Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the fmcsR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 670/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fmcsR 1.34.0 (landing page) Thomas Girke
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: fmcsR |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings fmcsR_1.34.0.tar.gz |
StartedAt: 2021-10-14 09:53:21 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:54:13 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 52.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: fmcsR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings fmcsR_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/fmcsR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fmcsR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fmcsR’ version ‘1.34.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘fmcsR’ can be installed ... WARNING Found the following significant warnings: MCSCompound.cpp:87:74: 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:123:68: 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/fmcsR.Rcheck/00install.out’ for details. * 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 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 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fmcsR-package 1.365 0.022 7.581 fmcsBatch 0.114 0.000 6.282 * 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 vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/fmcsR.Rcheck/00check.log’ for details.
fmcsR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL fmcsR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘fmcsR’ ... ** using staged installation 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 g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-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:381:69: 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++14 -I"/home/biocbuild/bbs-3.13-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:87:74: 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:123:68: 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++14 -I"/home/biocbuild/bbs-3.13-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:28:36: 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++14 -I"/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-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++14 -I"/home/biocbuild/bbs-3.13-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++14 -shared -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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)
fmcsR.Rcheck/fmcsR-Ex.timings
name | user | system | elapsed | |
MCS-class | 1.057 | 0.020 | 1.078 | |
fmcs | 1.363 | 0.013 | 1.375 | |
fmcsBatch | 0.114 | 0.000 | 6.282 | |
fmcsR-package | 1.365 | 0.022 | 7.581 | |
fmcstest | 0.012 | 0.012 | 0.024 | |
mcs2sdfset | 0.423 | 0.000 | 0.423 | |
plotMCS | 0.395 | 0.004 | 0.399 | |