Package: ChemmineR

Version: 2.11.19

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.11.19.tar.gz

StartedAt: 2013-03-24 03:27:53 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:30:43 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 170.1 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '2.11.19'
* 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 ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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'
* checking Rd files ... NOTE
prepare_Rd: batchByIndex.Rd:27-29: Dropping empty section \details
prepare_Rd: batchByIndex.Rd:30-36: Dropping empty section \value
prepare_Rd: batchByIndex.Rd:43-45: Dropping empty section \note
prepare_Rd: batchByIndex.Rd:40-42: Dropping empty section \author
prepare_Rd: batchByIndex.Rd:37-39: Dropping empty section \references
prepare_Rd: batchByIndex.Rd:49-51: Dropping empty section \seealso
prepare_Rd: bufferLines.Rd:25-27: Dropping empty section \details
prepare_Rd: bufferLines.Rd:28-34: Dropping empty section \value
prepare_Rd: bufferLines.Rd:41-43: Dropping empty section \note
prepare_Rd: bufferLines.Rd:38-40: Dropping empty section \author
prepare_Rd: bufferLines.Rd:35-37: Dropping empty section \references
prepare_Rd: bufferLines.Rd:47-49: Dropping empty section \seealso
prepare_Rd: bufferResultSet.Rd:28-30: Dropping empty section \details
prepare_Rd: bufferResultSet.Rd:31-37: Dropping empty section \value
prepare_Rd: bufferResultSet.Rd:44-46: Dropping empty section \note
prepare_Rd: bufferResultSet.Rd:41-43: Dropping empty section \author
prepare_Rd: bufferResultSet.Rd:38-40: Dropping empty section \references
prepare_Rd: bufferResultSet.Rd:50-52: Dropping empty section \seealso
prepare_Rd: findCompounds.Rd:27-29: Dropping empty section \details
prepare_Rd: findCompounds.Rd:30-36: Dropping empty section \value
prepare_Rd: findCompounds.Rd:43-45: Dropping empty section \note
prepare_Rd: findCompounds.Rd:40-42: Dropping empty section \author
prepare_Rd: findCompounds.Rd:37-39: Dropping empty section \references
prepare_Rd: findCompounds.Rd:49-51: Dropping empty section \seealso
prepare_Rd: findCompoundsByName.Rd:25-27: Dropping empty section \details
prepare_Rd: findCompoundsByName.Rd:28-34: Dropping empty section \value
prepare_Rd: findCompoundsByName.Rd:41-43: Dropping empty section \note
prepare_Rd: findCompoundsByName.Rd:38-40: Dropping empty section \author
prepare_Rd: findCompoundsByName.Rd:35-37: Dropping empty section \references
prepare_Rd: findCompoundsByName.Rd:47-49: Dropping empty section \seealso
prepare_Rd: getCompoundNames.Rd:22-24: Dropping empty section \details
prepare_Rd: getCompoundNames.Rd:25-31: Dropping empty section \value
prepare_Rd: getCompoundNames.Rd:38-40: Dropping empty section \note
prepare_Rd: getCompoundNames.Rd:35-37: Dropping empty section \author
prepare_Rd: getCompoundNames.Rd:32-34: Dropping empty section \references
prepare_Rd: getCompoundNames.Rd:44-46: Dropping empty section \seealso
prepare_Rd: getCompounds.Rd:25-27: Dropping empty section \details
prepare_Rd: getCompounds.Rd:28-34: Dropping empty section \value
prepare_Rd: getCompounds.Rd:41-43: Dropping empty section \note
prepare_Rd: getCompounds.Rd:38-40: Dropping empty section \author
prepare_Rd: getCompounds.Rd:35-37: Dropping empty section \references
prepare_Rd: getCompounds.Rd:47-49: Dropping empty section \seealso
prepare_Rd: initDb.Rd:21-23: Dropping empty section \details
prepare_Rd: initDb.Rd:24-30: Dropping empty section \value
prepare_Rd: initDb.Rd:37-39: Dropping empty section \note
prepare_Rd: initDb.Rd:34-36: Dropping empty section \author
prepare_Rd: initDb.Rd:31-33: Dropping empty section \references
prepare_Rd: initDb.Rd:43-45: Dropping empty section \seealso
prepare_Rd: jarvisPatrick_c.Rd:40-42: Dropping empty section \details
prepare_Rd: jarvisPatrick_c.Rd:43-49: Dropping empty section \value
prepare_Rd: jarvisPatrick_c.Rd:56-58: Dropping empty section \note
prepare_Rd: jarvisPatrick_c.Rd:53-55: Dropping empty section \author
prepare_Rd: jarvisPatrick_c.Rd:50-52: Dropping empty section \references
prepare_Rd: jarvisPatrick_c.Rd:62-64: Dropping empty section \seealso
prepare_Rd: jarvisPatrick_c.Rd:65-67: Dropping empty section \examples
prepare_Rd: loadSdf.Rd:31-33: Dropping empty section \details
prepare_Rd: loadSdf.Rd:34-40: Dropping empty section \value
prepare_Rd: loadSdf.Rd:47-49: Dropping empty section \note
prepare_Rd: loadSdf.Rd:44-46: Dropping empty section \author
prepare_Rd: loadSdf.Rd:41-43: Dropping empty section \references
prepare_Rd: loadSdf.Rd:53-55: Dropping empty section \seealso
prepare_Rd: loadSmiles.Rd:25-27: Dropping empty section \details
prepare_Rd: loadSmiles.Rd:28-34: Dropping empty section \value
prepare_Rd: loadSmiles.Rd:41-43: Dropping empty section \note
prepare_Rd: loadSmiles.Rd:38-40: Dropping empty section \author
prepare_Rd: loadSmiles.Rd:35-37: Dropping empty section \references
prepare_Rd: loadSmiles.Rd:47-49: Dropping empty section \seealso
prepare_Rd: selectInBatches.Rd:30-32: Dropping empty section \details
prepare_Rd: selectInBatches.Rd:33-39: Dropping empty section \value
prepare_Rd: selectInBatches.Rd:46-48: Dropping empty section \note
prepare_Rd: selectInBatches.Rd:43-45: Dropping empty section \author
prepare_Rd: selectInBatches.Rd:40-42: Dropping empty section \references
prepare_Rd: selectInBatches.Rd:52-54: Dropping empty section \seealso
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-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 installed files from 'inst/doc' ... OK
* checking examples ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
jarvisPatrick 7.441  0.446   7.973
trimNeighbors 5.515  0.028   5.561
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [27s/27s]
 [27s/27s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.

