rTANDEM 1.15.1
Frederic Fournier
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rTANDEM | | Last Changed Rev: 128693 / Revision: 129046 | | Last Changed Date: 2017-04-13 23:12:37 -0400 (Thu, 13 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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_1.15.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/rTANDEM.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.15.1’
* 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 ... 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 ‘new’
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 ‘new’
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’
ms2.plot: no visible global function definition for ‘is’
ms2.plot: no visible global function definition for ‘plot’
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’
Undefined global functions or variables:
addChildren data.table getNodeSet is new plot rbindlist saveXML set
setkey setnames xmlAttrs xmlChildren xmlEventParse xmlGetAttr xmlName
xmlNode xmlRoot xmlTreeParse xmlValue
Consider adding
importFrom("graphics", "plot")
importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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-3.5-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.
* installing *source* package ‘rTANDEM’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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:193:9: warning: unused variable 'fMaxIntens' [-Wunused-variable]
float fMaxIntens = 0;
^
PTMTreeSearchScore.cpp:195:8: warning: unused variable 'active' [-Wunused-variable]
bool active;
^
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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c dataLoader.cpp -o dataLoader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c masscalc.cpp -o masscalc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mbiomlreport.cpp -o mbiomlreport.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mplugin.cpp -o mplugin.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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:251:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
size_t tActiveNow = 0;
^
mrefine.cpp:250:9: warning: unused variable 'a' [-Wunused-variable]
size_t a = 0;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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:588:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
^
mscore_hrk.cpp:587:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfBScore;
^
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:658:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfXScore;
^
mscore_hrk.cpp:657:9: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
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:692:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
^
mscore_hrk.cpp:693:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
^
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:736:10: warning: unused variable 'pfScore' [-Wunused-variable]
float *pfScore = m_pSeqUtilFrag->m_pfYScore;
^
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:759:17: warning: unused variable 'lCount' [-Wunused-variable]
unsigned long lCount = 0;
^
mscore_hrk.cpp:758:17: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 0;
^
mscore_hrk.cpp:761:10: warning: unused variable 'b' [-Wunused-variable]
size_t b = 0;
^
mscore_hrk.cpp:760:8: warning: unused variable 'lType' [-Wunused-variable]
long lType = 0;
^
32 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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:380:6: warning: unused variable 'lType' [-Wunused-variable]
long lType = 0;
^
mscore_k.cpp:378:15: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 0;
^
mscore_k.cpp:381:8: warning: unused variable 'b' [-Wunused-variable]
size_t b = 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:631:7: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
^
mscore_k.cpp:638:8: warning: unused variable 'dZ' [-Wunused-variable]
double dZ = (double)_c;
^
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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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:582:16: warning: unused variable 'lCount' [-Wunused-variable]
unsigned long lCount = 0;
^
mscore_tandem.cpp:583:7: warning: unused variable 'lType' [-Wunused-variable]
long lType = 0;
^
mscore_tandem.cpp:581:16: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c msequencecollection.cpp -o msequencecollection.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c msequenceserver.cpp -o msequenceserver.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c stdafx.cpp -o stdafx.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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: /Library/Developer/CommandLineTools/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.5-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)