rTANDEM 1.10.0
Frederic Fournier
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rTANDEM | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rTANDEM_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rTANDEM.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rTANDEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rTANDEM’ version ‘1.10.0’
* 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 ‘rTANDEM’ can be installed ... [112s/112s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘Rcpp’ ‘XML’ ‘data.table’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetParamFromXML: no visible global function definition for
‘xmlTreeParse’
GetParamFromXML: no visible global function definition for ‘xmlRoot’
GetParamFromXML: no visible global function definition for
‘xmlChildren’
GetParamFromXML: no visible global function definition for ‘xmlName’
GetParamFromXML: no visible global function definition for ‘xmlAttrs’
GetParamFromXML: no visible global function definition for ‘xmlValue’
GetPeptides: no visible global function definition for ‘setnames’
GetProteins: no visible global function definition for ‘setkey’
GetResultsFromXML: no visible global function definition for
‘data.table’
GetResultsFromXML : protein: no visible global function definition for
‘data.table’
GetResultsFromXML : protein: no visible global function definition for
‘rbindlist’
GetResultsFromXML : protein: no visible global function definition for
‘set’
GetResultsFromXML : file: no visible global function definition for
‘set’
GetResultsFromXML : domain: no visible global function definition for
‘set’
GetResultsFromXML : domain: no visible global function definition for
‘data.table’
GetResultsFromXML : domain: no visible global function definition for
‘rbindlist’
GetResultsFromXML : aa: no visible global function definition for
‘data.table’
GetResultsFromXML : aa: no visible global function definition for
‘rbindlist’
GetResultsFromXML : aa: no visible global function definition for ‘set’
GetResultsFromXML : trace: no visible global function definition for
‘data.table’
GetResultsFromXML : trace: no visible global function definition for
‘rbindlist’
GetResultsFromXML : trace: no visible global function definition for
‘xmlChildren’
GetResultsFromXML : trace: no visible global function definition for
‘xmlGetAttr’
GetResultsFromXML : trace: no visible global function definition for
‘xmlValue’
GetResultsFromXML : trace: no visible global function definition for
‘set’
GetResultsFromXML : trace: no visible global function definition for
‘xmlAttrs’
GetResultsFromXML : note: no visible global function definition for
‘xmlAttrs’
GetResultsFromXML : note: no visible global function definition for
‘xmlValue’
GetResultsFromXML : note: no visible global function definition for
‘set’
GetResultsFromXML: no visible global function definition for
‘xmlEventParse’
GetResultsFromXML: no visible global function definition for ‘setkey’
GetResultsFromXML: no visible global function definition for ‘set’
GetTaxoFromXML: no visible global function definition for
‘xmlTreeParse’
GetTaxoFromXML: no visible global function definition for ‘getNodeSet’
GetTaxoFromXML: no visible global function definition for ‘xmlRoot’
GetTaxoFromXML: no visible global function definition for ‘xmlChildren’
GetTaxoFromXML: no visible global function definition for ‘xmlName’
GetTaxoFromXML: no visible global function definition for ‘xmlAttrs’
WriteParamToXML: no visible global function definition for ‘xmlNode’
WriteParamToXML: no visible global function definition for
‘addChildren’
WriteParamToXML: no visible global function definition for ‘saveXML’
WriteTaxoToXML: no visible global function definition for ‘xmlNode’
WriteTaxoToXML: no visible global function definition for ‘addChildren’
WriteTaxoToXML: no visible global function definition for ‘saveXML’
getParamFromXML: no visible global function definition for
‘xmlTreeParse’
getParamFromXML: no visible global function definition for ‘xmlRoot’
getParamFromXML: no visible global function definition for
‘xmlChildren’
getParamFromXML: no visible global function definition for ‘xmlName’
getParamFromXML: no visible global function definition for ‘xmlAttrs’
getParamFromXML: no visible global function definition for ‘xmlValue’
getPeptides: no visible global function definition for ‘setnames’
getProteins: no visible global function definition for ‘setkey’
getResultsFromXML: no visible global function definition for
‘data.table’
getResultsFromXML : protein: no visible global function definition for
‘data.table’
getResultsFromXML : protein: no visible global function definition for
‘rbindlist’
getResultsFromXML : protein: no visible global function definition for
‘set’
getResultsFromXML : file: no visible global function definition for
‘set’
getResultsFromXML : domain: no visible global function definition for
‘set’
getResultsFromXML : domain: no visible global function definition for
‘data.table’
getResultsFromXML : domain: no visible global function definition for
‘rbindlist’
getResultsFromXML : aa: no visible global function definition for
‘data.table’
getResultsFromXML : aa: no visible global function definition for
‘rbindlist’
getResultsFromXML : aa: no visible global function definition for ‘set’
getResultsFromXML : trace: no visible global function definition for
‘data.table’
getResultsFromXML : trace: no visible global function definition for
‘rbindlist’
getResultsFromXML : trace: no visible global function definition for
‘xmlChildren’
getResultsFromXML : trace: no visible global function definition for
‘xmlGetAttr’
getResultsFromXML : trace: no visible global function definition for
‘xmlValue’
getResultsFromXML : trace: no visible global function definition for
‘set’
getResultsFromXML : trace: no visible global function definition for
‘xmlAttrs’
getResultsFromXML : note: no visible global function definition for
‘xmlAttrs’
getResultsFromXML : note: no visible global function definition for
‘xmlValue’
getResultsFromXML : note: no visible global function definition for
‘set’
getResultsFromXML: no visible global function definition for
‘xmlEventParse’
getResultsFromXML: no visible global function definition for ‘setkey’
getResultsFromXML: no visible global function definition for ‘set’
getTaxoFromXML: no visible global function definition for
‘xmlTreeParse’
getTaxoFromXML: no visible global function definition for ‘getNodeSet’
getTaxoFromXML: no visible global function definition for ‘xmlRoot’
getTaxoFromXML: no visible global function definition for ‘xmlChildren’
getTaxoFromXML: no visible global function definition for ‘xmlName’
getTaxoFromXML: no visible global function definition for ‘xmlAttrs’
writeParamToXML: no visible global function definition for ‘xmlNode’
writeParamToXML: no visible global function definition for
‘addChildren’
writeParamToXML: no visible global function definition for ‘saveXML’
writeTaxoToXML: no visible global function definition for ‘xmlNode’
writeTaxoToXML: no visible global function definition for ‘addChildren’
writeTaxoToXML: no visible global function definition for ‘saveXML’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘rTANDEM/libs/rTANDEM.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘mreport.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Object: ‘mreport.o’
File ‘rTANDEM/libs/rTANDEM.so’:
Found non-API call to R: ‘R_CStackLimit’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.
