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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/fmcsR_1.22.0.tar.gz && rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fmcsR.buildbin-libdir fmcsR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL fmcsR_1.22.0.zip && rm fmcsR_1.22.0.tar.gz fmcsR_1.22.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'fmcsR' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 = 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) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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::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) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 = 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) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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()) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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]
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c util.cpp -o util.o
util.cpp: In function 'std::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) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'fmcsR'
finding HTML links ... done
MCS-class html
fmcs html
fmcsBatch html
fmcsR-package html
fmcstest html
mcs2sdfset html
plotMCS html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'fmcsR' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 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) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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::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) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 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) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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()) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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]
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c util.cpp -o util.o
util.cpp: In function 'std::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) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.22.0.zip
* DONE (fmcsR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'fmcsR' successfully unpacked and MD5 sums checked
In R CMD INSTALL