BioC 2.9: CHECK report for ChemmineR on pitt

Package: ChemmineR

Version: 2.6.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChemmineR_2.6.1.tar.gz

StartedAt: 2012-03-24 00:08:39 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:11:52 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 193.5 seconds

RetCode: 0

Status: OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ChemmineR.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '2.6.1'
* 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 whether package 'ChemmineR' can be installed ... OK
* checking installed package size ... 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 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
.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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'gplots' 'scatterplot3d'
* 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

* installing *source* package 'ChemmineR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'ChemmineR'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ChemmineR.Rnw' 
** testing if installed package can be loaded

* DONE (ChemmineR)

name	user	system	elapsed
AP-class	20.261	0.190	20.815
APset-class	19.958	0.160	20.462
SDF-class	0.126	0.011	0.137
SDF2apcmp	0.060	0.003	0.062
SDFset-class	0.961	0.048	1.015
SDFset2SDF	0.308	0.012	0.323
SDFset2list	0.137	0.050	0.193
SDFstr-class	0.585	0.006	0.599
ap	19.384	0.055	19.609
apset	0.016	0.002	0.017
apset2descdb	19.806	0.151	20.110
atomblock	0.396	0.026	0.424
atomcount	0.541	0.009	0.558
atomprop	0.006	0.001	0.007
atomsubset	0.080	0.002	0.084
bondblock	0.335	0.017	0.358
bonds	0.091	0.003	0.096
cid	2.297	0.005	2.315
cluster.sizestat	1.102	0.019	1.132
cluster.visualize	1.423	0.023	1.459
cmp.cluster	2.497	0.044	2.565
cmp.duplicated	0.081	0.002	0.085
cmp.parse	0.076	0.004	0.080
cmp.parse1	0.000	0.000	0.001
cmp.search	1.375	0.027	1.411
cmp.similarity	0.045	0.002	0.048
conMA	0.139	0.017	0.161
datablock	0.713	0.013	0.728
datablock2ma	0.085	0.003	0.089
db.explain	0.083	0.008	0.091
db.subset	0.013	0.001	0.013
fp2bit	1.082	0.290	1.387
fpSim	1.162	0.287	1.457
getIds	0	0	0
grepSDFset	0.113	0.001	0.116
groups	0.300	0.009	0.312
header	0.338	0.005	0.344
makeUnique	0.068	0.002	0.071
plotStruc	0.454	0.010	0.465
pubchemFPencoding	0.005	0.001	0.006
read.SDFset	1.275	0.006	1.300
read.SDFstr	1.744	0.005	1.763
rings	1.114	0.015	1.134
sdf.subset	0	0	0
sdf.visualize	0.053	0.002	0.055
sdf2ap	19.876	0.155	20.204
sdf2list	0.066	0.017	0.082
sdf2smiles	0.001	0.000	0.000
sdf2str	0.068	0.007	0.074
sdfid	0.071	0.002	0.073
sdfsample	0.118	0.005	0.124
sdfstr2list	0.868	0.503	1.401
searchSim	0	0	0
searchString	0	0	0
smiles2sdf	0.001	0.001	0.000
validSDF	0.085	0.002	0.086
view	4.063	0.015	4.088
write.SDF	0.419	0.006	0.427

Summary

Command output