BioC 2.12: CHECK report for ChemmineR on petty

Package: ChemmineR

Version: 2.12.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.12.3.tar.gz

StartedAt: 2013-10-08 21:54:14 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:57:58 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 224.4 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 3.0.1 (2013-05-16)
* 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 '2.12.3'
* 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 ... [15s/15s] 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: 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: 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [89s/91s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
jarvisPatrick    7.427  0.137   7.596
addNewFeatures   6.715  0.238   7.199
trimNeighbors    6.437  0.069   6.582
loadSdf          6.416  0.074   6.533
findCompounds    5.766  0.071   5.960
nearestNeighbors 4.958  0.039   5.022
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [32s/32s]
 [32s/33s] 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 -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
** testing if installed package can be loaded
* DONE (ChemmineR)

name	user	system	elapsed
AP-class	2.202	0.126	2.333
APset-class	2.024	0.154	2.189
FP-class	0.227	0.008	0.238
FPset-class	0.773	0.034	0.811
SDF-class	0.226	0.013	0.240
SDF2apcmp	0.048	0.003	0.051
SDFset-class	1.164	0.055	1.242
SDFset2SDF	0.280	0.012	0.293
SDFset2list	0.140	0.049	0.191
SDFstr-class	0.717	0.013	0.731
addNewFeatures	6.715	0.238	7.199
ap	1.457	0.027	1.484
apfp	0.020	0.001	0.021
apset	0.028	0.001	0.030
apset2descdb	1.888	0.122	2.017
atomblock	0.443	0.036	0.479
atomcount	0.527	0.015	0.543
atomprop	0.012	0.002	0.015
atomsubset	0.073	0.004	0.077
batchByIndex	0.015	0.002	0.017
bondblock	0.399	0.022	0.420
bonds	0.084	0.005	0.090
bufferLines	0.010	0.001	0.011
bufferResultSet	0.009	0.005	0.015
byCluster	1.977	0.086	2.066
cid	0.195	0.005	0.200
cluster.sizestat	1.342	0.032	1.451
cluster.visualize	1.522	0.029	1.629
cmp.cluster	4.727	0.059	4.912
cmp.duplicated	0.106	0.004	0.111
cmp.parse	0.063	0.002	0.066
cmp.parse1	0.009	0.001	0.010
cmp.search	1.629	0.060	1.712
cmp.similarity	0.049	0.005	0.055
conMA	0.134	0.016	0.153
datablock	0.896	0.019	0.979
datablock2ma	0.086	0.002	0.089
db.explain	0.097	0.009	0.107
db.subset	0.023	0.003	0.025
desc2fp	0.580	0.011	0.598
findCompounds	5.766	0.071	5.960
findCompoundsByName	0.904	0.022	0.976
fp2bit	1.765	0.060	1.924
fpSim	1.586	0.059	1.710
fromNNMatrix	2.064	0.035	2.203
getCompoundNames	0.854	0.022	0.922
getCompounds	0.903	0.022	0.977
getIds	0.006	0.002	0.009
grepSDFset	0.123	0.002	0.136
groups	0.324	0.009	0.417
header	0.427	0.006	0.534
initDb	0.087	0.011	0.104
jarvisPatrick	7.427	0.137	7.596
loadSdf	6.416	0.074	6.533
makeUnique	0.062	0.004	0.065
nearestNeighbors	4.958	0.039	5.022
plotStruc	0.622	0.012	0.636
pubchemFPencoding	0.010	0.003	0.013
read.AP	0.053	0.005	0.058
read.SDFindex	0.142	0.006	0.149
read.SDFset	1.427	0.012	1.446
read.SDFstr	2.091	0.008	2.107
rings	1.301	0.016	1.332
sdf.subset	0.104	0.002	0.106
sdf.visualize	0.040	0.005	0.046
sdf2ap	1.876	0.119	2.052
sdf2list	0.055	0.015	0.071
sdf2smiles	0.005	0.002	0.008
sdf2str	0.062	0.006	0.068
sdfStream	0.060	0.005	0.065
sdfid	0.073	0.004	0.077
sdfsample	0.128	0.005	0.132
sdfstr2list	0.938	0.462	1.473
searchSim	0.005	0.004	0.009
searchString	0.005	0.003	0.008
selectInBatches	0.006	0.005	0.012
smiles2sdf	0.005	0.003	0.007
trimNeighbors	6.437	0.069	6.582
validSDF	0.072	0.003	0.081
view	0.380	0.008	0.403
write.SDF	0.601	0.007	0.614
write.SDFsplit	0.039	0.005	0.044