CHECK report for ChemmineR on tokay1
This page was generated on 2021-05-06 12:30:11 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the ChemmineR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
|
| ChemmineR 3.42.2 (landing page)
Thomas Girke
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ChemmineR |
| Branch: RELEASE_3_12 |
| Last Commit: d1536d5 |
| Last Changed Date: 2021-02-25 13:09:29 -0400 (Thu, 25 Feb 2021) |
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |  | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | |
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | |
Summary
Command output
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChemmineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChemmineR_3.42.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '3.42.2'
* 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 'ChemmineR' can be installed ... WARNING
Found the following significant warnings:
formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'png'
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' calls in package code:
'ChemmineDrugs' 'ChemmineOB' 'RPostgreSQL' 'RSQLite' 'fmcsR' 'png'
'snow'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'BiocGenerics'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'ChemmineR/R/sim.R':
unlockBinding(".progress_bar_int_cnt", environment(.progress_bar))
.data.frame.to.str: no visible global function definition for
'write.table'
.data.frame.to.str: no visible binding for global variable 'string'
.parseV3000: no visible binding for global variable 'AW'
.rings: no visible global function definition for 'combn'
DUD: no visible global function definition for 'download.file'
DUD: no visible global function definition for 'untar'
applyOptions: no visible global function definition for 'convertFormat'
browseJob: no visible global function definition for 'browseURL'
canonicalNumbering: no visible global function definition for
'canonicalNumbering_OB'
canonicalNumberingOB: no visible global function definition for
'canonicalNumbering_OB'
cluster.visualize: no visible global function definition for 'rainbow'
cluster.visualize: no visible global function definition for 'pdf'
cluster.visualize: no visible global function definition for
'postscript'
cluster.visualize: no visible global function definition for 'dev.off'
desc2fp: no visible global function definition for 'data'
draw_sdf: no visible global function definition for 'rgb'
draw_sdf: no visible global function definition for 'fmcs'
exactMassOB: no visible global function definition for 'exactMass_OB'
fingerprintOB: no visible global function definition for
'fingerprint_OB'
getCompoundFeatures : <anonymous>: no visible global function
definition for 'write.table'
getCompounds: no visible global function definition for 'str'
getDbConn: no visible global function definition for 'error'
handle_segs: no visible binding for global variable 'C1'
handle_segs: no visible binding for global variable 'C2'
handle_segs: no visible binding for global variable 'C1.1'
handle_segs: no visible binding for global variable 'C2.1'
handle_text: no visible binding for global variable 'C1'
handle_text: no visible binding for global variable 'C2'
listCMTools: no visible global function definition for 'read.table'
parBatchByIndex: no visible global function definition for
'clusterExport'
parBatchByIndex: no visible global function definition for
'clusterApplyLB'
postgresqlWriteTable: no visible global function definition for
'postgresqlTableRef'
postgresqlWriteTable: no visible global function definition for
'postgresqlQuoteId'
postgresqlWriteTable: no visible global function definition for
'postgresqlpqExec'
postgresqlWriteTable: no visible global function definition for
'postgresqlCopyInDataframe'
postgresqlWriteTable: no visible global function definition for
'postgresqlgetResult'
propOB: no visible global function definition for 'prop_OB'
read.AP: no visible global function definition for 'read.delim'
sdf2OBMol: no visible global function definition for 'forEachMol'
sdf2image: no visible global function definition for 'convertToImage'
sdf2smiles: no visible global function definition for 'convertFormat'
sdf2smilesOB: no visible global function definition for 'convertFormat'
sdfStream: no visible global function definition for 'write.table'
setPriorities: no visible global function definition for
'clusterExport'
smartsSearchOB: no visible global function definition for
'smartsSearch_OB'
smile2sdfFile: no visible global function definition for
'convertFormatFile'
smiles2sdf: no visible global function definition for 'convertFormat'
smiles2sdfOB: no visible global function definition for 'convertFormat'
write.SMI: no visible global function definition for 'write.table'
Undefined global functions or variables:
AW C1 C1.1 C2 C2.1 browseURL canonicalNumbering_OB clusterApplyLB
clusterExport combn convertFormat convertFormatFile convertToImage
data dev.off download.file error exactMass_OB fingerprint_OB fmcs
forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId
postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript
prop_OB rainbow read.delim read.table rgb smartsSearch_OB str string
untar write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
"rgb")
importFrom("utils", "browseURL", "combn", "data", "download.file",
"read.delim", "read.table", "str", "untar", "write.table")
to your NAMESPACE file.
