Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for rTANDEM on malbec1

This page was generated on 2021-02-27 12:10:03 -0500 (Sat, 27 Feb 2021).

To the developers/maintainers of the rTANDEM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1589/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTANDEM 1.30.0
Frederic Fournier
Snapshot Date: 2021-02-26 14:50:01 -0500 (Fri, 26 Feb 2021)
URL: https://git.bioconductor.org/packages/rTANDEM
Branch: RELEASE_3_12
Last Commit: 96455bf
Last Changed Date: 2020-10-27 10:48:41 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    NA  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    NA  
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: rTANDEM
Version: 1.30.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:rTANDEM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings rTANDEM_1.30.0.tar.gz
StartedAt: 2021-02-27 06:44:47 -0500 (Sat, 27 Feb 2021)
EndedAt: 2021-02-27 06:45:16 -0500 (Sat, 27 Feb 2021)
EllapsedTime: 28.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: rTANDEM.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:rTANDEM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings rTANDEM_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/rTANDEM.Rcheck’
* using R version 4.0.4 (2021-02-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.30.0’
* 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:
  Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/rTANDEM.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 16.8Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs     13.3Mb
* 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’
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 rbindlist saveXML set setkey
  setnames xmlAttrs xmlChildren xmlEventParse xmlGetAttr xmlName
  xmlNode xmlRoot xmlTreeParse xmlValue
Consider adding
  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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rTANDEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accessors
> ### Title: Extract information from rTANDEM result object
> ### Aliases: GetProteins getProteins GetPeptides getPeptides GetDegeneracy
> ###   getDegeneracy
> 
> ### ** Examples
> 
> # To show how to use the accessor functions, we need an rTANDEM result.
> # We can produce one by running the example from the rTANDEM function,
> # and reading it to R with GetResultsFromXML:
> # output.file.path <- example(rTANDEM)
> ## Don't show: 
> output.file.path <- example(rTANDEM);

rTANDE> # X!Tandem call style: we call tandem(input) on a single
rTANDE> # rTParam object.
rTANDE> 
rTANDE> # We create rTParam from an X!Tandem xml file
rTANDE> # located in the installation folder: 
rTANDE> param <- GetParamFromXML(system.file("extdata/input.xml", package="rTANDEM"))

rTANDE> # We create a rTTaxo object and identify a database for yeast
rTANDE> taxonomy <- rTTaxo( 
rTANDE+   taxon="yeast",
rTANDE+   format="peptide",
rTANDE+   URL= system.file("extdata/fasta/scd.fasta.pro", package="rTANDEM")
rTANDE+   )

rTANDE> # We will adjust those two objects to use one another and to use
rTANDE> # the path of some data and configuration files located
rTANDE> # in the installation folder:
rTANDE> param <- setParamValue(param, 'list path', 'taxonomy information', taxonomy)

rTANDE> param <- setParamValue(param, 'list path', 'default parameters',
rTANDE+   value=system.file("extdata/default_input.xml", package="rTANDEM"))

rTANDE> param <- setParamValue(param, 'spectrum', 'path',
rTANDE+   value=system.file("extdata/test_spectra.mgf", package="rTANDEM"))

rTANDE> param <- setParamValue(param, 'output', 'xsl path',
rTANDE+   value=system.file("extdata/tandem-input-style.xsl", package="rTANDEM"))

rTANDE> param <- setParamValue(param, 'output', 'path',
rTANDE+   value=paste(getwd(), "output.xml", sep="/"))

rTANDE> # This is the main command to run rTANDEM. The output will be
rTANDE> # written to a file in the working directory and the function
rTANDE> # returns the path to this file.
rTANDE> output.file <- tandem(param)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
rTANDEM
 --- call from context --- 
NULL
 --- call from argument --- 
col %in% names(input) && !is.na(eval(substitute(input$COL, list(COL = col))))
 --- R stacktrace ---
where 1 at /tmp/RtmpN2pIQg/Rex54bf5b6b6e53#38: tandem(param)
where 2: eval(ei, envir)
where 3: eval(ei, envir)
where 4: withVisible(eval(ei, envir))
where 5: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix, 
    getOption("prompt")), continue.echo = paste0(prompt.prefix, 
    getOption("continue")), verbose = verbose, max.deparse.length = Inf, 
    encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
where 6: example(rTANDEM)

 --- value of length: 3 type: logical ---
     taxon format  URL
[1,]  TRUE   TRUE TRUE
 --- function from context --- 
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* 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 ERROR, 1 WARNING, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.


