Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:40 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 | WARNINGS | 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fmcsR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings fmcsR_1.47.0.tar.gz |
StartedAt: 2024-08-16 00:51:33 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 00:53:16 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 103.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: fmcsR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fmcsR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings fmcsR_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/fmcsR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'fmcsR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'fmcsR' version '1.47.0' * 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 whether package 'fmcsR' can be installed ... WARNING Found the following significant warnings: 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] 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] See 'F:/biocbuild/bbs-3.20-bioc/meat/fmcsR.Rcheck/00install.out' for details. * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 code 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 ... NOTE fmcs: no visible global function definition for 'as' fmcs: no visible global function definition for 'new' fmcsBatch: no visible global function definition for 'as' fmcsBatch : score: no visible global function definition for 'as' plotMCS: no visible global function definition for 'par' coerce,list-MCS: no visible global function definition for 'new' Undefined global functions or variables: as new par Consider adding importFrom("graphics", "par") importFrom("methods", "as", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/fmcsR/libs/x64/fmcsR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fmcsR-package 1.51 0.05 10.06 fmcsBatch 0.08 0.01 8.87 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/fmcsR.Rcheck/00check.log' for details.
fmcsR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL fmcsR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'fmcsR' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 long unsigned int'} [-Wsign-compare] 143 | for (int i = 0; i < length; ++i) { | ~~^~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here 26 | struct Atom { | ^~~~ MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const std::string&)': MCSCompound.cpp:157:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long 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 std::string&) const': MCSCompound.cpp:194:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long 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 long unsigned int'} [-Wsign-compare] 467 | for(int i = 0; i < bondCount; ++i) { | ~~^~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 long unsigned int'} [-Wsign-compare] 143 | for (int i = 0; i < length; ++i) { | ~~^~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 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 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 long unsigned int'} [-Wsign-compare] 194 | if (level > vertexPath.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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: 'matchType' may be used uninitialized [-Wmaybe-uninitialized] 74 | matchType, runningMode, *timeout); | ^ fmcs_R_wrap.cpp:42:24: note: 'matchType' was declared here 42 | MCS::MatchType matchType; | ^~~~~~~~~ fmcs_R_wrap.cpp:74:45: warning: 'runningMode' may be used uninitialized [-Wmaybe-uninitialized] 74 | matchType, runningMode, *timeout); | ^ fmcs_R_wrap.cpp:52:26: note: 'runningMode' was declared here 52 | MCS::RunningMode runningMode; | ^~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o util.cpp: In function 'std::string getUpper(const std::string&)': util.cpp:11:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 11 | for (int i = 0; i < upper.length(); ++i) { | ~~^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-fmcsR/00new/fmcsR/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fmcsR)
fmcsR.Rcheck/fmcsR-Ex.timings
name | user | system | elapsed | |
MCS-class | 1.85 | 0.60 | 1.57 | |
fmcs | 1.97 | 0.00 | 1.97 | |
fmcsBatch | 0.08 | 0.01 | 8.87 | |
fmcsR-package | 1.51 | 0.05 | 10.06 | |
fmcstest | 0.02 | 0.00 | 0.02 | |
mcs2sdfset | 0.43 | 0.00 | 0.42 | |
plotMCS | 0.46 | 0.01 | 0.54 | |