BioC 2.7: CHECK report for ChemmineR on pelham

Package: ChemmineR

Version: 2.2.19

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.2.19.tar.gz

StartedAt: 2011-03-31 05:08:58 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 05:12:56 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 237.5 seconds

RetCode: 0

Status: OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/ChemmineR.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘2.2.19’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘ChemmineR’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
.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 ... 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘ChemmineR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "ChemmineR"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	29.080	0.219	30.314
APset-class	28.786	0.179	29.295
SDF-class	0.145	0.010	0.154
SDF2apcmp	0.056	0.003	0.058
SDFset-class	1.232	0.050	1.310
SDFset2SDF	0.329	0.013	0.345
SDFset2list	0.169	0.049	0.219
SDFstr-class	0.633	0.007	0.653
ap	28.343	0.118	28.747
apset	0.018	0.002	0.020
apset2descdb	28.797	0.183	29.342
atomblock	0.418	0.026	0.447
atomcount	0.609	0.008	0.623
atomprop	0.007	0.001	0.009
bondblock	0.422	0.016	0.442
cid	3.373	0.009	3.402
cluster.sizestat	1.210	0.019	1.262
cluster.visualize	1.408	0.021	1.456
cmp.cluster	2.833	0.052	2.916
cmp.duplicated	0.084	0.001	0.087
cmp.parse	0.071	0.003	0.076
cmp.parse1	0	0	0
cmp.search	1.635	0.036	1.723
cmp.similarity	0.049	0.002	0.051
conMA	0.144	0.016	0.160
datablock	0.949	0.017	0.966
datablock2ma	0.105	0.003	0.108
db.explain	0.157	0.008	0.166
db.subset	0.013	0.002	0.015
fp2bit	1.280	0.324	1.622
fpSim	1.191	0.283	1.497
getIds	0.000	0.000	0.001
grepSDFset	0.113	0.002	0.115
header	0.341	0.011	0.354
makeUnique	0.072	0.002	0.074
plotStruc	0.506	0.008	0.522
pubchemFPencoding	0.007	0.001	0.008
read.SDFset	1.357	0.008	1.375
read.SDFstr	1.921	0.008	1.948
sdf.subset	0.001	0.000	0.001
sdf.visualize	0.052	0.002	0.054
sdf2ap	28.976	0.185	29.471
sdf2list	0.073	0.015	0.088
sdf2smiles	0.000	0.001	0.000
sdf2str	0.093	0.006	0.099
sdfid	0.074	0.002	0.076
sdfsample	0.151	0.005	0.156
sdfstr2list	3.257	0.520	3.825
searchSim	0.001	0.001	0.000
searchString	0	0	0
smiles2sdf	0.001	0.000	0.001
validSDF	0.068	0.001	0.070
view	5.829	0.022	5.934
write.SDF	0.565	0.007	0.575

Summary

Command output