Installation output

rTANDEM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL rTANDEM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘rTANDEM’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from PTMTreeSearch.h:16,
                 from PTMTreeSearch.cpp:14:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
PTMTreeSearch.cpp: In member function ‘virtual bool PTMTreeSearch::refine()’:
PTMTreeSearch.cpp:304:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < m_pProcess->m_vSpectra[a].m_vMI.size(); ++i){
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:308:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 1; i < spectraIntTMP.size(); ++i){
                 ~~^~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:382:12: warning: unused variable ‘dMaxExpect’ [-Wunused-variable]
     double dMaxExpect = atof(strValue.c_str());
            ^~~~~~~~~~
PTMTreeSearch.cpp:402:67: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
                                                                   ^
PTMTreeSearch.cpp:403:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
      if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
                                  ^
PTMTreeSearch.cpp:405:37: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
                                     ^
PTMTreeSearch.cpp:406:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
                                         ^
PTMTreeSearch.cpp:407:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
                                       ^
PTMTreeSearch.cpp:408:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
                                         ^
PTMTreeSearch.cpp:409:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
                                       ^
PTMTreeSearch.cpp:585:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (modCnt > noptmhitlimit){
       ~~~~~~~^~~~~~~~~~~~~~~
PTMTreeSearch.cpp:54:10: warning: unused variable ‘tActiveNow’ [-Wunused-variable]
   size_t tActiveNow = 0;
          ^~~~~~~~~~
PTMTreeSearch.cpp:66:10: warning: variable ‘dPTMMinEval’ set but not used [-Wunused-but-set-variable]
   double dPTMMinEval;
          ^~~~~~~~~~~
PTMTreeSearch.cpp:380:10: warning: unused variable ‘dMaxExpect’ [-Wunused-variable]
   double dMaxExpect = 0.1;
          ^~~~~~~~~~
PTMTreeSearch.cpp: In member function ‘bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification>*)’:
PTMTreeSearch.cpp:751:31: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    m_vmodModificationsDB[resid].push_back(mod);
                               ^
PTMTreeSearch.cpp:676:16: warning: variable ‘m_uiId’ set but not used [-Wunused-but-set-variable]
   unsigned int m_uiId;  //unique id of the modification
                ^~~~~~
PTMTreeSearch.cpp: In member function ‘virtual void SAXModsHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:875:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function ‘virtual void SAXResidHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1018:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function ‘virtual void SAXUnimodHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1170:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
       m_vmodModificationsDB[resid].push_back(mod);
                                  ^
PTMTreeSearch.cpp:1156:10: warning: unused variable ‘pos’ [-Wunused-variable]
   size_t pos = 0;
          ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
PTMTreeSearchScore.cpp:1264:1: warning: "/*" within comment [-Wcomment]
 /*
  
