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INSTALL report for fmcsR on malbec2

This page was generated on 2018-10-17 08:24:33 -0400 (Wed, 17 Oct 2018).

Package 526/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fmcsR 1.22.0
Thomas Girke
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/fmcsR
Branch: RELEASE_3_7
Last Commit: 4fdec21
Last Changed Date: 2018-04-30 10:35:26 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: fmcsR
Version: 1.22.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL fmcsR
StartedAt: 2018-10-15 18:03:30 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 18:03:43 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 13.0 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL fmcsR
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* 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... /bin/grep
checking for egrep... /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
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c MCS.cpp -o MCS.o
MCS.cpp: In member function ‘void FMCS::MCS::calculate()’:
MCS.cpp:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountOne; ++i) {
                                   ^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountTwo; ++i) {
                                   ^
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In instantiation of ‘bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]’:
MCS.cpp:381:69:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:5:0:
MCSRingDetector.h: In constructor ‘FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)’:
MCSRingDetector.h:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                   ^
MCSRingDetector.h: In member function ‘int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const’:
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                                 ^
MCSCompound.cpp: In member function ‘void FMCS::MCSCompound::read(const string&)’:
MCSCompound.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < bondCount; ++i) {
                           ^
MCSCompound.cpp: In member function ‘std::__cxx11::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const’:
MCSCompound.cpp:194:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < indexLength; ++i) {
                           ^
MCSCompound.cpp: In member function ‘const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const’:
MCSCompound.cpp:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int i = 0; i < bondCount; ++i) {
                          ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8:0,
                 from MCSMap.cpp:3:
MCSList.h: In instantiation of ‘bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]’:
MCSMap.cpp:28:36:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:0:
MCSRingDetector.h: In constructor ‘FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)’:
MCSRingDetector.h:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                   ^
MCSRingDetector.h: In member function ‘int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const’:
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                                 ^
MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::sortVertexQueue()’:
MCSRingDetector.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < vertexQueue.size(); ++i) {
                           ^
MCSRingDetector.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < queueSize-1-i; ++j ) {
                               ^
MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::convert()’:
MCSRingDetector.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < degree; ++j) {
                               ^
MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::detect()’:
MCSRingDetector.cpp:175:13: warning: unused variable ‘aromaticCount’ [-Wunused-variable]
         int aromaticCount = 0;
             ^
MCSRingDetector.cpp: In member function ‘bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const’:
MCSRingDetector.cpp:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (level > vertexPath.size()) {
                   ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
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:74:45: warning: ‘runningMode’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             matchType, runningMode, *timeout);
                                             ^
fmcs_R_wrap.cpp:74:45: warning: ‘matchType’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c util.cpp -o util.o
util.cpp: In function ‘std::__cxx11::string getUpper(const string&)’:
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < upper.length(); ++i) {
                       ^
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/fmcsR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fmcsR)