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Package 234/658HostnameOS / ArchBUILDCHECKBUILD BIN
fmcsR 1.1.3
ChemmineR Team
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/fmcsR
Last Changed Rev: 74467 / Revision: 74774
Last Changed Date: 2013-03-16 12:18:01 -0700 (Sat, 16 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: fmcsR
Version: 1.1.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch fmcsR_1.1.3.tar.gz
StartedAt: 2013-03-25 02:30:08 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:31:26 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 78.1 seconds
RetCode: 0
Status:  OK 
CheckDir: fmcsR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/fmcsR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'fmcsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fmcsR' version '1.1.3'
* 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 ... [20s/21s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
fmcsR-package 6.772  0.017    6.79
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/fmcsR.Rcheck/00check.log'
for details.

fmcsR.Rcheck/00install.out:

* 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
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCS.cpp -o MCS.o
In file included from MCS.h:11,
                 from MCS.cpp:3:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
MCS.h: In constructor 'FMCS::MCS::MCS(const FMCS::MCSCompound&, const FMCS::MCSCompound&, size_t, size_t, size_t, size_t, size_t, size_t, FMCS::MCS::MatchType, FMCS::MCS::RunningMode, int)':
MCS.h:157: warning: 'FMCS::MCS::compoundTwo' will be initialized after
MCS.h:141: warning:   'size_t FMCS::MCS::userDefinedLowerBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:148: warning: 'FMCS::MCS::atomMismatchLowerBound' will be initialized after
MCS.h:145: warning:   'size_t FMCS::MCS::atomMismatchUpperBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:149: warning: 'FMCS::MCS::bondMismatchLowerBound' will be initialized after
MCS.h:146: warning:   'size_t FMCS::MCS::bondMismatchUpperBound'
MCS.cpp:43: warning:   when initialized here
MCS.h:146: warning: 'FMCS::MCS::bondMismatchUpperBound' will be initialized after
MCS.h:139: warning:   'FMCS::MCS::MatchType FMCS::MCS::matchType'
MCS.cpp:43: warning:   when initialized here
MCS.h:139: warning: 'FMCS::MCS::matchType' will be initialized after
MCS.h:126: warning:   'FMCS::MCS::RunningMode FMCS::MCS::runningMode'
MCS.cpp:43: warning:   when initialized here
MCS.h:126: warning: 'FMCS::MCS::runningMode' will be initialized after
MCS.h:122: warning:   'int FMCS::MCS::_timeout'
MCS.cpp:43: warning:   when initialized here
MCS.h:152: warning: 'FMCS::MCS::bondMismatchCurr' will be initialized after
MCS.h:143: warning:   'size_t FMCS::MCS::currSubstructureNum'
MCS.cpp:43: warning:   when initialized here
MCS.h:143: warning: 'FMCS::MCS::currSubstructureNum' will be initialized after
MCS.h:133: warning:   'double FMCS::MCS::timeUsed'
MCS.cpp:43: warning:   when initialized here
MCS.h:133: warning: 'FMCS::MCS::timeUsed' will be initialized after
MCS.h:130: warning:   'size_t FMCS::MCS::bestSize'
MCS.cpp:43: warning:   when initialized here
MCS.h:130: warning: 'FMCS::MCS::bestSize' will be initialized after
MCS.h:128: warning:   'bool FMCS::MCS::identicalGraph'
MCS.cpp:43: warning:   when initialized here
MCS.h:128: warning: 'FMCS::MCS::identicalGraph' will be initialized after
MCS.h:124: warning:   'bool FMCS::MCS::_isTimeout'
MCS.cpp:43: warning:   when initialized here
MCS.h:124: warning: 'FMCS::MCS::_isTimeout' will be initialized after
MCS.h:120: warning:   'bool FMCS::MCS::haveBeenSwapped'
MCS.cpp:43: warning:   when initialized here
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:105: warning: comparison between signed and unsigned integer expressions
MCS.cpp:113: warning: comparison between signed and unsigned integer expressions
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]':
MCS.cpp:371:   instantiated from here
MCSList.h:143: warning: comparison between signed and unsigned integer expressions
MCS.cpp: In member function 'size_t FMCS::MCS::top(FMCS::MCSList<long unsigned int>&)':
MCS.cpp:262: warning: 'candidateIdx' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:4:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
In file included from MCSCompound.cpp:5:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168: warning: 'FMCS::MCSRingDetector::compound' will be initialized after
MCSRingDetector.h:165: warning:   'int FMCS::MCSRingDetector::vertexId'
MCSRingDetector.h:191: warning:   when initialized here
MCSCompound.h: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.h:98: warning: 'FMCS::MCSCompound::bonds' will be initialized after
MCSCompound.h:88: warning:   'std::string FMCS::MCSCompound::SdfContentString'
MCSCompound.cpp:82: warning:   when initialized here
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const std::string&)':
MCSCompound.cpp:157: warning: comparison between signed and unsigned integer expressions
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const std::string&) const':
MCSCompound.cpp:194: warning: comparison between signed and unsigned integer expressions
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSMap.cpp -o MCSMap.o
MCSList.h: In member function 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]':
MCSMap.cpp:28:   instantiated from here
MCSList.h:143: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.h:16,
                 from MCSRingDetector.cpp:13:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
In file included from MCSRingDetector.cpp:13:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::MCSRingDetector(FMCS::MCSCompound&)':
MCSRingDetector.h:168: warning: 'FMCS::MCSRingDetector::compound' will be initialized after
MCSRingDetector.h:165: warning:   'int FMCS::MCSRingDetector::vertexId'
MCSRingDetector.h:191: warning:   when initialized here
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp:94: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149: warning: comparison between signed and unsigned integer expressions
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175: warning: unused variable 'aromaticCount'
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
In file included from MCS.h:11,
                 from fmcs_R_wrap.cpp:11:
MCSCompound.h: In constructor 'FMCS::MCSCompound::Atom::Atom(size_t, size_t, int, std::string)':
MCSCompound.h:38: warning: 'FMCS::MCSCompound::Atom::originalId' will be initialized after
MCSCompound.h:33: warning:   'int FMCS::MCSCompound::Atom::atomType'
MCSCompound.h:46: warning:   when initialized here
fmcs_R_wrap.cpp: In function 'void fmcs_R_wrap(const char**, const char**, int*, int*, int*, int*, int*, int*, int*, const char**, const char**, const char**, const char**, const char**)':
fmcs_R_wrap.cpp:42: warning: 'matchType' may be used uninitialized in this function
fmcs_R_wrap.cpp:52: warning: 'runningMode' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const std::string&)':
util.cpp:11: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.12-bioc/meat/fmcsR.Rcheck/fmcsR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'fmcsR.Rnw' 
** testing if installed package can be loaded
* DONE (fmcsR)

fmcsR.Rcheck/fmcsR-Ex.timings:

nameusersystemelapsed
MCS-class2.8870.0282.945
fmcs3.1890.0263.224
fmcsBatch3.4380.0153.453
fmcsR-package6.7720.0176.790
fmcstest0.0490.0090.058
mcs2sdfset1.0520.0141.066
plotMCS0.9110.0100.922