BioC 2.12: CHECK report for ChemmineR on lamb2

Package: ChemmineR

Version: 2.11.9

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.11.9.tar.gz

StartedAt: 2013-01-16 01:24:43 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:27:42 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 179.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ChemmineR.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (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 ‘2.11.9’
* 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 ... 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’
.gen_atom_pair: no visible global function definition for
  ‘Descriptors_get_len’
.gen_atom_pair: no visible global function definition for
  ‘Descriptors_get_descriptor’
.parse: no visible global function definition for ‘Descriptors’
.parse: no visible global function definition for
  ‘Descriptors_parse_sdf’
cmp.parse: no visible global function definition for ‘batch_parse’
cmp.parse1: no visible global function definition for
  ‘delete_Descriptors’
datablock2ma: no visible binding for global variable ‘sdfset’
sdf_to_desc: no visible global function definition for
  ‘delete_Descriptors’
sdfs_to_desc: no visible global function definition for ‘batch_parse’
* 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: 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
sdf2ap        13.268  0.036  13.305
APset-class   13.245  0.036  13.286
AP-class      13.048  0.060  13.115
ap            12.833  0.004  12.840
apset2descdb  12.781  0.048  12.837
jarvisPatrick  5.696  0.364   6.060
* checking for unstated dependencies in tests ... WARNING
‘::’ or ‘:::’ import not declared from: ‘BiocGenerics’
* checking tests ...
  Running ‘runTests.R’
 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineR’ ...
** 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’
** 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	13.048	0.060	13.115
APset-class	13.245	0.036	13.286
FP-class	0.192	0.000	0.193
FPset-class	0.672	0.020	0.691
SDF-class	0.088	0.008	0.094
SDF2apcmp	0.028	0.000	0.027
SDFset-class	0.820	0.016	0.837
SDFset2SDF	0.180	0.000	0.178
SDFset2list	0.084	0.024	0.109
SDFstr-class	0.440	0.000	0.439
ap	12.833	0.004	12.840
apfp	0.004	0.004	0.010
apset	0.108	0.000	0.108
apset2descdb	12.781	0.048	12.837
atomblock	0.404	0.004	0.410
atomcount	0.436	0.000	0.434
atomprop	0.012	0.004	0.015
atomsubset	0.064	0.000	0.062
batchByIndex	0.024	0.000	0.026
bondblock	0.412	0.000	0.409
bonds	0.060	0.004	0.065
bufferLines	0.016	0.000	0.016
bufferResultSet	0.016	0.000	0.013
cid	1.456	0.004	1.464
cluster.sizestat	0.840	0.000	0.842
cluster.visualize	1.072	0.016	1.085
cmp.cluster	3.092	0.020	3.112
cmp.duplicated	0.1	0.0	0.1
cmp.parse	0.040	0.004	0.044
cmp.parse1	0.004	0.004	0.007
cmp.search	1.005	0.004	1.006
cmp.similarity	0.040	0.000	0.039
conMA	0.092	0.004	0.095
datablock	0.704	0.016	0.718
datablock2ma	0.060	0.000	0.062
db.explain	0.092	0.004	0.095
db.subset	0.016	0.000	0.015
desc2fp	2.688	0.000	2.694
findCompounds	0.020	0.000	0.018
findCompoundsByName	0.008	0.000	0.012
fp2bit	1.544	0.008	1.552
fpSim	1.348	0.048	1.392
getCompoundNames	0.016	0.000	0.014
getCompounds	0.040	0.000	0.038
getIds	0.004	0.000	0.006
grepSDFset	0.088	0.004	0.094
groups	0.196	0.000	0.196
header	0.204	0.004	0.208
initDb	0.024	0.000	0.023
jarvisPatrick	5.696	0.364	6.060
loadSdf	0.036	0.000	0.035
loadSmiles	0.012	0.000	0.012
makeUnique	0.044	0.000	0.041
plotStruc	0.372	0.000	0.375
pubchemFPencoding	0.012	0.000	0.013
read.AP	0.044	0.000	0.044
read.SDFindex	0.036	0.004	0.043
read.SDFset	0.980	0.000	0.979
read.SDFstr	1.313	0.012	1.324
rings	0.764	0.000	0.765
sdf.subset	0.008	0.000	0.008
sdf.visualize	0.036	0.004	0.040
sdf2ap	13.268	0.036	13.305
sdf2list	0.032	0.016	0.045
sdf2smiles	0.008	0.000	0.010
sdf2str	0.060	0.004	0.061
sdfStream	0.044	0.000	0.048
sdfid	0.060	0.000	0.059
sdfsample	0.168	0.008	0.174
sdfstr2list	0.929	0.200	1.128
searchSim	0.008	0.004	0.010
searchString	0.004	0.004	0.006
selectInBatches	0.008	0.000	0.007
smiles2sdf	0.008	0.000	0.007
validSDF	0.048	0.000	0.056
view	2.524	0.008	2.535
write.SDF	0.316	0.004	0.318
write.SDFsplit	0.124	0.000	0.126

Summary

Command output