* installing *source* package ‘rTANDEM’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from PTMTreeSearch.cpp:14:
In file included from ./PTMTreeSearch.h:16:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
PTMTreeSearch.cpp:382:12: warning: unused variable 'dMaxExpect' [-Wunused-variable]
double dMaxExpect = atof(strValue.c_str());
^
PTMTreeSearch.cpp:402:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:403:21: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:405:24: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:406:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:407:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:408:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:409:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
^˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
size_t tActiveNow = 0;
^
PTMTreeSearch.cpp:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
double dMaxExpect = 0.1;
^
PTMTreeSearch.cpp:751:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[resid].push_back(mod);
^˜˜˜˜˜
PTMTreeSearch.cpp:875:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[resid].push_back(mod);
^˜˜˜˜˜
PTMTreeSearch.cpp:1003:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (pos = m_strResidues.find(',')>m_strResidues.npos){
˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:1003:18: note: place parentheses around the assignment to silence this warning
while (pos = m_strResidues.find(',')>m_strResidues.npos){
^
( )
PTMTreeSearch.cpp:1003:18: note: use '==' to turn this assignment into an equality comparison
while (pos = m_strResidues.find(',')>m_strResidues.npos){
^
==
PTMTreeSearch.cpp:1006:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (pos = m_strResidues.find(' ')>m_strResidues.npos){
˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:1006:18: note: place parentheses around the assignment to silence this warning
while (pos = m_strResidues.find(' ')>m_strResidues.npos){
^
( )
PTMTreeSearch.cpp:1006:18: note: use '==' to turn this assignment into an equality comparison
while (pos = m_strResidues.find(' ')>m_strResidues.npos){
^
==
PTMTreeSearch.cpp:1018:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[resid].push_back(mod);
^˜˜˜˜˜
PTMTreeSearch.cpp:1170:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_vmodModificationsDB[resid].push_back(mod);
^˜˜˜˜˜
PTMTreeSearch.cpp:1156:10: warning: unused variable 'pos' [-Wunused-variable]
size_t pos = 0;
^
18 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
In file included from PTMTreeSearchScore.cpp:13:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
PTMTreeSearchScore.cpp:369:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:373:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:528:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:568:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:587:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:195:8: warning: unused variable 'active' [-Wunused-variable]
bool active;
^
PTMTreeSearchScore.cpp:193:9: warning: unused variable 'fMaxIntens' [-Wunused-variable]
float fMaxIntens = 0;
^
PTMTreeSearchScore.cpp:309:16: warning: unused variable 'ScoreOffset' [-Wunused-variable]
unsigned int ScoreOffset;
^
PTMTreeSearchScore.cpp:624:16: warning: unused variable 'lValue' [-Wunused-variable]
unsigned long lValue = 0;
^
PTMTreeSearchScore.cpp:871:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
^˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:895:49: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[0] += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:897:52: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[0] += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:903:49: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
^˜˜
PTMTreeSearchScore.cpp:903:85: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
^˜˜
PTMTreeSearchScore.cpp:905:53: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
^˜˜
PTMTreeSearchScore.cpp:921:49: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:923:52: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:952:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:954:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:1029:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:1031:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:1068:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
^˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:1116:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:1118:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
PTMTreeSearchScore.cpp:1157:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
^˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:1183:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:1185:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:1199:8: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
PTMTreeSearchScore.cpp:1259:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:1261:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:1264:1: warning: '/*' within block comment [-Wcomment]
/*
^
PTMTreeSearchScore.cpp:1305:47: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:1314:46: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:1271:8: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
PTMTreeSearchScore.cpp:1362:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:1364:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
PTMTreeSearchScore.cpp:1366:1: warning: '/*' within block comment [-Wcomment]
/*
^
PTMTreeSearchScore.cpp:1405:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearchScore.cpp:1374:8: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
40 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c base64.cpp -o base64.o
base64.cpp:11:28: warning: unused variable 'b64_pad' [-Wunused-const-variable]
static const unsigned char b64_pad = '=';
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c dataLoader.cpp -o dataLoader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c loadmspectrum.cpp -o loadmspectrum.o
In file included from loadmspectrum.cpp:142:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c masscalc.cpp -o masscalc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mbiomlreport.cpp -o mbiomlreport.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mpam.cpp -o mpam.o
In file included from mpam.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mplugin.cpp -o mplugin.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mpmods.cpp -o mpmods.o
In file included from mpmods.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mprocess.cpp -o mprocess.o
In file included from mprocess.cpp:157:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
bool bC = false;
^
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
size_t tLast = 0;
^
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
size_t c = 0;
^
mprocess.cpp:3253:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dNt = m_pScore->m_seqUtil.m_pdAaMod['['];
^˜˜˜
mprocess.cpp:3254:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dNtAve = m_pScore->m_seqUtilAvg.m_pdAaMod['['];
^˜˜˜
mprocess.cpp:3255:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dNg = m_pScore->m_seqUtil.m_pdAaMod['n'];
^˜˜˜
mprocess.cpp:3256:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dNgAve = m_pScore->m_seqUtilAvg.m_pdAaMod['n'];
^˜˜˜
mprocess.cpp:3342:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = dAcetyl;
^˜˜˜
mprocess.cpp:3343:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = dAcetylAve;
^˜˜˜
mprocess.cpp:3352:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = dAcetyl;
^˜˜˜
mprocess.cpp:3353:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = dAcetylAve;
^˜˜˜
mprocess.cpp:3360:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
^˜˜˜
mprocess.cpp:3361:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
^˜˜˜
mprocess.cpp:3366:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['n'] = dDeamidate;
^˜˜˜
mprocess.cpp:3367:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = dDeamidateAve;
^˜˜˜
mprocess.cpp:3390:46: warning: '&&' within '||' [-Wlogical-op-parentheses]
if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