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* 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-3.12-bioc/R/library/ChemmineR/libs/i386/ChemmineR.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-3.12-bioc/R/library/ChemmineR/libs/x64/ChemmineR.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
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addNewFeatures 5.18 0.22 5.39
loadSdf 5.02 0.03 5.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.
Installation output
ChemmineR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ChemmineR_3.42.2.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.42.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.42.2.zip && rm ChemmineR_3.42.2.tar.gz ChemmineR_3.42.2.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
100 780k 100 780k 0 0 2236k 0 --:--:-- --:--:-- --:--:-- 2241k
install for i386
* installing *source* package 'ChemmineR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
~~^~~~~~~~~~~~~~
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:17: 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 < list.size(); i++)
~~^~~~~~~~~~~~~
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int j = 0; j < nbr_list[i].size(); j ++) {
~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
~^~
cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
~^~
cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for(unsigned i=0; i<N; i++){
~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cstrsplit.cc:2:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int i=0; i < descs.size(); i++)
~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int i=0; i < aps.size(); i++)
~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o
formats.cc: In function 'int sdf_iter(std::fstream&, std::__cxx11::string&, int&)':
formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
strncpy(buf_4, line, 4);
~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
const char *p = typeName;
^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o
In file included from script.cc:2:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
static char elements[112][3] = {
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
static char elements[112][3] = {
^~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ChemmineR'
finding HTML links ... done
AP-class html
APset-class html
ExtSDF-class html
FP-class html
FPset-class html
SDF-class html
SDF2apcmp html
SDFDataTable html
SDFset-class html
SDFset2SDF html
SDFset2list html
SDFstr-class html
SMI-class html
SMIset-class html
addDescriptorType html
addNewFeatures html
ap html
apfp html
apset html
apset2descdb html
atomblock html
atomcount html
atomprop html
atomsubset html
batchByIndex html
bondblock html
bonds html
browseJob html
bufferLines html
bufferResultSet html
byCluster html
canonicalNumbering html
canonicalize html
cid html
cluster.sizestat html
cluster.visualize html
cmp.cluster html
cmp.duplicated html
cmp.parse html
cmp.parse1 html
cmp.search html
cmp.similarity html
conMA html
connections html
datablock html
datablock2ma html
db.explain html
db.subset html
dbTransaction html
desc2fp html
draw_sdf html
exactMassOB html
findCompounds html
findCompoundsByName html
fingerprintOB html
fold html
foldCount html
fp2bit html
fpSim html
fptype html
fromNNMatrix html
genAPDescriptors html
genParameters html
generate3DCoords html
getAllCompoundIds html
getCompoundFeatures html
getCompoundNames html
getCompounds html
getIds html
grepSDFset html
groups html
header html
initDb html
jarvisPatrick html
jarvisPatrick_c html
jobToken-class html
largestComponent html
launchCMTool html
listCMTools html
listFeatures html
loadSdf html
makeUnique html
maximallyDissimilar html
nearestNeighbors html
numBits html
obmol html
openBabelPlot html
parBatchByIndex html
plotStruc html
propOB html
pubchemCidToSDF html
pubchemFPencoding html
pubchemName2CID html
pubchemSDFSearch html
pubchemSmilesSearch html
read.AP html
read.SDFindex html
read.SDFset html
read.SDFstr html
read.SMIset html
regenerateCoords html
result html
rings html
sdf.subset html
sdf.visualize html
sdf2ap html
sdf2list html
sdf2smiles html
sdf2str html
sdfStream html
sdfid html
sdfsample html
sdfstr2list html
searchSim html
searchString html
selectInBatches html
setPriorities html
smartsSearchOB html
smiles2sdf html
smisample html
status html
toolDetails html
trimNeighbors html
validSDF html
view html
write.SDF html
write.SDFsplit html
write.SMI 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 'ChemmineR' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
~~^~~~~~~~~~~~~~
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:17: 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 < list.size(); i++)
~~^~~~~~~~~~~~~
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int j = 0; j < nbr_list[i].size(); j ++) {
~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
~^~
cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
~^~
cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
for(unsigned i=0; i<N; i++){
~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cstrsplit.cc:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i=0; i < descs.size(); i++)
~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i=0; i < aps.size(); i++)
~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o
formats.cc: In function 'int sdf_iter(std::fstream&, std::__cxx11::string&, int&)':
formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
strncpy(buf_4, line, 4);
~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
const char *p = typeName;
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o
In file included from script.cc:2:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
static char elements[112][3] = {
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
static char elements[112][3] = {
^~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_3.42.2.zip
* DONE (ChemmineR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ChemmineR' successfully unpacked and MD5 sums checked
Tests output
|
ChemmineR.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ChemmineR")
======= testing fpset ===============================================
======= folding...
