BioC 3.2: CHECK report for fmcsR on oaxaca

Package: fmcsR

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fmcsR_1.12.2.tar.gz

StartedAt: 2016-04-23 00:13:56 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:15:07 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 71.3 seconds

RetCode: 0

Status:  OK

CheckDir: fmcsR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fmcsR_1.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/fmcsR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fmcsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmcsR’ version ‘1.12.2’
* 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 ‘fmcsR’ can be installed ... [13s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘ChemmineR’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to ‘ChemmineR’ which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘RUnit’ ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/22s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
fmcsR-package 1.778  0.042   9.327
fmcsBatch     0.067  0.011   6.549
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/fmcsR.Rcheck/00check.log’
for details.

* installing *source* package ‘fmcsR’ ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MCS.cpp -o MCS.o
In file included from MCS.cpp:3:
In file included from ./MCS.h:12:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
MCS.cpp:48:11: warning: field 'compoundTwo' will be initialized after field 'userDefinedLowerBound' [-Wreorder]
          compoundTwo(compoundOne.size() > compoundTwo.size() ? compoundOne : compoundTwo),
          ^
MCS.cpp:50:8: warning: field 'atomMismatchLowerBound' will be initialized after field 'atomMismatchUpperBound' [-Wreorder]
          atomMismatchLowerBound(atomMishmatchLower), atomMismatchUpperBound(atomMismatchUpper),
          ^
MCS.cpp:51:8: warning: field 'bondMismatchLowerBound' will be initialized after field 'bondMismatchUpperBound' [-Wreorder]
          bondMismatchLowerBound(bondMismatchLower), bondMismatchUpperBound(bondMismatchUpper),
          ^
MCS.cpp:51:51: warning: field 'bondMismatchUpperBound' will be initialized after field 'matchType' [-Wreorder]
          bondMismatchLowerBound(bondMismatchLower), bondMismatchUpperBound(bondMismatchUpper),
                                                     ^
MCS.cpp:52:8: warning: field 'matchType' will be initialized after field 'runningMode' [-Wreorder]
          matchType(matchType), runningMode(runningMode), _timeout(timeout),
          ^
MCS.cpp:52:30: warning: field 'runningMode' will be initialized after field '_timeout' [-Wreorder]
          matchType(matchType), runningMode(runningMode), _timeout(timeout),
                                ^
MCS.cpp:53:29: warning: field 'bondMismatchCurr' will be initialized after field 'currSubstructureNum' [-Wreorder]
          atomMismatchCurr(0), bondMismatchCurr(0), currSubstructureNum(0),
                               ^
MCS.cpp:53:50: warning: field 'currSubstructureNum' will be initialized after field 'timeUsed' [-Wreorder]
          atomMismatchCurr(0), bondMismatchCurr(0), currSubstructureNum(0),
                                                    ^
MCS.cpp:54:22: warning: field 'startTime' will be initialized after field 'bestSize' [-Wreorder]
          timeUsed(0.0),startTime(0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                        ^
MCS.cpp:54:37: warning: field 'bestSize' will be initialized after field 'identicalGraph' [-Wreorder]
          timeUsed(0.0),startTime(0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                                       ^
MCS.cpp:54:50: warning: field 'identicalGraph' will be initialized after field '_isTimeout' [-Wreorder]
          timeUsed(0.0),startTime(0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                                                    ^
MCS.cpp:54:73: warning: field '_isTimeout' will be initialized after field 'haveBeenSwapped' [-Wreorder]
          timeUsed(0.0),startTime(0),  bestSize(0), identicalGraph(false), _isTimeout(false),
                                                                           ^
13 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
In file included from MCSCompound.cpp:5:
./MCSRingDetector.h:191:50: warning: field 'compound' will be initialized after field 'vertexId' [-Wreorder]
        MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
                                                 ^
MCSCompound.cpp:83:56: warning: field 'bonds' will be initialized after field 'SdfContentString' [-Wreorder]
            : bondCount(0), atomCount(0), atoms(NULL), bonds(NULL), SdfContentString(other.SdfContentString) {
                                                       ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MCSMap.cpp -o MCSMap.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:
In file included from ./MCSRingDetector.h:16:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
In file included from MCSRingDetector.cpp:13:
./MCSRingDetector.h:191:50: warning: field 'compound' will be initialized after field 'vertexId' [-Wreorder]
        MCSRingDetector(MCSCompound& compound) : compound(compound), vertexId(-1), edgeId(-1) {
                                                 ^
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
        int aromaticCount = 0;
            ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from fmcs_R_wrap.cpp:11:
In file included from ./MCS.h:12:
./MCSCompound.h:47:31: warning: field 'originalId' will be initialized after field 'atomType' [-Wreorder]
                : atomId(id), originalId(originalId), atomType(atomType), atomSymbol(atomSymbol) {}
                              ^
fmcs_R_wrap.cpp:47:13: warning: variable 'matchType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default: 
            ^˜˜˜˜˜˜
fmcs_R_wrap.cpp:74:13: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
            ^˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:42:6: note: variable 'matchType' is declared here
        MCS::MatchType matchType;
        ^
fmcs_R_wrap.cpp:56:13: warning: variable 'runningMode' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default:
            ^˜˜˜˜˜˜
fmcs_R_wrap.cpp:74:24: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
                       ^˜˜˜˜˜˜˜˜˜˜
fmcs_R_wrap.cpp:52:9: note: variable 'runningMode' is declared here
        MCS::RunningMode runningMode;
        ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c util.cpp -o util.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/fmcsR.Rcheck/fmcsR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fmcsR)

name	user	system	elapsed
MCS-class	1.583	0.031	1.615
fmcs	1.800	0.030	1.832
fmcsBatch	0.067	0.011	6.549
fmcsR-package	1.778	0.042	9.327
fmcstest	0.034	0.006	0.040
mcs2sdfset	0.612	0.010	0.622
plotMCS	0.517	0.008	0.526