mprocess.cpp:3390:46: note: place parentheses around the '&&' expression to silence this warning
if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
^
( )
mprocess.cpp:3403:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['n'] = m_dNg;
^˜˜˜
mprocess.cpp:3404:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = m_dNgAve;
^˜˜˜
mprocess.cpp:3415:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
^˜˜˜
mprocess.cpp:3416:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
^˜˜˜
mprocess.cpp:3427:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = dAcetyl;
^˜˜˜
mprocess.cpp:3428:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = dAcetylAve;
^˜˜˜
mprocess.cpp:3436:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['n'] = dDeamidate;
^˜˜˜
mprocess.cpp:3437:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = dDeamidateAve;
^˜˜˜
mprocess.cpp:3459:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
^˜˜˜
mprocess.cpp:3460:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
^˜˜˜
mprocess.cpp:3462:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['n'] = m_dNg;
^˜˜˜
mprocess.cpp:3463:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = m_dNgAve;
^˜˜˜
mprocess.cpp:3520:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_pScore->m_seqUtil.m_pdAaMod['['] != 0.0 || !m_bQuickPyro) {
^˜˜˜
mprocess.cpp:3526:32: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_pyroState.m_dModMass;
^˜˜˜
mprocess.cpp:3527:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = -1.0*m_pScore->m_seqUtilAvg.m_dAmmonia;
^˜˜˜
mprocess.cpp:3537:32: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_pyroState.m_dModMass;
^˜˜˜
mprocess.cpp:3538:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = -1.0*m_pScore->m_seqUtilAvg.m_dWater;
^˜˜˜
mprocess.cpp:3546:63: warning: array subscript is of type 'char' [-Wchar-subscripts]
else if(_c == 'C' && (long)(m_pScore->m_seqUtil.m_pdAaFullMod['C']) == 57) {
^˜˜˜
mprocess.cpp:3548:32: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_pyroState.m_dModMass;
^˜˜˜
mprocess.cpp:3549:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = -1.0*m_pScore->m_seqUtilAvg.m_dAmmonia;
^˜˜˜
mprocess.cpp:3567:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
^˜˜˜
mprocess.cpp:3568:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
^˜˜˜
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
uint64_t crc = INITIALCRC, part = 0;
^
40 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mrefine.cpp -o mrefine.o
In file included from mrefine.cpp:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mrefine.cpp:334:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pProcess->m_pScore->m_seqUtil.m_pdAaMod['['] = 0.0;
^˜˜˜
mrefine.cpp:355:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pProcess->m_pScore->m_seqUtil.m_pdAaMod[']'] = 0.0;
^˜˜˜
mrefine.cpp:250:9: warning: unused variable 'a' [-Wunused-variable]
size_t a = 0;
^
mrefine.cpp:251:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
size_t tActiveNow = 0;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mreport.cpp -o mreport.o
In file included from mreport.cpp:143:
In file included from ./saxsaphandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mreport.cpp:655:74: warning: array subscript is of type 'char' [-Wchar-subscripts]
sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
^˜˜˜
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
size_t a = 0;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mscore.cpp -o mscore.o
In file included from mscore.cpp:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mscore.cpp:301:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:303:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore.cpp:372:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:374:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore.cpp:450:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:452:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore.cpp:514:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:516:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore.cpp:586:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:588:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore.cpp:678:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:680:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore.cpp:867:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:867:64: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:994:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(a == '[' && m_seqUtil.m_pdAaFullMod['['] != 0.0) {
^˜˜˜
mscore.cpp:997:51: warning: array subscript is of type 'char' [-Wchar-subscripts]
aaValue.m_dMod = (float)m_seqUtil.m_pdAaFullMod['['];
^˜˜˜
mscore.cpp:1001:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(a == ']' && m_seqUtil.m_pdAaFullMod[']'] != 0.0) {
^˜˜˜
mscore.cpp:1004:51: warning: array subscript is of type 'char' [-Wchar-subscripts]
aaValue.m_dMod = (float)m_seqUtil.m_pdAaFullMod[']'];
^˜˜˜
mscore.cpp:1244:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1244:65: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1245:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:1246:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:1259:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:1272:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:1287:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:1288:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1288:66: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1293:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:1294:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:1306:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore.cpp:1307:47: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_pSeqUtilFrag->m_pdAaMod['['],m_pSeqUtilFrag->m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1307:78: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_pSeqUtilFrag->m_pdAaMod['['],m_pSeqUtilFrag->m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1310:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore.cpp:1635:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_plAA['s'] = 0;
^˜˜˜
mscore.cpp:1636:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_plAA['t'] = 0;
^˜˜˜
mscore.cpp:1637:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_plAA['n'] = 0;
^˜˜˜
mscore.cpp:1638:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_plAA['q'] = 0;
^˜˜˜
mscore.cpp:1639:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_plAA['y'] = 0;
^˜˜˜
mscore.cpp:1650:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
^˜˜˜
mscore.cpp:1650:50: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
^˜˜˜
mscore.cpp:1650:64: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
^˜˜˜
mscore.cpp:1650:83: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
^˜˜˜
mscore.cpp:1650:97: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
^˜˜˜
mscore.cpp:1912:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1912:64: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
^˜˜˜
mscore.cpp:1951:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_seqUtil.m_pdAaMod['['];
^˜˜˜
mscore.cpp:1954:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_seqUtil.m_pdAaMod[']'];
^˜˜˜
mscore.cpp:1963:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_seqUtil.m_pdAaFullMod['['];
^˜˜˜
mscore.cpp:1964:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_dSeqMH += m_seqUtil.m_pdAaFullMod[']'];
^˜˜˜
50 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mscore_hrk.cpp:24:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mscore_hrk.cpp:352:7: warning: unused variable 'iTotI' [-Wunused-variable]
int iTotI = 0;
^
mscore_hrk.cpp:371:7: warning: unused variable 'peakCount' [-Wunused-variable]
int peakCount = 0;
^
mscore_hrk.cpp:544:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_Term.m_lN) dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore_hrk.cpp:545:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore_hrk.cpp:550:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfAScore;
^
mscore_hrk.cpp:580:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_Term.m_lN) dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore_hrk.cpp:581:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore_hrk.cpp:587:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
