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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings fmcsR_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/fmcsR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘fmcsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmcsR’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:87:23: 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/fmcsR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 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 loading without being on the library search path ... 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 1.249  0.032   7.378
fmcsBatch     0.058  0.010   6.182
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/fmcsR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL fmcsR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-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 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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);
      |             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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 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-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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 unsigned int’} [-Wsign-compare]
   11 |     for (int i = 0; i < upper.length(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)