BioC 2.9: CHECK report for ChemmineR on wilson2

Package: ChemmineR

Version: 2.5.3

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.5.3.tar.gz

StartedAt: 2011-07-06 23:59:28 -0700 (Wed, 06 Jul 2011)

EndedAt: 2011-07-07 00:01:26 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 118.0 seconds

RetCode: 0

Status: OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ChemmineR.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘2.5.3’
* 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 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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	12.520	0.076	12.614
APset-class	12.233	0.040	12.289
SDF-class	0.096	0.000	0.094
SDF2apcmp	0.028	0.000	0.026
SDFset-class	0.956	0.028	0.985
SDFset2SDF	0.244	0.004	0.248
SDFset2list	0.088	0.012	0.102
SDFstr-class	0.536	0.004	0.540
ap	11.877	0.008	11.890
apset	0.008	0.004	0.011
apset2descdb	12.297	0.028	12.321
atomblock	0.492	0.020	0.513
atomcount	0.448	0.008	0.456
atomprop	0.004	0.000	0.006
bondblock	0.400	0.000	0.402
bonds	0.056	0.000	0.059
cid	1.408	0.000	1.414
cluster.sizestat	0.820	0.004	0.822
cluster.visualize	0.960	0.012	0.978
cmp.cluster	1.880	0.004	1.885
cmp.duplicated	0.068	0.000	0.067
cmp.parse	0.040	0.000	0.037
cmp.parse1	0	0	0
cmp.search	1.008	0.004	1.013
cmp.similarity	0.040	0.000	0.037
conMA	0.084	0.012	0.094
datablock	0.840	0.008	0.850
datablock2ma	0.048	0.000	0.051
db.explain	0.068	0.000	0.071
db.subset	0.008	0.000	0.007
fp2bit	0.960	0.092	1.057
fpSim	0.980	0.012	0.990
getIds	0	0	0
grepSDFset	0.076	0.000	0.078
header	0.304	0.000	0.305
makeUnique	0.124	0.004	0.127
plotStruc	0.312	0.004	0.312
pubchemFPencoding	0.000	0.004	0.005
read.SDFset	0.860	0.008	0.872
read.SDFstr	1.385	0.000	1.381
sdf.subset	0	0	0
sdf.visualize	0.024	0.000	0.025
sdf2ap	12.368	0.044	12.424
sdf2list	0.032	0.004	0.038
sdf2smiles	0.000	0.004	0.000
sdf2str	0.044	0.000	0.044
sdfid	0.044	0.000	0.043
sdfsample	0.088	0.000	0.087
sdfstr2list	0.960	0.216	1.181
searchSim	0	0	0
searchString	0	0	0
smiles2sdf	0	0	0
validSDF	0.048	0.000	0.046
view	2.609	0.004	2.648
write.SDF	0.384	0.000	0.410

Summary

Command output