^
mscore_hrk.cpp:588:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
^
mscore_hrk.cpp:615:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_Term.m_lN) dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore_hrk.cpp:616:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore_hrk.cpp:623:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
^
mscore_hrk.cpp:622:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
^
mscore_hrk.cpp:648:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_Term.m_lC) dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore_hrk.cpp:649:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore_hrk.cpp:657:9: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
mscore_hrk.cpp:658:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfXScore;
^
mscore_hrk.cpp:685:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_Term.m_lC) dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore_hrk.cpp:686:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore_hrk.cpp:693:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
^
mscore_hrk.cpp:692:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
^
mscore_hrk.cpp:691:9: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
mscore_hrk.cpp:729:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(m_Term.m_lC) dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore_hrk.cpp:730:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore_hrk.cpp:735:9: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
mscore_hrk.cpp:737:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
^
mscore_hrk.cpp:736:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
^
mscore_hrk.cpp:760:8: warning: unused variable 'lType' [-Wunused-variable]
long lType = 0;
^
mscore_hrk.cpp:761:10: warning: unused variable 'b' [-Wunused-variable]
size_t b = 0;
^
mscore_hrk.cpp:758:17: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 0;
^
mscore_hrk.cpp:759:17: warning: unused variable 'lCount' [-Wunused-variable]
unsigned long lCount = 0;
^
32 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mscore_k.cpp -o mscore_k.o
In file included from mscore_k.cpp:24:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mscore_k.cpp:379:15: warning: unused variable 'lCount' [-Wunused-variable]
unsigned long lCount = 0;
^
mscore_k.cpp:381:8: warning: unused variable 'b' [-Wunused-variable]
size_t b = 0;
^
mscore_k.cpp:378:15: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 0;
^
mscore_k.cpp:380:6: warning: unused variable 'lType' [-Wunused-variable]
long lType = 0;
^
mscore_k.cpp:449:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore_k.cpp:451:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore_k.cpp:466:14: warning: unused variable 'dZ' [-Wunused-variable]
const double dZ = (double)_c;
^
mscore_k.cpp:505:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore_k.cpp:507:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore_k.cpp:529:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
^˜˜˜˜˜˜˜˜˜˜˜
mscore_k.cpp:523:14: warning: unused variable 'dZ' [-Wunused-variable]
const double dZ = (double)_c;
^
mscore_k.cpp:567:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
^˜˜˜
mscore_k.cpp:569:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
^˜˜˜
mscore_k.cpp:591:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
^˜˜˜˜˜˜˜˜˜˜˜
mscore_k.cpp:584:8: warning: unused variable 'dZ' [-Wunused-variable]
double dZ = (double)_c;
^
mscore_k.cpp:615:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore_k.cpp:617:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore_k.cpp:638:8: warning: unused variable 'dZ' [-Wunused-variable]
double dZ = (double)_c;
^
mscore_k.cpp:631:7: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
mscore_k.cpp:673:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore_k.cpp:675:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore_k.cpp:677:1: warning: '/*' within block comment [-Wcomment]
/*
^
mscore_k.cpp:706:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
mscore_k.cpp:712:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
mscore_k.cpp:694:8: warning: unused variable 'dZ' [-Wunused-variable]
double dZ = (double)_c;
^
mscore_k.cpp:684:7: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
mscore_k.cpp:749:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
^˜˜˜
mscore_k.cpp:751:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
^˜˜˜
mscore_k.cpp:753:1: warning: '/*' within block comment [-Wcomment]
/*
^
mscore_k.cpp:776:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
mscore_k.cpp:779:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
^˜˜˜˜˜˜˜˜˜˜˜
mscore_k.cpp:761:7: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
33 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mscore_tandem.cpp:135:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
mscore_tandem.cpp:362:9: warning: unused variable 'b' [-Wunused-variable]
size_t b = 0;
^
mscore_tandem.cpp:358:8: warning: unused variable 'fValue0' [-Wunused-variable]
float fValue0 = 0.0;
^
mscore_tandem.cpp:581:16: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 0;
^
mscore_tandem.cpp:583:7: warning: unused variable 'lType' [-Wunused-variable]
long lType = 0;
^
mscore_tandem.cpp:582:16: warning: unused variable 'lCount' [-Wunused-variable]
unsigned long lCount = 0;
^
mscore_tandem.cpp:584:9: warning: unused variable 'b' [-Wunused-variable]
size_t b = 0;
^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c msequencecollection.cpp -o msequencecollection.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c msequenceserver.cpp -o msequenceserver.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c msequtilities.cpp -o msequtilities.o
msequtilities.cpp:336:15: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pdAaFullMod[']'] = 0.0;
^˜˜˜
msequtilities.cpp:337:15: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pdAaFullMod['['] = 0.0;
^˜˜˜
msequtilities.cpp:384:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pdAaMod['['] = 0.0;
^˜˜˜
msequtilities.cpp:385:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pdAaMod[']'] = 0.0;
^˜˜˜
msequtilities.cpp:443:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pdAaMod['['] = 0.0;
^˜˜˜
msequtilities.cpp:444:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pdAaMod[']'] = 0.0;
^˜˜˜
msequtilities.cpp:488:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(fabs(m_pdAaMod['t']-79.966331) < 0.1) {
^˜˜˜
msequtilities.cpp:492:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(fabs(m_pdAaMod['s']-79.966331) < 0.1) {
^˜˜˜
msequtilities.cpp:496:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
if(fabs(m_pdAaMod['y']-79.966331) < 0.1) {
^˜˜˜
msequtilities.cpp:615:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['a'] = pdValue['A'] = m_calc.calcMass("C3H5ON");
^˜˜˜
msequtilities.cpp:615:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['a'] = pdValue['A'] = m_calc.calcMass("C3H5ON");
^˜˜˜
msequtilities.cpp:616:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['a'] = pValue['A'] = (float)pdValue['A'];
^˜˜˜
msequtilities.cpp:616:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['a'] = pValue['A'] = (float)pdValue['A'];
^˜˜˜
msequtilities.cpp:616:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['a'] = pValue['A'] = (float)pdValue['A'];
^˜˜˜
msequtilities.cpp:618:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['b'] = pdValue['B'] = m_calc.calcMass("C4H6O2N2"); // Same as N
^˜˜˜
msequtilities.cpp:618:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['b'] = pdValue['B'] = m_calc.calcMass("C4H6O2N2"); // Same as N
^˜˜˜
msequtilities.cpp:619:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:619:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:619:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:621:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['c'] = pdValue['C'] = m_calc.calcMass("C3H5ONS");
^˜˜˜
msequtilities.cpp:621:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['c'] = pdValue['C'] = m_calc.calcMass("C3H5ONS");
^˜˜˜
msequtilities.cpp:622:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['c'] = pValue['C'] = (float)pdValue['C'];
