Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for ChemmineR on perceval

This page was generated on 2015-04-10 09:54:13 -0700 (Fri, 10 Apr 2015).

Package 144/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 2.18.1
ChemmineR Team
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ChemmineR
Last Changed Rev: 99651 / Revision: 102249
Last Changed Date: 2015-02-20 09:21:18 -0800 (Fri, 20 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: ChemmineR
Version: 2.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.18.1.tar.gz
StartedAt: 2015-04-09 23:38:43 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:42:30 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 226.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChemmineR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChemmineR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.18.1’
* 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/25s] OK
* 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’ ‘ChemmineOB’ ‘ChemmineDrugs’
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’ ‘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’
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’
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’
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’
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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* 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 ... [68s/75s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
generate3DCoords 14.012  0.041  14.267
addNewFeatures    3.952  0.296   8.804
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [40s/49s]
 [40s/49s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘RefManageR’
* 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

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

ChemmineR.Rcheck/00install.out:

* installing *source* package ‘ChemmineR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c DisjointSets.cpp -o DisjointSets.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&)’:
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc:118: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘int contains(int, std::vector<int, std::allocator<int> >&)’:
cluster.cc:131: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXPREC*)’:
cluster.cc:284: warning: comparison between signed and unsigned integer expressions
cluster.cc:298: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘void loadNNList(int, int, SEXPREC*)’:
cluster.cc:314: warning: comparison between signed and unsigned integer expressions
cluster.cc:332: warning: comparison between signed and unsigned integer expressions
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
cluster.cc:390: warning: comparison between signed and unsigned integer expressions
cluster.cc: At global scope:
cluster.cc:49: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXPREC*)’:
desc.cc:249: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXPREC*)’:
fingerprints.cc:137: warning: comparison between signed and unsigned integer expressions
fingerprints.cc:144: warning: comparison between signed and unsigned integer expressions
fingerprints.cc:157: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c formats.cc -o formats.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c molecule.cc -o molecule.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c r_wrap.cc -o r_wrap.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c script.cc -o script.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -DNO_MAIN -DNO_DEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c similarity.cc -o similarity.o
desc.h:39: warning: ‘elements’ defined but not used
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-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)

ChemmineR.Rcheck/ChemmineR-Ex.timings:

nameusersystemelapsed
AP-class0.6690.1050.774
APset-class0.4490.0890.549
FP-class0.0840.0030.087
FPset-class0.4330.0320.465
SDF-class0.0720.0080.093
SDF2apcmp0.0320.0010.033
SDFset-class0.5910.0380.641
SDFset2SDF0.1800.0100.191
SDFset2list0.0930.0420.135
SDFstr-class0.5020.0110.514
SMI-class0.0050.0000.005
SMIset-class0.0100.0010.011
addDescriptorType0.0000.0000.001
addNewFeatures3.9520.2968.804
ap0.2780.0180.297
apfp0.0040.0010.004
apset0.0070.0010.008
apset2descdb0.4470.0940.559
atomblock0.1450.0200.164
atomcount0.2860.0080.304
atomprop0.0050.0010.005
atomsubset0.0360.0020.038
batchByIndex0.0010.0000.001
bondblock0.1370.0120.150
bonds0.0420.0030.045
browseJob0.0010.0000.001
bufferLines0.0010.0000.001
bufferResultSet0.0020.0010.002
byCluster1.2250.0071.233
canonicalNumbering1.1020.0972.067
canonicalize0.0720.0030.074
cid0.0260.0010.027
cluster.sizestat0.7860.0110.800
cluster.visualize1.0960.0131.217
cmp.cluster3.2920.0373.330
cmp.duplicated0.0520.0020.054
cmp.parse0.0340.0020.043
cmp.parse10.0000.0010.001
cmp.search1.0220.0191.043
cmp.similarity0.0270.0010.028
conMA0.0770.0130.095
connections0.3460.0140.419
datablock0.4290.0110.440
datablock2ma0.0520.0030.054
db.explain0.0970.0080.104
db.subset0.0050.0010.006
dbTransaction0.0930.0110.157
desc2fp0.1340.0050.145
exactMassOB1.0690.0161.087
findCompounds3.4820.0653.617
findCompoundsByName0.5040.0250.592
fingerprintOB0.0000.0000.001
fold0.0030.0010.002
foldCount0.0030.0000.003
fp2bit0.6570.0240.691
fpSim0.8080.0120.830
fptype0.0020.0000.002
fromNNMatrix1.1720.0041.176
genAPDescriptors0.0200.0010.022
generate3DCoords14.012 0.04114.267
getAllCompoundIds0.4910.0210.582
getCompoundFeatures3.3800.0373.495
getCompoundNames0.5140.0200.603
getCompounds0.5180.0200.606
getIds0.0000.0000.001
grepSDFset0.0710.0010.073
groups0.3560.0060.364
header0.1330.0040.137
initDb0.0960.0130.165
jarvisPatrick2.7640.0142.778
jobToken-class0.0020.0000.002
launchCMTool0.0010.0000.001
listCMTools0.0010.0000.001
listFeatures0.5690.0240.649
loadSdf3.7050.0433.879
makeUnique0.0220.0010.022
maximallyDissimilar0.3920.0010.393
nearestNeighbors1.9610.0061.966
numBits0.0020.0000.002
obmol0.0630.0020.065
parBatchByIndex0.0010.0000.001
plotStruc0.3790.0130.421
propOB0.0000.0000.001
pubchemFPencoding0.0040.0010.005
read.AP0.0200.0020.022
read.SDFindex0.0200.0010.022
read.SDFset0.8130.0030.817
read.SDFstr1.2010.0051.206
read.SMIset0.0020.0010.003
regenerateCoords0.0000.0000.001
result0.0010.0000.001
rings0.7050.0050.722
sdf.subset0.0010.0000.001
sdf.visualize0.0190.0010.020
sdf2ap0.5290.0890.624
sdf2list0.0420.0120.053
sdf2smiles000
sdf2str0.0440.0050.049
sdfStream0.0220.0010.023
sdfid0.0350.0010.036
sdfsample0.0680.0040.073
sdfstr2list1.9550.4032.435
searchSim0.0000.0000.001
searchString0.0010.0000.001
selectInBatches0.0020.0000.002
setPriorities0.0000.0000.001
smartsSearchOB0.0010.0010.000
smiles2sdf0.0010.0000.001
smisample0.0060.0000.007
status0.0010.0000.001
toolDetails0.0010.0000.001
trimNeighbors2.1990.0072.206
validSDF0.0260.0010.028
view0.0960.0070.102
write.SDF0.2430.0050.248
write.SDFsplit0.0190.0010.020
write.SMI0.0020.0010.003