PTMTreeSearchScore.cpp:1366:1: warning: "/*" within comment [-Wcomment]
 /*
  
In file included from mspectrum.h:142:0,
                 from PTMTreeSearchScore.cpp:13:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
PTMTreeSearchScore.cpp: In member function ‘virtual float PTMTreeSearchScore::score(size_t)’:
PTMTreeSearchScore.cpp:369:35: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
                                   ^
PTMTreeSearchScore.cpp:373:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
                                               ^
PTMTreeSearchScore.cpp:528:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:568:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:587:47: warning: array subscript has 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: In member function ‘virtual bool PTMTreeSearchScore::get_aa(std::vector<maa>&, size_t, double&)’:
PTMTreeSearchScore.cpp:871:40: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
                                        ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::AnchorFixedModification()’:
PTMTreeSearchScore.cpp:903:52: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                    ^
PTMTreeSearchScore.cpp:903:88: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                                                        ^
PTMTreeSearchScore.cpp:905:56: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
                                                        ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dB(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1068:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dC(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1157:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dX(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1199:8: warning: unused variable ‘fSub’ [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dY(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1305:59: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                           ^
PTMTreeSearchScore.cpp:1314:58: warning: array subscript has 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: In member function ‘bool PTMTreeSearchScore::add_dZ(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1405:57: warning: array subscript has 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;
        ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c base64.cpp -o base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dataLoader.cpp -o dataLoader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142:0,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c masscalc.cpp -o masscalc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mbiomlreport.cpp -o mbiomlreport.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mplugin.cpp -o mplugin.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142:0,
                 from mprocess.cpp:157:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mprocess.cpp: In member function ‘virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)’:
mprocess.cpp:440:7: warning: unused variable ‘bC’ [-Wunused-variable]
  bool bC = false;
       ^~
mprocess.cpp: In member function ‘bool mprocess::report_valid(double)’:
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: In member function ‘bool mprocess::score_single(const msequence&)’:
mprocess.cpp:3390:46: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
       if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
                                   ~~~~~~~~~~~^~~~~~~~~~~~~~
mprocess.cpp: In member function ‘bool mprocess::initialize_crc()’:
mprocess.cpp:4843:14: warning: unused variable ‘crc’ [-Wunused-variable]
     uint64_t crc = INITIALCRC, part = 0;
              ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142:0,
                 from mrefine.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mrefine.cpp: In member function ‘virtual bool mrefine::refine()’:
mrefine.cpp:250:9: warning: unused variable ‘a’ [-Wunused-variable]
  size_t a = 0;
         ^
mrefine.cpp:251:9: warning: unused variable ‘tActiveNow’ [-Wunused-variable]
  size_t tActiveNow = 0;
         ^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mreport.cpp: In member function ‘bool mreport::masses(msequtilities&)’:
mreport.cpp:655:78: warning: array subscript has 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;
         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142:0,
                 from mscore.cpp:153:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore.cpp: In constructor ‘mscore::mscore()’:
mscore.cpp:200:16: warning: iteration 16 invokes undefined behavior [-Waggressive-loop-optimizations]
   m_plCount[a] = 0;
   ~~~~~~~~~~~~~^~~
mscore.cpp:199:10: note: within this loop
  while(a < 20) {
        ~~^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mspectrum.h:142:0,
                 from mscore_hrk.cpp:24:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_hrk.cpp: In member function ‘virtual double mscore_hrk::dot(long unsigned int*)’:
mscore_hrk.cpp:305:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (itType != itEnd && iIon == itType->m_lM) {
                            ~~~~~^~~~~~~~~~~~~~~
mscore_hrk.cpp:314:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                              ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_hrk.cpp:321:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                               ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_hrk.cpp: In member function ‘bool mscore_hrk::add_mi_hr(mspectrum&)’:
mscore_hrk.cpp:443:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(ii==tempLookup.size()-1) break;
          ~~^~~~~~~~~~~~~~~~~~~~~
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: In member function ‘double mscore_hrk::dot_hr(long unsigned int*)’:
mscore_hrk.cpp:491:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i==m_vmiType[m_lId].size()){
          ~^~~~~~~~~~~~~~~~~~~~~~~~~
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_A(long unsigned int, long int)’:
mscore_hrk.cpp:550:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfAScore;
          ^~~~~~~
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_B(long unsigned int, long int)’:
mscore_hrk.cpp:587:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~
mscore_hrk.cpp:588:10: warning: unused variable ‘pfScorePlus’ [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~~~~~
