ChemmineR 2.25.5
Thomas Girke
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR | | Last Changed Rev: 119808 / Revision: 121152 | | Last Changed Date: 2016-08-01 09:07:37 -0700 (Mon, 01 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | ERROR | skipped | skipped | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineR_2.25.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.25.5’
* 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 ... 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 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’
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’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
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_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’
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’
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’
updatePriorities: no visible global function definition for
‘dbGetPreparedQuery’
write.SMI: no visible global function definition for ‘write.table’
Undefined global functions or variables:
AW C1 C1.1 C2 C2.1 arrangeGrob browseURL canonicalNumbering_OB
clusterApplyLB clusterExport combn convertFormat convertFormatFile
data dbGetPreparedQuery dev.off error exactMass_OB fingerprint_OB
fmcs forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId
postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript
prop_OB rainbow rasterGrob read.delim read.table readPNG rgb
smartsSearch_OB str string write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
"rgb")
importFrom("utils", "browseURL", "combn", "data", "read.delim",
"read.table", "str", "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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
-stdlib=libstdc++
* 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’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.
* installing *source* package ‘ChemmineR’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c DisjointSets.cpp -o DisjointSets.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c cstrsplit.cc -o cstrsplit.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c desc.cc -o desc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c fingerprints.cc -o fingerprints.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c formats.cc -o formats.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c molecule.cc -o molecule.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c r_wrap.cc -o r_wrap.o
r_wrap.cc:1689:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c script.cc -o script.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -stdlib=libstdc++ -DNO_MAIN -DNO_DEBUG -fPIC -Wall -mtune=core2 -g -O2 -c similarity.cc -o similarity.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -stdlib=libstdc++ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
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)