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: 2013-03-25 01:41:13 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:43:53 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 160.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [14s/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/i386/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 examples ... [56s/57s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
jarvisPatrick 6.499  1.926   8.451
trimNeighbors 6.214  0.060   6.275
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [22s/23s]
 [23s/23s] 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
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c DisjointSets.cpp -o DisjointSets.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -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
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c desc.cc -o desc.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c formats.cc -o formats.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c molecule.cc -o molecule.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c r_wrap.cc -o r_wrap.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c script.cc -o script.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -DNO_MAIN  -fPIC  -g -O2 -Wall -fasm-blocks  -c similarity.cc -o similarity.o
g++ -arch i386 -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/i386
** 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	1.701	0.119	1.821
APset-class	1.812	0.134	1.947
FP-class	0.152	0.017	0.170
FPset-class	0.514	0.056	0.571
SDF-class	0.113	0.023	0.136
SDF2apcmp	0.048	0.008	0.057
SDFset-class	0.794	0.071	0.864
SDFset2SDF	0.229	0.016	0.245
SDFset2list	0.109	0.056	0.165
SDFstr-class	0.456	0.015	0.473
ap	1.080	0.029	1.112
apfp	0.010	0.006	0.015
apset	0.017	0.006	0.024
apset2descdb	1.332	0.097	1.434
atomblock	0.286	0.029	0.316
atomcount	0.383	0.018	0.401
atomprop	0.012	0.007	0.019
atomsubset	0.049	0.009	0.059
batchByIndex	0.009	0.010	0.019
bondblock	0.239	0.022	0.262
bonds	0.102	0.012	0.114
bufferLines	0.007	0.008	0.015
bufferResultSet	0.007	0.007	0.015
cid	0.134	0.014	0.148
cluster.sizestat	0.891	0.020	0.911
cluster.visualize	1.327	0.030	1.357
cmp.cluster	3.704	0.050	3.755
cmp.duplicated	0.071	0.013	0.084
cmp.parse	0.053	0.011	0.064
cmp.parse1	0.003	0.004	0.008
cmp.search	1.627	0.034	1.661
cmp.similarity	0.055	0.014	0.068
conMA	0.103	0.022	0.125
datablock	0.604	0.026	0.632
datablock2ma	0.120	0.014	0.133
db.explain	0.065	0.014	0.080
db.subset	0.016	0.011	0.027
desc2fp	0.471	0.038	0.509
findCompounds	0.012	0.008	0.020
findCompoundsByName	0.015	0.008	0.024
fp2bit	1.862	0.518	2.392
fpSim	1.614	0.463	2.079
getCompoundNames	0.007	0.007	0.014
getCompounds	0.016	0.014	0.031
getIds	0.004	0.005	0.008
grepSDFset	0.077	0.010	0.087
groups	0.253	0.016	0.269
header	0.260	0.016	0.278
initDb	0.019	0.017	0.035
jarvisPatrick	6.499	1.926	8.451
loadSdf	0.029	0.020	0.049
loadSmiles	0.009	0.010	0.019
makeUnique	0.049	0.011	0.060
nearestNeighbors	3.615	0.023	3.642
plotStruc	0.423	0.021	0.444
pubchemFPencoding	0.056	0.007	0.063
read.AP	0.037	0.015	0.052
read.SDFindex	0.035	0.013	0.048
read.SDFset	1.267	0.010	1.277
read.SDFstr	1.945	0.014	1.959
rings	1.104	0.027	1.133
sdf.subset	0.008	0.008	0.016
sdf.visualize	0.050	0.017	0.068
sdf2ap	2.007	0.148	2.164
sdf2list	0.062	0.026	0.088
sdf2smiles	0.011	0.008	0.019
sdf2str	0.070	0.018	0.088
sdfStream	0.061	0.020	0.081
sdfid	0.085	0.018	0.104
sdfsample	0.131	0.014	0.145
sdfstr2list	0.972	0.566	1.570
searchSim	0.009	0.007	0.017
searchString	0.010	0.007	0.017
selectInBatches	0.016	0.010	0.026
smiles2sdf	0.009	0.007	0.016
trimNeighbors	6.214	0.060	6.275
validSDF	0.067	0.010	0.077
view	0.393	0.016	0.409
write.SDF	0.507	0.017	0.525
write.SDFsplit	0.051	0.013	0.064