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BioC 2.13: CHECK report for ChemmineR on perceval

This page was generated on 2014-04-05 09:52:10 -0700 (Sat, 05 Apr 2014).

Package 128/750HostnameOS / ArchBUILDCHECKBUILD BIN
ChemmineR 2.14.3
ChemmineR Team
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ChemmineR
Last Changed Rev: 87755 / Revision: 88450
Last Changed Date: 2014-03-22 19:42:23 -0700 (Sat, 22 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ChemmineR
Version: 2.14.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.14.3.tar.gz
StartedAt: 2014-04-05 00:10:48 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:13:31 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 163.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ChemmineR.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ChemmineR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.14.3’
* 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 ... [11s/11s] 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:
  ‘methods’
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
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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’
fingerprintOB: no visible global function definition for
  ‘fingerprint_OB’
propOB: no visible global function definition for ‘prop_OB’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
smile2sdfFile: no visible global function definition for
  ‘convertFormatFile’
smiles2sdf: no visible global function definition for ‘convertFormat’
smiles2sdfOB: no visible global function definition for ‘convertFormat’
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/ChemmineR.Rcheck/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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ChemmineR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [61s/61s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
jarvisPatrick 5.702  0.121    5.84
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [26s/28s]
 [27s/28s] 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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   -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   -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   -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:202: warning: unused variable ‘id’
desc.cc:253: warning: comparison between signed and unsigned integer expressions
desc.cc:180: warning: unused variable ‘d’
desc.cc:218: warning: unused variable ‘Rf_ncols’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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   -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   -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   -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   -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/usr/local/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o desc.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-2.13-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-class0.9290.1061.035
APset-class0.8410.1050.946
FP-class0.1960.0080.204
FPset-class0.5990.0360.634
SDF-class0.1000.0110.112
SDF2apcmp0.0470.0020.049
SDFset-class0.9240.0570.987
SDFset2SDF0.2200.0170.238
SDFset2list0.1320.0470.180
SDFstr-class0.5950.0120.622
SMI-class0.0130.0010.013
SMIset-class0.0390.0050.044
addNewFeatures4.4440.1744.650
ap0.5510.0240.576
apfp0.0170.0010.018
apset0.0190.0020.021
apset2descdb0.9690.0951.065
atomblock0.3740.0280.407
atomcount0.5610.0130.574
atomprop0.0110.0020.012
atomsubset0.0630.0020.065
batchByIndex0.0080.0010.009
bondblock0.3410.0200.360
bonds0.0610.0110.071
bufferLines0.0060.0030.008
bufferResultSet0.0100.0030.013
byCluster1.3200.0241.345
cid0.0990.0060.105
cluster.sizestat0.7840.0200.805
cluster.visualize0.9370.0180.956
cmp.cluster2.9650.0513.020
cmp.duplicated0.0710.0090.079
cmp.parse0.0410.0060.048
cmp.parse10.0090.0020.011
cmp.search1.0640.0271.090
cmp.similarity0.0320.0060.039
conMA0.1000.0210.121
datablock0.6370.0150.654
datablock2ma0.0700.0070.077
db.explain0.1100.0100.123
db.subset0.1210.0080.128
dbTransaction0.0900.0140.104
desc2fp0.2090.0190.231
findCompounds3.8820.0663.952
findCompoundsByName0.6500.0210.673
fingerprintOB0.0190.0020.020
fp2bit1.4700.1191.592
fpSim1.3290.1081.450
fromNNMatrix1.4310.0091.440
genAPDescriptors0.0360.0020.039
getCompoundNames0.6610.0220.686
getCompounds0.6220.0270.651
getIds0.0050.0020.008
grepSDFset0.0960.0030.100
groups0.2350.0100.245
header0.2390.0100.249
initDb0.0870.0080.097
jarvisPatrick5.7020.1215.840
listFeatures0.6250.0200.646
loadSdf4.2360.0864.327
makeUnique0.0590.0050.064
nearestNeighbors2.4910.0192.511
parBatchByIndex0.0140.0060.020
plotStruc0.3810.0110.392
propOB0.0120.0030.015
pubchemFPencoding0.0090.0040.012
read.AP0.0310.0080.039
read.SDFindex0.0350.0080.044
read.SDFset0.8880.0060.895
read.SDFstr1.4770.0041.480
read.SMIset0.0090.0040.013
rings0.8150.0160.831
sdf.subset0.0090.0020.012
sdf.visualize0.0380.0020.040
sdf2ap0.8580.1210.981
sdf2list0.0420.0150.057
sdf2smiles0.0080.0020.009
sdf2str0.0600.0120.072
sdfStream0.0360.0090.045
sdfid0.0520.0050.057
sdfsample0.0800.0040.085
sdfstr2list1.8420.4362.293
searchSim0.0100.0050.014
searchString0.0120.0040.017
selectInBatches0.0110.0040.016
smiles2sdf0.0130.0030.015
smisample0.0170.0040.021
trimNeighbors3.2760.0193.297
validSDF0.0520.0020.054
view0.1610.0080.169
write.SDF0.3570.0090.365
write.SDFsplit0.0290.0080.037
write.SMI0.0110.0050.016