ChemmineR 2.22.0
Thomas Girke
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ChemmineR | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘2.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChemmineR’ can be installed ... [16s/17s] OK
* 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:
‘ChemmineOB’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘grid’
‘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 binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
applyOptions: no visible global function definition for ‘convertFormat’
canonicalNumbering: no visible global function definition for
‘canonicalNumbering_OB’
canonicalNumberingOB: no visible global function definition for
‘canonicalNumbering_OB’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
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’
getDbConn: no visible global function definition for ‘error’
handle_raster: no visible global function definition for ‘readPNG’
handle_raster: no visible global function definition for ‘rasterGrob’
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’
insertDef: no visible global function definition for
‘dbGetPreparedQuery’
insertDescriptor: no visible global function definition for
‘dbGetPreparedQuery’
insertDescriptorType: no visible global function definition for
‘dbGetPreparedQuery’
insertFeature: no visible global function definition for
‘dbGetPreparedQuery’
insertNamedDef: no visible global function definition for
‘dbGetPreparedQuery’
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’
sdf2OBMol: no visible global function definition for ‘forEachMol’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
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’
updatePriorities: no visible global function definition for
‘dbGetPreparedQuery’
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘ChemmineR/libs/ChemmineR.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Objects: ‘desc.o’, ‘formats.o’, ‘script.o’
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘cluster.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [33s/33s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [15s/15s]
[15s/16s] 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: 6 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.
* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
^
cluster.cc:118:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
^
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < list.size(); i++)
^
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < nbr_list[i].size(); j ++) {
^
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
^
cluster.cc:298:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
^
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
^
cluster.cc:332:20: warning: comparison between signed and unsigned integer expressions [-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:390:22: warning: comparison between signed and unsigned integer expressions [-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)
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c cstrsplit.cc -o cstrsplit.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < descs.size(); i++)
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < aps.size(); i++)
^
fingerprints.cc:145:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
^
fingerprints.cc:158:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -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;
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c script.cc -o script.o
In file included from script.cc:2:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
static char elements[112][3] = {
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c similarity.cc -o similarity.o
In file included from similarity.cc:1:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
static char elements[112][3] = {
^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘ChemmineR’
Creating a generic function for ‘print’ from package ‘base’ in package ‘ChemmineR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)