* 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  -fPIC  -mtune=core2 -g -O2  -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  -fPIC  -mtune=core2 -g -O2  -c cluster.cc -o cluster.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -mtune=core2 -g -O2  -c desc.cc -o desc.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -mtune=core2 -g -O2  -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  -fPIC  -mtune=core2 -g -O2  -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  -fPIC  -mtune=core2 -g -O2  -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  -fPIC  -mtune=core2 -g -O2  -c script.cc -o script.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -mtune=core2 -g -O2  -c similarity.cc -o similarity.o
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 -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-2.12-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
   'ChemmineR.Rnw' 
** testing if installed package can be loaded
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	1.995	0.156	2.161
APset-class	1.668	0.147	1.826
FP-class	0.193	0.008	0.202
FPset-class	0.610	0.041	0.653
SDF-class	0.199	0.014	0.214
SDF2apcmp	0.042	0.005	0.047
SDFset-class	0.851	0.061	0.919
SDFset2SDF	0.209	0.014	0.223
SDFset2list	0.118	0.053	0.172
SDFstr-class	0.674	0.010	0.686
ap	1.320	0.045	1.371
apfp	0.011	0.003	0.013
apset	0.018	0.002	0.021
apset2descdb	1.604	0.127	1.740
atomblock	0.532	0.040	0.574
atomcount	0.434	0.021	0.458
atomprop	0.016	0.002	0.018
atomsubset	0.068	0.004	0.072
batchByIndex	0.019	0.002	0.021
bondblock	0.332	0.020	0.354
bonds	0.072	0.007	0.078
bufferLines	0.012	0.004	0.016
bufferResultSet	0.010	0.006	0.015
cid	0.177	0.007	0.186
cluster.sizestat	1.003	0.016	1.022
cluster.visualize	1.293	0.024	1.328
cmp.cluster	3.611	0.062	3.686
cmp.duplicated	0.091	0.006	0.098
cmp.parse	0.059	0.007	0.067
cmp.parse1	0.009	0.002	0.011
cmp.search	1.335	0.027	1.365
cmp.similarity	0.046	0.008	0.054
conMA	0.121	0.023	0.145
datablock	0.726	0.027	0.758
datablock2ma	0.075	0.007	0.081
db.explain	0.087	0.010	0.097
db.subset	0.104	0.008	0.112
desc2fp	0.408	0.013	0.424
findCompounds	0.017	0.002	0.019
findCompoundsByName	0.015	0.001	0.015
fp2bit	1.597	0.107	1.710
fpSim	1.679	0.107	1.794
getCompoundNames	0.017	0.004	0.022
getCompounds	0.031	0.007	0.038
getIds	0.019	0.004	0.023
grepSDFset	0.124	0.006	0.133
groups	0.277	0.010	0.287
header	0.456	0.012	0.469
initDb	0.023	0.004	0.028
jarvisPatrick	7.441	0.446	7.973
loadSdf	0.036	0.011	0.053
loadSmiles	0.009	0.003	0.012
makeUnique	0.145	0.007	0.156
nearestNeighbors	4.257	0.034	4.338
plotStruc	0.523	0.017	0.561
pubchemFPencoding	0.012	0.003	0.018
read.AP	0.054	0.005	0.066
read.SDFindex	0.051	0.008	0.064
read.SDFset	1.280	0.013	1.389
read.SDFstr	1.896	0.011	1.911
rings	1.031	0.023	1.061
sdf.subset	0.018	0.001	0.020
sdf.visualize	0.047	0.004	0.051
sdf2ap	1.744	0.121	1.872
sdf2list	0.049	0.020	0.070
sdf2smiles	0.008	0.002	0.010
sdf2str	0.057	0.006	0.063
sdfStream	0.052	0.010	0.062
sdfid	0.080	0.004	0.086
sdfsample	0.104	0.007	0.111
sdfstr2list	0.820	0.503	1.323
searchSim	0.016	0.001	0.016
searchString	0.018	0.001	0.019
selectInBatches	0.025	0.007	0.096
smiles2sdf	0.013	0.002	0.015
trimNeighbors	5.515	0.028	5.561
validSDF	0.075	0.006	0.082
view	0.319	0.011	0.332
write.SDF	0.556	0.016	0.576
write.SDFsplit	0.132	0.004	0.137