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 ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=AffyTiling.buildbin-libdir AffyTiling_1.18.0.tar.gz'
>>>>>>>
* 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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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);
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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 -g -O2 -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();
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R_affx_parseBPMAP.cpp:291:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
bd[NPROBES].pmx = seqHit.PMX;
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R_affx_parseBPMAP.cpp:292:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
bd[NPROBES].pmy = seqHit.PMY;
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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());
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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());
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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);
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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 -g -O2 -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
installing to /Users/biocbuild/bbs-2.12-bioc/meat/AffyTiling.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR AffyTiling.buildbin-libdir/AffyTiling/libs//AffyTiling.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "AffyTiling.buildbin-libdir/AffyTiling/libs//AffyTiling.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "AffyTiling.buildbin-libdir/AffyTiling/libs//AffyTiling.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "AffyTiling.buildbin-libdir/AffyTiling/libs//AffyTiling.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "AffyTiling.buildbin-libdir/AffyTiling/libs//AffyTiling.so"