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_C(long unsigned int, long int)’:
mscore_hrk.cpp:622:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~
mscore_hrk.cpp:623:10: warning: unused variable ‘pfScorePlus’ [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~~~~~
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_X(long unsigned int, long int)’:
mscore_hrk.cpp:657:9: warning: unused variable ‘fSub’ [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:658:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfXScore;
          ^~~~~~~
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_Y(long unsigned int, long int)’:
mscore_hrk.cpp:691:9: warning: unused variable ‘fSub’ [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
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: In member function ‘virtual bool mscore_hrk::add_Z(long unsigned int, long int)’:
mscore_hrk.cpp:735:9: warning: unused variable ‘fSub’ [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:736:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~
mscore_hrk.cpp:737:10: warning: unused variable ‘pfScoreMinus’ [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~~~~~~
mscore_hrk.cpp: In member function ‘virtual float mscore_hrk::ion_check(long unsigned int, size_t)’:
mscore_hrk.cpp:758:17: warning: unused variable ‘a’ [-Wunused-variable]
   unsigned long a = 0;
                 ^
mscore_hrk.cpp:759:17: warning: unused variable ‘lCount’ [-Wunused-variable]
   unsigned long lCount = 0;
                 ^~~~~~
mscore_hrk.cpp:760:8: warning: unused variable ‘lType’ [-Wunused-variable]
   long lType = 0;
        ^~~~~
mscore_hrk.cpp:761:10: warning: unused variable ‘b’ [-Wunused-variable]
   size_t b = 0;
          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_k.cpp -o mscore_k.o
mscore_k.cpp:677:1: warning: "/*" within comment [-Wcomment]
 /*
  
mscore_k.cpp:753:1: warning: "/*" within comment [-Wcomment]
 /*
  
In file included from mspectrum.h:142:0,
                 from mscore_k.cpp:24:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_k.cpp: In member function ‘virtual double mscore_k::dot(long unsigned int*)’:
mscore_k.cpp:344:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itType != itEnd && iIon == itType->m_lM) {
                                ~~~~~^~~~~~~~~~~~~~~
mscore_k.cpp:355:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                                  ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_k.cpp:363:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                                   ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_k.cpp: In member function ‘virtual float mscore_k::ion_check(long unsigned int, size_t)’:
mscore_k.cpp:378:15: warning: unused variable ‘a’ [-Wunused-variable]
 unsigned long a = 0;
               ^
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:381:8: warning: unused variable ‘b’ [-Wunused-variable]
 size_t b = 0;
        ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_A(long unsigned int, long int)’:
mscore_k.cpp:466:14: warning: unused variable ‘dZ’ [-Wunused-variable]
 const double dZ = (double)_c;
              ^~
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_B(long unsigned int, long int)’:
mscore_k.cpp:529:54: warning: array subscript has 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: In member function ‘virtual bool mscore_k::add_C(long unsigned int, long int)’:
mscore_k.cpp:591:54: warning: array subscript has 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: In member function ‘virtual bool mscore_k::add_X(long unsigned int, long int)’:
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: In member function ‘virtual bool mscore_k::add_Y(long unsigned int, long int)’:
mscore_k.cpp:706:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:712:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:684:7: warning: unused variable ‘fSub’ [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
mscore_k.cpp:694:8: warning: unused variable ‘dZ’ [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Z(long unsigned int, long int)’:
mscore_k.cpp:776:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:779:55: warning: array subscript has 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;
       ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142:0,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_tandem.cpp: In member function ‘bool mscore_tandem::blur(std::vector<mi>&)’:
mscore_tandem.cpp:288:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(uType.m_lM == lValue + a) {
        ~~~~~~~~~~~^~~~~~~~~~~~~
mscore_tandem.cpp: In member function ‘virtual double mscore_tandem::dot(long unsigned int*)’:
mscore_tandem.cpp:358:8: warning: unused variable ‘fValue0’ [-Wunused-variable]
  float fValue0 = 0.0;
        ^~~~~~~
mscore_tandem.cpp:362:9: warning: unused variable ‘b’ [-Wunused-variable]
  size_t b = 0;
         ^
mscore_tandem.cpp: In member function ‘virtual float mscore_tandem::ion_check(long unsigned int, size_t)’:
mscore_tandem.cpp:581:16: warning: unused variable ‘a’ [-Wunused-variable]
  unsigned long a = 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:584:9: warning: unused variable ‘b’ [-Wunused-variable]
  size_t b = 0;
         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msequencecollection.cpp -o msequencecollection.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msequenceserver.cpp -o msequenceserver.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msequtilities.cpp -o msequtilities.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stdafx.cpp -o stdafx.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142:0,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
tandem.cpp: In function ‘SEXPREC* tandem(SEXP, SEXP, SEXP, SEXP, SEXP)’:
tandem.cpp:277:12: warning: unused variable ‘tCount’ [-Wunused-variable]
     size_t tCount = pProcess[0]->m_vSpectra.size();
            ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/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 -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-rTANDEM/00new/rTANDEM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘rTANDEM.Rnw’ 
** testing if installed package can be loaded from temporary location
Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (rTANDEM)

Tests output


Example timings

rTANDEM.Rcheck/rTANDEM-Ex.timings

nameusersystemelapsed