^˜˜˜
msequtilities.cpp:622:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['c'] = pValue['C'] = (float)pdValue['C'];
^˜˜˜
msequtilities.cpp:622:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['c'] = pValue['C'] = (float)pdValue['C'];
^˜˜˜
msequtilities.cpp:624:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['d'] = pdValue['D'] = m_calc.calcMass("C4H5O3N");
^˜˜˜
msequtilities.cpp:624:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['d'] = pdValue['D'] = m_calc.calcMass("C4H5O3N");
^˜˜˜
msequtilities.cpp:625:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['d'] = pValue['D'] = (float)pdValue['D'];
^˜˜˜
msequtilities.cpp:625:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['d'] = pValue['D'] = (float)pdValue['D'];
^˜˜˜
msequtilities.cpp:625:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['d'] = pValue['D'] = (float)pdValue['D'];
^˜˜˜
msequtilities.cpp:627:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['e'] = pdValue['E'] = m_calc.calcMass("C5H7O3N");
^˜˜˜
msequtilities.cpp:627:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['e'] = pdValue['E'] = m_calc.calcMass("C5H7O3N");
^˜˜˜
msequtilities.cpp:628:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['e'] = pValue['E'] = (float)pdValue['E'];
^˜˜˜
msequtilities.cpp:628:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['e'] = pValue['E'] = (float)pdValue['E'];
^˜˜˜
msequtilities.cpp:628:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['e'] = pValue['E'] = (float)pdValue['E'];
^˜˜˜
msequtilities.cpp:630:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['f'] = pdValue['F'] = m_calc.calcMass("C9H9ON");
^˜˜˜
msequtilities.cpp:630:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['f'] = pdValue['F'] = m_calc.calcMass("C9H9ON");
^˜˜˜
msequtilities.cpp:631:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['f'] = pValue['F'] = (float)pdValue['F'];
^˜˜˜
msequtilities.cpp:631:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['f'] = pValue['F'] = (float)pdValue['F'];
^˜˜˜
msequtilities.cpp:631:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['f'] = pValue['F'] = (float)pdValue['F'];
^˜˜˜
msequtilities.cpp:633:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['g'] = pdValue['G'] = m_calc.calcMass("C2H3ON");
^˜˜˜
msequtilities.cpp:633:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['g'] = pdValue['G'] = m_calc.calcMass("C2H3ON");
^˜˜˜
msequtilities.cpp:634:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['g'] = pValue['G'] = (float)pdValue['G'];
^˜˜˜
msequtilities.cpp:634:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['g'] = pValue['G'] = (float)pdValue['G'];
^˜˜˜
msequtilities.cpp:634:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['g'] = pValue['G'] = (float)pdValue['G'];
^˜˜˜
msequtilities.cpp:636:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['h'] = pdValue['H'] = m_calc.calcMass("C6H7ON3");
^˜˜˜
msequtilities.cpp:636:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['h'] = pdValue['H'] = m_calc.calcMass("C6H7ON3");
^˜˜˜
msequtilities.cpp:637:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['h'] = pValue['H'] = (float)pdValue['H'];
^˜˜˜
msequtilities.cpp:637:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['h'] = pValue['H'] = (float)pdValue['H'];
^˜˜˜
msequtilities.cpp:637:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['h'] = pValue['H'] = (float)pdValue['H'];
^˜˜˜
msequtilities.cpp:639:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['i'] = pdValue['I'] = m_calc.calcMass("C6H11ON");
^˜˜˜
msequtilities.cpp:639:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['i'] = pdValue['I'] = m_calc.calcMass("C6H11ON");
^˜˜˜
msequtilities.cpp:640:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['i'] = pValue['I'] = (float)pdValue['I'];
^˜˜˜
msequtilities.cpp:640:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['i'] = pValue['I'] = (float)pdValue['I'];
^˜˜˜
msequtilities.cpp:640:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['i'] = pValue['I'] = (float)pdValue['I'];
^˜˜˜
msequtilities.cpp:642:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['j'] = pdValue['J'] = 0.0;
^˜˜˜
msequtilities.cpp:642:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['j'] = pdValue['J'] = 0.0;
^˜˜˜
msequtilities.cpp:643:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['j'] = pValue['J'] = (float)pdValue['J'];
^˜˜˜
msequtilities.cpp:643:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['j'] = pValue['J'] = (float)pdValue['J'];
^˜˜˜
msequtilities.cpp:643:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['j'] = pValue['J'] = (float)pdValue['J'];
^˜˜˜
msequtilities.cpp:645:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['k'] = pdValue['K'] = m_calc.calcMass("C6H12ON2");
^˜˜˜
msequtilities.cpp:645:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['k'] = pdValue['K'] = m_calc.calcMass("C6H12ON2");
^˜˜˜
msequtilities.cpp:646:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['k'] = pValue['K'] = (float)pdValue['K'];
^˜˜˜
msequtilities.cpp:646:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['k'] = pValue['K'] = (float)pdValue['K'];
^˜˜˜
msequtilities.cpp:646:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['k'] = pValue['K'] = (float)pdValue['K'];
^˜˜˜
msequtilities.cpp:648:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['l'] = pdValue['L'] = m_calc.calcMass("C6H11ON");
^˜˜˜
msequtilities.cpp:648:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['l'] = pdValue['L'] = m_calc.calcMass("C6H11ON");
^˜˜˜
msequtilities.cpp:649:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['l'] = pValue['L'] = (float)pdValue['L'];
^˜˜˜
msequtilities.cpp:649:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['l'] = pValue['L'] = (float)pdValue['L'];
^˜˜˜
msequtilities.cpp:649:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['l'] = pValue['L'] = (float)pdValue['L'];
^˜˜˜
msequtilities.cpp:651:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['m'] = pdValue['M'] = m_calc.calcMass("C5H9ONS");
^˜˜˜
msequtilities.cpp:651:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['m'] = pdValue['M'] = m_calc.calcMass("C5H9ONS");
^˜˜˜
msequtilities.cpp:652:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['m'] = pValue['M'] = (float)pdValue['M'];
^˜˜˜
msequtilities.cpp:652:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['m'] = pValue['M'] = (float)pdValue['M'];
^˜˜˜
msequtilities.cpp:652:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['m'] = pValue['M'] = (float)pdValue['M'];
^˜˜˜
msequtilities.cpp:654:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['n'] = pdValue['N'] = m_calc.calcMass("C4H6O2N2");
^˜˜˜
msequtilities.cpp:654:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['n'] = pdValue['N'] = m_calc.calcMass("C4H6O2N2");
^˜˜˜
msequtilities.cpp:655:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['n'] = pValue['N'] = (float)pdValue['N'];
^˜˜˜
msequtilities.cpp:655:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['n'] = pValue['N'] = (float)pdValue['N'];
^˜˜˜
msequtilities.cpp:655:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['n'] = pValue['N'] = (float)pdValue['N'];
^˜˜˜
msequtilities.cpp:657:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['o'] = pdValue['O'] = m_calc.calcMass("C4H6O2N2"); // Same as N
^˜˜˜
msequtilities.cpp:657:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['o'] = pdValue['O'] = m_calc.calcMass("C4H6O2N2"); // Same as N
^˜˜˜
msequtilities.cpp:658:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['o'] = pValue['O'] = (float)pdValue['O'];
^˜˜˜
msequtilities.cpp:658:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['o'] = pValue['O'] = (float)pdValue['O'];
^˜˜˜
msequtilities.cpp:658:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['o'] = pValue['O'] = (float)pdValue['O'];
^˜˜˜
msequtilities.cpp:660:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['p'] = pdValue['P'] = m_calc.calcMass("C5H7ON");
^˜˜˜
msequtilities.cpp:660:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['p'] = pdValue['P'] = m_calc.calcMass("C5H7ON");
^˜˜˜
msequtilities.cpp:661:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['p'] = pValue['P'] = (float)pdValue['P'];
