Frederic Fournier
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rTANDEM |
| Branch: RELEASE_3_9 |
| Last Commit: 4815e9d |
| Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:56 -0400 (Wed, 16 Oct 2019).
| Package 1427/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rTANDEM 1.24.0 Frederic Fournier
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: rTANDEM |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rTANDEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rTANDEM_1.24.0.tar.gz |
| StartedAt: 2019-10-16 06:27:18 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:28:07 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 48.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rTANDEM.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rTANDEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rTANDEM_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rTANDEM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rTANDEM’ can be installed ... WARNING
Found the following significant warnings:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
base64.cpp:100:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
base64.cpp:101:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./loadmspectrum.h:185:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:498:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:567:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:575:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:698:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:754:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:766:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:777:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:786:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:820:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:903:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:958:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:971:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:980:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:1011:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:1059:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:1114:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
loadmspectrum.cpp:1167:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:798:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:1370:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:1768:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:1814:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:2273:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:2605:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:2967:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:2968:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:3759:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:3775:6: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:3788:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:3810:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mprocess.cpp:3815:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mrefine.cpp:206:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mreport.cpp:264:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mreport.cpp:667:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mreport.cpp:732:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
mreport.cpp:874:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
msequenceserver.cpp:605:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
msequtilities.cpp:533:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
saxhandler.cpp:335:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
tandem.cpp:323:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
tandem.cpp:404:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
tandem.cpp:720:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
tandem.cpp:721:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
tandem.cpp:722:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/rTANDEM.Rcheck/00install.out’ for details.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
print.rTParam
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rTANDEM/libs/rTANDEM.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Found ‘_srand’, possibly from ‘srand’ (C)
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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.
rTANDEM.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rTANDEM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘rTANDEM’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from PTMTreeSearch.cpp:16:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
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:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
double dMaxExpect = 0.1;
^
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
size_t tActiveNow = 0;
^
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: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;
^
23 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
In file included from PTMTreeSearchScore.cpp:13:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from PTMTreeSearchScore.cpp:14:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
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;
^
47 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c base64.cpp -o base64.o
base64.cpp:100:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
int register a;
^~~~~~~~~
base64.cpp:101:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
int register b;
^~~~~~~~~
base64.cpp:11:28: warning: unused variable 'b64_pad' [-Wunused-const-variable]
static const unsigned char b64_pad = '=';
^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c dataLoader.cpp -o dataLoader.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c loadmspectrum.cpp -o loadmspectrum.o
In file included from loadmspectrum.cpp:142:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from loadmspectrum.cpp:143:
./loadmspectrum.h:185:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
./loadmspectrum.h:176:17: note: allocated with 'new[]' here
char *pLine = new char[tBuffer];
^
loadmspectrum.cpp:498:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:423:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:567:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:539:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:575:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:539:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:698:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:614:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:754:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:766:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:777:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:786:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:820:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:808:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:903:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:834:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:958:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:937:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:971:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:937:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:980:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:937:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:1011:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:1002:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
loadmspectrum.cpp:1059:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:1028:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
loadmspectrum.cpp:1114:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:1028:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
loadmspectrum.cpp:1167:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
loadmspectrum.cpp:1151:16: note: allocated with 'new[]' here
char *pLine = new char[m_tSize];
^
25 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c masscalc.cpp -o masscalc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mbiomlreport.cpp -o mbiomlreport.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from mpam.cpp:138:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mplugin.cpp -o mplugin.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from mpmods.cpp:138:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mprocess.cpp -o mprocess.o
In file included from mprocess.cpp:156:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
In file included from mprocess.cpp:157:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from mprocess.cpp:158:
./loadmspectrum.h:185:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
./loadmspectrum.h:176:17: note: allocated with 'new[]' here
char *pLine = new char[tBuffer];
^
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
bool bC = false;
^
mprocess.cpp:798:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
mprocess.cpp:790:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
mprocess.cpp:1370:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
mprocess.cpp:1361:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
mprocess.cpp:1768:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
mprocess.cpp:1762:15: note: allocated with 'new[]' here
char *pOut = new char[256];
^
mprocess.cpp:1814:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
mprocess.cpp:1762:15: note: allocated with 'new[]' here
char *pOut = new char[256];
^
mprocess.cpp:2273:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
mprocess.cpp:2088:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
mprocess.cpp:2605:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
mprocess.cpp:2573:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
size_t c = 0;
^
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
size_t tLast = 0;
^
mprocess.cpp:2967:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plCount;
^
[]
mprocess.cpp:2765:27: note: allocated with 'new[]' here
unsigned long *plCount = new unsigned long[tMaxUid];
^
mprocess.cpp:2968:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pdExpect;
^
[]
mprocess.cpp:2764:21: note: allocated with 'new[]' here
double *pdExpect = new double[tMaxUid];
^
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:3759:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pValue;
^
[]
mprocess.cpp:3744:17: note: allocated with 'new[]' here
char *pValue = new char[1028];
^
mprocess.cpp:3775:6: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pValue;
^
[]
mprocess.cpp:3744:17: note: allocated with 'new[]' here
char *pValue = new char[1028];
^
mprocess.cpp:3788:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pValue;
^
[]
mprocess.cpp:3744:17: note: allocated with 'new[]' here
char *pValue = new char[1028];
^
mprocess.cpp:3810:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pValue;
^
[]
mprocess.cpp:3744:17: note: allocated with 'new[]' here
char *pValue = new char[1028];
^
mprocess.cpp:3815:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pValue;
^
[]
mprocess.cpp:3744:17: note: allocated with 'new[]' here
char *pValue = new char[1028];
^
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
uint64_t crc = INITIALCRC, part = 0;
^
61 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mrefine.cpp -o mrefine.o
In file included from mrefine.cpp:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from mrefine.cpp:139:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
mrefine.cpp:206:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
mrefine.cpp:197:17: note: allocated with 'new[]' here
char *pLine = new char[256];
^
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;
^
13 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete plValues;
^
[]
./mhistogram.h:345:19: note: allocated with 'new[]' here
int *plValues = new int[m_lLength];
^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pTempList;
^
[]
./mhistogram.h:349:21: note: allocated with 'new[]' here
int *pTempList = new int[m_lLength];
^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfX;
^
[]
./mhistogram.h:417:16: note: allocated with 'new[]' here
float *pfX = new float[m_lLength];
^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pfT;
^
[]
./mhistogram.h:418:16: note: allocated with 'new[]' here
float *pfT = new float[m_lLength];
^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
int lZeros = m_lHigh - a - 1;
^
In file included from mreport.cpp:147:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pOut;
^
[]
./mmotif.h:295:16: note: allocated with 'new[]' here
char *pOut = new char[256];
^
mreport.cpp:264:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete pLine;
^
[]
mreport.cpp:228:16: note: allocated with 'new[]' here
char *pLine = new char[256];
^
mreport.cpp:655:74: warning: array subscript is of type 'char' [-Wchar-subscripts]
sprintf(pLine,"\t
rTANDEM.Rcheck/rTANDEM-Ex.timings
| name | user | system | elapsed | |
| accessors | 2.426 | 0.130 | 1.338 | |
| converters | 0.004 | 0.005 | 0.002 | |
| parameters | 0.133 | 0.116 | 0.035 | |
| rTANDEM-package | 0.939 | 0.482 | 0.551 | |
| rTResult-class | 0.004 | 0.001 | 0.004 | |
| tandem | 0.485 | 0.021 | 0.506 | |
| visualizers | 0.342 | 0.177 | 0.189 | |