Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:40 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 740/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fmcsR 1.47.0 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the fmcsR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fmcsR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: fmcsR |
Version: 1.47.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL fmcsR |
StartedAt: 2024-08-26 15:53:35 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 15:53:52 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 17.8 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL fmcsR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘fmcsR’ ... ** using staged installation 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++ -std=gnu++17 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 using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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 of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 108 | for (int i = 0; i < atomCountOne; ++i) { | ~~^~~~~~~~~~~~~~ MCS.cpp:116:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 116 | for (int i = 0; i < atomCountTwo; ++i) { | ~~^~~~~~~~~~~~~~ In file included from MCSCompound.h:15, 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:381:44: required from here MCSList.h:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 143 | for (int i = 0; i < length; ++i) { | ~~^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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: MCSRingDetector.h: In constructor ‘FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)’: MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | 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 of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 142 | if (vertexIndex < vertexPath.size()-1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ MCSCompound.cpp: In copy constructor ‘FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)’: MCSCompound.cpp:87:23: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct FMCS::MCSCompound::Atom’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 87 | memcpy(atoms, other.atoms, sizeof(Atom) * other.atomCount); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from MCSCompound.cpp:4: MCSCompound.h:26:16: note: ‘struct FMCS::MCSCompound::Atom’ declared here 26 | struct Atom { | ^~~~ MCSCompound.cpp: In member function ‘const FMCS::MCSCompound& FMCS::MCSCompound::operator=(const FMCS::MCSCompound&)’: MCSCompound.cpp:123:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct FMCS::MCSCompound::Atom’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 123 | memcpy(atoms, that.atoms, sizeof(Atom) * that.atomCount); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from MCSCompound.cpp:4: MCSCompound.h:26:16: note: ‘struct FMCS::MCSCompound::Atom’ declared here 26 | struct Atom { | ^~~~ MCSCompound.cpp: In member function ‘void FMCS::MCSCompound::read(const string&)’: MCSCompound.cpp:157:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 157 | 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 of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 194 | 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 of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 467 | for(int i = 0; i < bondCount; ++i) { | ~~^~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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, from MCSMap.cpp:3: MCSList.h: In instantiation of ‘bool FMCS::MCSList<T>::contains(const T&) const [with T = long unsigned int]’: MCSMap.cpp:28:32: required from here MCSList.h:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 143 | for (int i = 0; i < length; ++i) { | ~~^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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: MCSRingDetector.h: In constructor ‘FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)’: MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | 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 of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 142 | if (vertexIndex < vertexPath.size()-1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::sortVertexQueue()’: MCSRingDetector.cpp:93:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 93 | for (int i = 0; i < vertexQueue.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~ MCSRingDetector.cpp:94:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 94 | for (int j = 0; j < queueSize-1-i; ++j ) { | ~~^~~~~~~~~~~~~~~ MCSRingDetector.cpp: In member function ‘void FMCS::MCSRingDetector::convert()’: MCSRingDetector.cpp:149:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 149 | 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] 175 | int aromaticCount = 0; | ^~~~~~~~~~~~~ MCSRingDetector.cpp: In member function ‘bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const’: MCSRingDetector.cpp:194:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 194 | if (level > vertexPath.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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] 74 | matchType, runningMode, *timeout); | ^ fmcs_R_wrap.cpp:74:45: warning: ‘matchType’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o util.cpp: In function ‘std::string getUpper(const string&)’: util.cpp:11:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 11 | for (int i = 0; i < upper.length(); ++i) { | ~~^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-fmcsR/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fmcsR)