Thomas Girke
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/fmcsR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9440089 |
| git_last_commit_date: 2021-05-19 11:53:39 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:05 -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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fmcsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fmcsR_1.34.0.tar.gz |
| StartedAt: 2021-10-14 23:17:59 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:20:07 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 127.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: fmcsR.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fmcsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fmcsR_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fmcsR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/Users/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 ... WARNING
Invalid citation information in 'inst/CITATION':
Failed with error: 'there is no package called 'bibtex''
Error in (function (bibtype, textVersion = NULL, header = NULL, footer = NULL, key = NULL, ..., other = list(), mheader = NULL, mfooter = NULL) { BibTeX_names <- names(BibLaTeX_entry_field_db) args <- c(list(...), other) if (!length(args)) return(structure(list(), class = "bibentry")) if (any(vapply(names(args), .is_not_nonempty_text, FALSE))) stop("all fields have to be named") args <- c(list(bibtype = bibtype, textVersion = textVersion, header = header, footer = footer, key = key), list(...)) args <- lapply(args, .listify) other <- lapply(other, .listify) max_length <- max(vapply(c(args, other), length, 0L)) args_length <- vapply(args, length, 0L) if (!all(args_length_ok <- args_length %in% c(1L, max_length))) warning(gettextf("Not all arguments are of the same length, %s: %s", "the following need to be recycled", paste(names(args)[!args_length_ok], collapse = ", ")), domain = NA) args <- lapply(args, function(x) rep(x, length.out = max_length)) other_length <- vapply(other, length, 0L) if (!all(other_length_ok <- other_length %in% c(1L, max_length))) warning(gettextf("Not all arguments are of the same length, %s: %s", "the following need to be recycled", paste(names(other)[!other_length_ok], collapse = ", ")), domain = NA) other <- lapply(other, function(x) rep(x, length.out = max_length)) bibentry1 <- function(bibtype, textVersion, header = NULL, footer = NULL, key = NULL, ..., other = list()) { bibtype <- as.character(bibtype) stopifnot(length(bibtype) == 1L) pos <- match(tolower(bibtype), tolower(BibTeX_names)) if (is.na(pos)) stop(gettextf("%s has to be one of %s", sQuote("bibtype"), paste(BibTeX_names, collapse = ", ")), domain = NA) bibtype <- BibTeX_names[pos] rval <- c(list(...), other) rval <- rval[!vapply(rval, .is_not_nonempty_text, FALSE)] fields <- tolower(names(rval)) names(rval) <- fields attr(rval, "bibtype") <- bibtype .BibEntryCheckBibEntry1(rval) pos <- fields %in% .BibEntryNameList if (any(pos)) { for (i in which(pos)) if (!inherits(rval[[i]], "person")) rval[[i]] <- ArrangeAuthors(rval[[i]]) } pos <- fields %in% c("dateobj") | pos if (any(!pos)) { for (i in which(!pos)) rval[[i]] <- as.character(rval[[i]]) } attr(rval, "key") <- if (is.null(key)) NULL else as.character(key) if (is.null(rval[["dateobj"]])) { tdate <- try(ProcessDates(rval), TRUE) if (!inherits(tdate, "try-error")) attr(rval, "dateobj") <- tdate } else { attr(rval, "dateobj") <- rval[["dateobj"]] rval[["dateobj"]] <- NULL } if (!is.null(textVersion)) attr(rval, "textVersion") <- as.character(textVersion) if (!.is_not_nonempty_text(header)) attr(rval, "header") <- paste(header, collapse = "\n") if (!.is_not_nonempty_text(footer)) attr(rval, "footer") <- paste(footer, collapse = "\n") return(rval) } rval <- lapply(seq_along(args$bibtype), function(i) do.call("bibentry1", c(lapply(args, "[[", i), list(other = lapply(other, "[[", i))))) if (!.is_not_nonempty_text(mheader)) attr(rval, "mheader") <- paste(mheader, collapse = "\n") if (!.is_not_nonempty_text(mfooter)) attr(rval, "mfooter") <- paste(mfooter, collapse = "\n") class(rval) <- c("BibEntry", "bibentry") rval})(year = "2021", key = "_2021"): argument "bibtype" is missing, with no default
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/fmcsR/libs/i386/fmcsR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/fmcsR/libs/x64/fmcsR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fmcsR-package 1.63 0.01 9.77
fmcsBatch 0.08 0.00 8.15
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fmcsR-package 1.68 0.02 10.11
fmcsBatch 0.07 0.00 8.22
* 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: 2 WARNINGs, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/fmcsR.Rcheck/00check.log'
for details.
fmcsR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/fmcsR_1.34.0.tar.gz && rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fmcsR.buildbin-libdir fmcsR_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL fmcsR_1.34.0.zip && rm fmcsR_1.34.0.tar.gz fmcsR_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
3 80732 3 2488 0 0 30423 0 0:00:02 --:--:-- 0:00:02 30341
100 80732 100 80732 0 0 510k 0 --:--:-- --:--:-- --:--:-- 508k
install for i386
* installing *source* package 'fmcsR' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/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 'unsigned int'} [-Wsign-compare]
for (int i = 0; i < atomCountOne; ++i) {
~~^~~~~~~~~~~~~~
MCS.cpp:116:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 = 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 unsigned int'} [-Wsign-compare]
for (int i = 0; i < length; ++i) {
~~^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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]
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
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]
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
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 'unsigned int'} [-Wsign-compare]
for (int i = 0; i < bondCount; ++i) {
~~^~~~~~~~~~~
MCSCompound.cpp: In member function 'std::__cxx11::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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < bondCount; ++i) {
~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/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 = 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 unsigned int'} [-Wsign-compare]
for (int i = 0; i < length; ++i) {
~~^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
if (level > vertexPath.size()) {
~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/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: '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:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
util.cpp: In function 'std::__cxx11::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 'unsigned int'} [-Wsign-compare]
for (int i = 0; i < upper.length(); ++i) {
~~^~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/fmcsR.buildbin-libdir/00LOCK-fmcsR/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'fmcsR' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/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]
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]
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:381:69: 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]
for (int i = 0; i < length; ++i) {
~~^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/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]
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]
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]
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
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]
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
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 long unsigned int'} [-Wsign-compare]
for (int i = 0; i < bondCount; ++i) {
~~^~~~~~~~~~~
MCSCompound.cpp: In member function 'std::__cxx11::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 long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
for(int i = 0; i < bondCount; ++i) {
~~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/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:28:36: 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]
for (int i = 0; i < length; ++i) {
~~^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/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]
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]
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]
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]
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]
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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
if (level > vertexPath.size()) {
~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/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: '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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
util.cpp: In function 'std::__cxx11::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 long unsigned int'} [-Wsign-compare]
for (int i = 0; i < upper.length(); ++i) {
~~^~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.34.0.zip
* DONE (fmcsR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'fmcsR' successfully unpacked and MD5 sums checked
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fmcsR.Rcheck/examples_i386/fmcsR-Ex.timings
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fmcsR.Rcheck/examples_x64/fmcsR-Ex.timings
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