Loading required package: RSQLite
[1] "createing db"
[1] "createing db"
[1] "loading first half, no features"
[1] "createing db"
[1] "loading first half,with features"
adding new features to existing compounds. This could take a while
[1] "loading incomplete features"
[1] "loading second half"
adding new features to existing compounds. This could take a while
[1] "done loading"
[1] "createing db"
adding new features to existing compounds. This could take a while
[1] "found 70 compounds"
[1] "found 20 compounds"
Timing stopped at: 0 0 0
Error in DEACTIVATED("local test") : local test
In addition: There were 14 warnings (use warnings() to see them)
Timing stopped at: 0 0 0
Error in DEACTIVATED("local test only") : local test only
found 100 ids
[1] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
[19] 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236
[37] 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
[55] 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272
[73] 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290
[91] 291 292 293 294 295 296 297 298 299 300
starting parBatchByIndex
Loading required package: snow
int [1:100] 201 202 203 204 205 206 207 208 209 210 ...
NULL
[1] "results: parBench-sub-1,parBench-sub-2,parBench-sub-3,parBench-sub-4,parBench-sub-5,parBench-sub-6,parBench-sub-7,parBench-sub-8,parBench-sub-9,parBench-sub-10"
[1] "loading duplications"
loading 1 new compounds, updating 1 compounds
fetching features:
Timing stopped at: 0 0 0
Error in DEACTIVATED("causing timeout on bioc, disabling for now") :
causing timeout on bioc, disabling for now
In addition: Warning messages:
1: In .quickCoerceSelect(thisClass, Class, coerceFun, coerceMethods, :
closing unused connection 6 (<-TOKAY1:11675)
2: In .quickCoerceSelect(thisClass, Class, coerceFun, coerceMethods, :
closing unused connection 5 (<-TOKAY1:11675)
3: In .quickCoerceSelect(thisClass, Class, coerceFun, coerceMethods, :
closing unused connection 4 (<-TOKAY1:11675)
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") :
this test requires ChemmineOB, but not installed
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") :
this test requires ChemmineOB, but not installed
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") :
this test requires ChemmineOB, but not installed
Timing stopped at: 0 0 0
Error in DEACTIVATED("removed old version of function") :
removed old version of function
Timing stopped at: 0 0 0
Error in DEACTIVATED("just for manual testing") : just for manual testing
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") :
this test requires ChemmineOB, but not installed
Timing stopped at: 0 0 0
Error in DEACTIVATED("requires local files") : requires local files
Timing stopped at: 0 0 0
Error in DEACTIVATED("fails on ubuntu 16.04") : fails on ubuntu 16.04
Timing stopped at: 0 0 0
Error in DEACTIVATED("Causes SSL protocol version error on BioC") :
Causes SSL protocol version error on BioC
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") :
this test requires ChemmineOB, but not installed
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") :
this test requires ChemmineOB, but not installed
RUNIT TEST PROTOCOL -- Thu May 06 01:24:25 2021
***********************************************
Number of test functions: 17
Number of deactivated test functions: 14
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChemmineR RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of deactivated test functions: 14
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.56 1.09 19.62
|
ChemmineR.Rcheck/tests_x64/runTests.Rout
|
Example timings
|
ChemmineR.Rcheck/examples_i386/ChemmineR-Ex.timings
|
ChemmineR.Rcheck/examples_x64/ChemmineR-Ex.timings
|