].sequence, sizeSEQ+1, "%s\0", seqHit.PMProbe.c_str());
                                                                          ˜˜˜^˜˜
R_affx_parseBPMAP.cpp:367:23: warning: format string contains '\0' within the string body [-Wformat]
                        sprintf(TMP, "%s-%i\0", bd[i].chr, bd[i].start);
                                     ˜˜˜˜˜˜^˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -imacros R_affx_constants.h -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/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp:10:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
installing to /Users/biocbuild/bbs-2.12-bioc/meat/AffyTiling.Rcheck/AffyTiling/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AffyTiling)

AffyTiling.Rcheck/AffyTiling-Ex.timings:

nameusersystemelapsed
AnalyzeTilingCelFiles0.0160.0020.020
AssociateWithGenes0.2600.0130.283
AssociateWithInterval0.0510.0020.054
TilingCelFiles2Probesets0.0340.0010.036
parseBPMAP0.0240.0020.027