^˜˜˜
msequtilities.cpp:661:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['p'] = pValue['P'] = (float)pdValue['P'];
^˜˜˜
msequtilities.cpp:661:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['p'] = pValue['P'] = (float)pdValue['P'];
^˜˜˜
msequtilities.cpp:663:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['q'] = pdValue['Q'] = m_calc.calcMass("C5H8O2N2");
^˜˜˜
msequtilities.cpp:663:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['q'] = pdValue['Q'] = m_calc.calcMass("C5H8O2N2");
^˜˜˜
msequtilities.cpp:664:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
^˜˜˜
msequtilities.cpp:664:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
^˜˜˜
msequtilities.cpp:664:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
^˜˜˜
msequtilities.cpp:666:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['r'] = pdValue['R'] = m_calc.calcMass("C6H12ON4");
^˜˜˜
msequtilities.cpp:666:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['r'] = pdValue['R'] = m_calc.calcMass("C6H12ON4");
^˜˜˜
msequtilities.cpp:667:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['r'] = pValue['R'] = (float)pdValue['R'];
^˜˜˜
msequtilities.cpp:667:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['r'] = pValue['R'] = (float)pdValue['R'];
^˜˜˜
msequtilities.cpp:667:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['r'] = pValue['R'] = (float)pdValue['R'];
^˜˜˜
msequtilities.cpp:669:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['s'] = pdValue['S'] = m_calc.calcMass("C3H5O2N");
^˜˜˜
msequtilities.cpp:669:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['s'] = pdValue['S'] = m_calc.calcMass("C3H5O2N");
^˜˜˜
msequtilities.cpp:670:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['s'] = pValue['S'] = (float)pdValue['S'];
^˜˜˜
msequtilities.cpp:670:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['s'] = pValue['S'] = (float)pdValue['S'];
^˜˜˜
msequtilities.cpp:670:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['s'] = pValue['S'] = (float)pdValue['S'];
^˜˜˜
msequtilities.cpp:672:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['t'] = pdValue['T'] = m_calc.calcMass("C4H7O2N");
^˜˜˜
msequtilities.cpp:672:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['t'] = pdValue['T'] = m_calc.calcMass("C4H7O2N");
^˜˜˜
msequtilities.cpp:673:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['t'] = pValue['T'] = (float)pdValue['T'];
^˜˜˜
msequtilities.cpp:673:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['t'] = pValue['T'] = (float)pdValue['T'];
^˜˜˜
msequtilities.cpp:673:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['t'] = pValue['T'] = (float)pdValue['T'];
^˜˜˜
msequtilities.cpp:675:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['u'] = pdValue['U'] = m_calc.calcMass("C3H5ONSe"); // selenocysteine
^˜˜˜
msequtilities.cpp:675:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['u'] = pdValue['U'] = m_calc.calcMass("C3H5ONSe"); // selenocysteine
^˜˜˜
msequtilities.cpp:676:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['u'] = pValue['U'] = (float)pdValue['U'];
^˜˜˜
msequtilities.cpp:676:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['u'] = pValue['U'] = (float)pdValue['U'];
^˜˜˜
msequtilities.cpp:676:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['u'] = pValue['U'] = (float)pdValue['U'];
^˜˜˜
msequtilities.cpp:678:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['v'] = pdValue['V'] = m_calc.calcMass("C5H9ON");
^˜˜˜
msequtilities.cpp:678:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['v'] = pdValue['V'] = m_calc.calcMass("C5H9ON");
^˜˜˜
msequtilities.cpp:679:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['v'] = pValue['V'] = (float)pdValue['V'];
^˜˜˜
msequtilities.cpp:679:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['v'] = pValue['V'] = (float)pdValue['V'];
^˜˜˜
msequtilities.cpp:679:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['v'] = pValue['V'] = (float)pdValue['V'];
^˜˜˜
msequtilities.cpp:681:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['w'] = pdValue['W'] = m_calc.calcMass("C11H10ON2");
^˜˜˜
msequtilities.cpp:681:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['w'] = pdValue['W'] = m_calc.calcMass("C11H10ON2");
^˜˜˜
msequtilities.cpp:682:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['w'] = pValue['W'] = (float)pdValue['W'];
^˜˜˜
msequtilities.cpp:682:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['w'] = pValue['W'] = (float)pdValue['W'];
^˜˜˜
msequtilities.cpp:682:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['w'] = pValue['W'] = (float)pdValue['W'];
^˜˜˜
msequtilities.cpp:684:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['x'] = pdValue['X'] = 111.060000; // Why?
^˜˜˜
msequtilities.cpp:684:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['x'] = pdValue['X'] = 111.060000; // Why?
^˜˜˜
msequtilities.cpp:685:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['x'] = pValue['X'] = (float)pdValue['X'];
^˜˜˜
msequtilities.cpp:685:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['x'] = pValue['X'] = (float)pdValue['X'];
^˜˜˜
msequtilities.cpp:685:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['x'] = pValue['X'] = (float)pdValue['X'];
^˜˜˜
msequtilities.cpp:687:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['y'] = pdValue['Y'] = m_calc.calcMass("C9H9O2N");
^˜˜˜
msequtilities.cpp:687:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['y'] = pdValue['Y'] = m_calc.calcMass("C9H9O2N");
^˜˜˜
msequtilities.cpp:688:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
^˜˜˜
msequtilities.cpp:688:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
^˜˜˜
msequtilities.cpp:688:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
^˜˜˜
msequtilities.cpp:690:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['z'] = pdValue['Z'] = m_calc.calcMass("C5H8O2N2"); // Same as Q
^˜˜˜
msequtilities.cpp:690:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['z'] = pdValue['Z'] = m_calc.calcMass("C5H8O2N2"); // Same as Q
^˜˜˜
msequtilities.cpp:691:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
^˜˜˜
msequtilities.cpp:691:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
^˜˜˜
msequtilities.cpp:691:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
^˜˜˜
msequtilities.cpp:693:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['b'] = pdValue['B'] = m_calc.calcMass("C10H21O2N3"); // Hypusine
^˜˜˜
msequtilities.cpp:693:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['b'] = pdValue['B'] = m_calc.calcMass("C10H21O2N3"); // Hypusine
^˜˜˜
msequtilities.cpp:694:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:694:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:694:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:705:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['a'] = pdValue['A'] = 71.0788;
^˜˜˜
msequtilities.cpp:705:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['a'] = pdValue['A'] = 71.0788;
^˜˜˜
msequtilities.cpp:706:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['a'] = pValue['A'] = (float)pdValue['A'];
^˜˜˜
msequtilities.cpp:706:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['a'] = pValue['A'] = (float)pdValue['A'];
^˜˜˜
msequtilities.cpp:706:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['a'] = pValue['A'] = (float)pdValue['A'];
^˜˜˜
msequtilities.cpp:708:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['b'] = pdValue['B'] = 114.1038; // Same as N
^˜˜˜
msequtilities.cpp:708:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['b'] = pdValue['B'] = 114.1038; // Same as N
^˜˜˜
msequtilities.cpp:709:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:709:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:709:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['b'] = pValue['B'] = (float)pdValue['B'];
^˜˜˜
msequtilities.cpp:711:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['c'] = pdValue['C'] = 103.1388;
^˜˜˜
msequtilities.cpp:711:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['c'] = pdValue['C'] = 103.1388;
^˜˜˜
msequtilities.cpp:712:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['c'] = pValue['C'] = (float)pdValue['C'];
^˜˜˜
msequtilities.cpp:712:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['c'] = pValue['C'] = (float)pdValue['C'];
^˜˜˜
msequtilities.cpp:712:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['c'] = pValue['C'] = (float)pdValue['C'];
^˜˜˜
msequtilities.cpp:714:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['d'] = pdValue['D'] = 115.0886;
^˜˜˜
msequtilities.cpp:714:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['d'] = pdValue['D'] = 115.0886;
^˜˜˜
msequtilities.cpp:715:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['d'] = pValue['D'] = (float)pdValue['D'];
^˜˜˜
msequtilities.cpp:715:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['d'] = pValue['D'] = (float)pdValue['D'];
^˜˜˜
msequtilities.cpp:715:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['d'] = pValue['D'] = (float)pdValue['D'];
^˜˜˜
msequtilities.cpp:717:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['e'] = pdValue['E'] = 129.1155;
^˜˜˜
msequtilities.cpp:717:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['e'] = pdValue['E'] = 129.1155;
^˜˜˜
msequtilities.cpp:718:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['e'] = pValue['E'] = (float)pdValue['E'];
^˜˜˜
msequtilities.cpp:718:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['e'] = pValue['E'] = (float)pdValue['E'];
^˜˜˜
msequtilities.cpp:718:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['e'] = pValue['E'] = (float)pdValue['E'];
^˜˜˜
msequtilities.cpp:720:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['f'] = pdValue['F'] = 147.1766;
^˜˜˜
msequtilities.cpp:720:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['f'] = pdValue['F'] = 147.1766;
^˜˜˜
msequtilities.cpp:721:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['f'] = pValue['F'] = (float)pdValue['F'];
^˜˜˜
msequtilities.cpp:721:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['f'] = pValue['F'] = (float)pdValue['F'];
^˜˜˜
msequtilities.cpp:721:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['f'] = pValue['F'] = (float)pdValue['F'];
^˜˜˜
msequtilities.cpp:723:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['g'] = pdValue['G'] = 57.0519;
^˜˜˜
msequtilities.cpp:723:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['g'] = pdValue['G'] = 57.0519;
^˜˜˜
msequtilities.cpp:724:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['g'] = pValue['G'] = (float)pdValue['G'];
^˜˜˜
msequtilities.cpp:724:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['g'] = pValue['G'] = (float)pdValue['G'];
^˜˜˜
msequtilities.cpp:724:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['g'] = pValue['G'] = (float)pdValue['G'];
^˜˜˜
msequtilities.cpp:726:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['h'] = pdValue['H'] = 137.1411;
^˜˜˜
msequtilities.cpp:726:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['h'] = pdValue['H'] = 137.1411;
^˜˜˜
msequtilities.cpp:727:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['h'] = pValue['H'] = (float)pdValue['H'];
^˜˜˜
msequtilities.cpp:727:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['h'] = pValue['H'] = (float)pdValue['H'];
^˜˜˜
msequtilities.cpp:727:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['h'] = pValue['H'] = (float)pdValue['H'];
^˜˜˜
msequtilities.cpp:729:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['i'] = pdValue['I'] = 113.1594;
^˜˜˜
msequtilities.cpp:729:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['i'] = pdValue['I'] = 113.1594;
^˜˜˜
msequtilities.cpp:730:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['i'] = pValue['I'] = (float)pdValue['I'];
^˜˜˜
msequtilities.cpp:730:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['i'] = pValue['I'] = (float)pdValue['I'];
^˜˜˜
msequtilities.cpp:730:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['i'] = pValue['I'] = (float)pdValue['I'];
^˜˜˜
msequtilities.cpp:732:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['j'] = pdValue['J'] = 0.0;
^˜˜˜
msequtilities.cpp:732:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['j'] = pdValue['J'] = 0.0;
^˜˜˜
msequtilities.cpp:733:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['j'] = pValue['J'] = (float)pdValue['J'];
^˜˜˜
msequtilities.cpp:733:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['j'] = pValue['J'] = (float)pdValue['J'];
^˜˜˜
msequtilities.cpp:733:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['j'] = pValue['J'] = (float)pdValue['J'];
^˜˜˜
msequtilities.cpp:735:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['k'] = pdValue['K'] = 128.1741;
^˜˜˜
msequtilities.cpp:735:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['k'] = pdValue['K'] = 128.1741;
^˜˜˜
msequtilities.cpp:736:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['k'] = pValue['K'] = (float)pdValue['K'];
^˜˜˜
msequtilities.cpp:736:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['k'] = pValue['K'] = (float)pdValue['K'];
^˜˜˜
msequtilities.cpp:736:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['k'] = pValue['K'] = (float)pdValue['K'];
^˜˜˜
msequtilities.cpp:738:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['l'] = pdValue['L'] = 113.1594;
^˜˜˜
msequtilities.cpp:738:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['l'] = pdValue['L'] = 113.1594;
^˜˜˜
msequtilities.cpp:739:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['l'] = pValue['L'] = (float)pdValue['L'];
^˜˜˜
msequtilities.cpp:739:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['l'] = pValue['L'] = (float)pdValue['L'];
^˜˜˜
msequtilities.cpp:739:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['l'] = pValue['L'] = (float)pdValue['L'];
^˜˜˜
msequtilities.cpp:741:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['m'] = pdValue['M'] = 131.1926;
^˜˜˜
msequtilities.cpp:741:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['m'] = pdValue['M'] = 131.1926;
^˜˜˜
msequtilities.cpp:742:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['m'] = pValue['M'] = (float)pdValue['M'];
^˜˜˜
msequtilities.cpp:742:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['m'] = pValue['M'] = (float)pdValue['M'];
^˜˜˜
msequtilities.cpp:742:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['m'] = pValue['M'] = (float)pdValue['M'];
^˜˜˜
msequtilities.cpp:744:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['n'] = pdValue['N'] = 114.1038;
^˜˜˜
msequtilities.cpp:744:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['n'] = pdValue['N'] = 114.1038;
^˜˜˜
msequtilities.cpp:745:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['n'] = pValue['N'] = (float)pdValue['N'];
^˜˜˜
msequtilities.cpp:745:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['n'] = pValue['N'] = (float)pdValue['N'];
^˜˜˜
msequtilities.cpp:745:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['n'] = pValue['N'] = (float)pdValue['N'];
^˜˜˜
msequtilities.cpp:747:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['o'] = pdValue['O'] = 114.1038; // Same as N
^˜˜˜
msequtilities.cpp:747:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['o'] = pdValue['O'] = 114.1038; // Same as N
^˜˜˜
msequtilities.cpp:748:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['o'] = pValue['O'] = (float)pdValue['O'];
^˜˜˜
msequtilities.cpp:748:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['o'] = pValue['O'] = (float)pdValue['O'];
^˜˜˜
msequtilities.cpp:748:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['o'] = pValue['O'] = (float)pdValue['O'];
^˜˜˜
msequtilities.cpp:750:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['p'] = pdValue['P'] = 97.1167;
^˜˜˜
msequtilities.cpp:750:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['p'] = pdValue['P'] = 97.1167;
^˜˜˜
msequtilities.cpp:751:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['p'] = pValue['P'] = (float)pdValue['P'];
^˜˜˜
msequtilities.cpp:751:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['p'] = pValue['P'] = (float)pdValue['P'];
^˜˜˜
msequtilities.cpp:751:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['p'] = pValue['P'] = (float)pdValue['P'];
^˜˜˜
msequtilities.cpp:753:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['q'] = pdValue['Q'] = 128.1307;
^˜˜˜
msequtilities.cpp:753:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['q'] = pdValue['Q'] = 128.1307;
^˜˜˜
msequtilities.cpp:754:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
^˜˜˜
msequtilities.cpp:754:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
^˜˜˜
msequtilities.cpp:754:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
^˜˜˜
msequtilities.cpp:756:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['r'] = pdValue['R'] = 156.1875;
^˜˜˜
msequtilities.cpp:756:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['r'] = pdValue['R'] = 156.1875;
^˜˜˜
msequtilities.cpp:757:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['r'] = pValue['R'] = (float)pdValue['R'];
^˜˜˜
msequtilities.cpp:757:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['r'] = pValue['R'] = (float)pdValue['R'];
^˜˜˜
msequtilities.cpp:757:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['r'] = pValue['R'] = (float)pdValue['R'];
^˜˜˜
msequtilities.cpp:759:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['s'] = pdValue['S'] = 87.0782;
^˜˜˜
msequtilities.cpp:759:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['s'] = pdValue['S'] = 87.0782;
^˜˜˜
msequtilities.cpp:760:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['s'] = pValue['S'] = (float)pdValue['S'];
^˜˜˜
msequtilities.cpp:760:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['s'] = pValue['S'] = (float)pdValue['S'];
^˜˜˜
msequtilities.cpp:760:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['s'] = pValue['S'] = (float)pdValue['S'];
^˜˜˜
msequtilities.cpp:762:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['t'] = pdValue['T'] = 101.1051;
^˜˜˜
msequtilities.cpp:762:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['t'] = pdValue['T'] = 101.1051;
^˜˜˜
msequtilities.cpp:763:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['t'] = pValue['T'] = (float)pdValue['T'];
^˜˜˜
msequtilities.cpp:763:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['t'] = pValue['T'] = (float)pdValue['T'];
^˜˜˜
msequtilities.cpp:763:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['t'] = pValue['T'] = (float)pdValue['T'];
^˜˜˜
msequtilities.cpp:765:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['u'] = pdValue['U'] = 103.1388 - 32.066 + 78.96; // selenocysteine
^˜˜˜
msequtilities.cpp:765:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['u'] = pdValue['U'] = 103.1388 - 32.066 + 78.96; // selenocysteine
^˜˜˜
msequtilities.cpp:766:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['u'] = pValue['U'] = (float)pdValue['U'];
^˜˜˜
msequtilities.cpp:766:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['u'] = pValue['U'] = (float)pdValue['U'];
^˜˜˜
msequtilities.cpp:766:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['u'] = pValue['U'] = (float)pdValue['U'];
^˜˜˜
msequtilities.cpp:768:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['v'] = pdValue['V'] = 99.1326;
^˜˜˜
msequtilities.cpp:768:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['v'] = pdValue['V'] = 99.1326;
^˜˜˜
msequtilities.cpp:769:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['v'] = pValue['V'] = (float)pdValue['V'];
^˜˜˜
msequtilities.cpp:769:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['v'] = pValue['V'] = (float)pdValue['V'];
^˜˜˜
msequtilities.cpp:769:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['v'] = pValue['V'] = (float)pdValue['V'];
^˜˜˜
msequtilities.cpp:771:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['w'] = pdValue['W'] = 186.2132;
^˜˜˜
msequtilities.cpp:771:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['w'] = pdValue['W'] = 186.2132;
^˜˜˜
msequtilities.cpp:772:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['w'] = pValue['W'] = (float)pdValue['W'];
^˜˜˜
msequtilities.cpp:772:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['w'] = pValue['W'] = (float)pdValue['W'];
^˜˜˜
msequtilities.cpp:772:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['w'] = pValue['W'] = (float)pdValue['W'];
^˜˜˜
msequtilities.cpp:774:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['x'] = pdValue['X'] = 113.1594; // Why?
^˜˜˜
msequtilities.cpp:774:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['x'] = pdValue['X'] = 113.1594; // Why?
^˜˜˜
msequtilities.cpp:775:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['x'] = pValue['X'] = (float)pdValue['X'];
^˜˜˜
msequtilities.cpp:775:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['x'] = pValue['X'] = (float)pdValue['X'];
^˜˜˜
msequtilities.cpp:775:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['x'] = pValue['X'] = (float)pdValue['X'];
^˜˜˜
msequtilities.cpp:777:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['y'] = pdValue['Y'] = 163.1760;
^˜˜˜
msequtilities.cpp:777:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['y'] = pdValue['Y'] = 163.1760;
^˜˜˜
msequtilities.cpp:778:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
^˜˜˜
msequtilities.cpp:778:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
^˜˜˜
msequtilities.cpp:778:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
^˜˜˜
msequtilities.cpp:780:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['z'] = pdValue['Z'] = 128.1307; // Same as Q
^˜˜˜
msequtilities.cpp:780:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
pdValue['z'] = pdValue['Z'] = 128.1307; // Same as Q
^˜˜˜
msequtilities.cpp:781:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
^˜˜˜
msequtilities.cpp:781:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
^˜˜˜
msequtilities.cpp:781:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
^˜˜˜
274 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrumcondition.cpp:154:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mtermmods.cpp -o mtermmods.o
In file included from mtermmods.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mxxcleavage.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from saxbiomlhandler.cpp:140:
In file included from ./saxbiomlhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from saxgamlhandler.cpp:139:
In file included from ./saxgamlhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxhandler.cpp -o saxhandler.o
In file included from saxhandler.cpp:132:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxmodhandler.cpp -o saxmodhandler.o
In file included from saxmodhandler.cpp:140:
In file included from ./saxmodhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from saxmzdatahandler.cpp:28:
In file included from ./saxmzdatahandler.h:4:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from saxmzmlhandler.cpp:33:
In file included from ./saxmzmlhandler.h:4:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from saxmzxmlhandler.cpp:20:
In file included from ./saxmzxmlhandler.h:4:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxsaphandler.cpp -o saxsaphandler.o
In file included from saxsaphandler.cpp:140:
In file included from ./saxsaphandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from saxtandeminputhandler.cpp:139:
In file included from ./saxtandeminputhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from saxtaxhandler.cpp:139:
In file included from ./saxtaxhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c stdafx.cpp -o stdafx.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c tandem.cpp -o tandem.o
In file included from tandem.cpp:143:
In file included from ./tandem.h:15:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
tandem.cpp:225:62: warning: if statement has empty body [-Wempty-body]
if(!pProcess[0]->load(param, peptide, saps, mods, spectrum));
^
tandem.cpp:225:62: note: put the semicolon on a separate line to silence this warning
tandem.cpp:277:12: warning: unused variable 'tCount' [-Wunused-variable]
size_t tCount = pProcess[0]->m_vSpectra.size();
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c xmlparameter.cpp -o xmlparameter.o
In file included from xmlparameter.cpp:144:
In file included from ./saxtandeminputhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from xmltaxonomy.cpp:160:
In file included from ./saxtaxhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rTANDEM.so PTMTreeSearch.o PTMTreeSearchScore.o base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_hrk.o mscore_k.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -lpthread -lexpat -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.2-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rTANDEM)