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Package 105/609HostnameOS / ArchBUILDCHECKBUILD BIN
ChemmineR 2.10.9
ChemmineR Team
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/ChemmineR
Last Changed Rev: 71850 / Revision: 74773
Last Changed Date: 2012-12-11 18:15:09 -0800 (Tue, 11 Dec 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ChemmineR
Version: 2.10.9
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.10.9.tar.gz
StartedAt: 2013-03-25 00:02:43 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:05:05 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 141.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ChemmineR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ChemmineR.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.10.9’
* 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 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 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 'R/sim.R':
  found 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
AP-class      11.948  0.052  12.415
sdf2ap        11.521  0.052  11.779
apset2descdb  11.429  0.036  11.811
APset-class   11.341  0.064  11.500
ap            11.325  0.024  12.282
jarvisPatrick  5.221  0.304   5.540
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘fmcsR’ ‘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

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.

ChemmineR.Rcheck/00install.out:

* 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)

ChemmineR.Rcheck/ChemmineR-Ex.timings:

nameusersystemelapsed
AP-class11.948 0.05212.415
APset-class11.341 0.06411.500
FP-class0.0960.0000.112
FPset-class0.6080.0080.730
SDF-class0.0680.0000.067
SDF2apcmp0.0160.0040.032
SDFset-class0.6800.0120.733
SDFset2SDF0.2520.0000.293
SDFset2list0.0840.0160.188
SDFstr-class0.3960.0080.559
ap11.325 0.02412.282
apfp0.0000.0000.013
apset0.0040.0000.007
apset2descdb11.429 0.03611.811
atomblock0.2680.0040.334
atomcount0.3720.0040.586
atomprop0.0000.0040.009
atomsubset0.0440.0000.064
bondblock0.2000.0000.215
bonds0.0520.0040.057
cid1.3880.0081.488
cluster.sizestat0.7560.0040.855
cluster.visualize0.8520.0120.872
cmp.cluster2.8280.0162.845
cmp.duplicated0.0720.0000.074
cmp.parse0.0320.0000.031
cmp.parse1000
cmp.search0.9840.0201.010
cmp.similarity0.0280.0000.029
conMA0.0680.0080.077
datablock0.5520.0040.554
datablock2ma0.0480.0040.052
db.explain0.1360.0080.145
db.subset0.0000.0040.004
desc2fp2.3760.0042.401
fp2bit1.2000.0521.268
fpSim1.2120.0481.270
getIds0.0000.0000.001
grepSDFset0.0720.0040.089
groups0.1760.0040.185
header0.2760.0000.278
jarvisPatrick5.2210.3045.540
makeUnique0.0240.0000.025
plotStruc0.3160.0040.342
pubchemFPencoding0.0000.0040.015
read.AP0.0160.0000.017
read.SDFindex0.0200.0000.017
read.SDFset0.8840.0041.003
read.SDFstr1.3960.0041.435
rings0.7240.0040.776
sdf.subset0.0000.0000.001
sdf.visualize0.0200.0000.031
sdf2ap11.521 0.05211.779
sdf2list0.0280.0000.044
sdf2smiles000
sdf2str0.0280.0000.031
sdfStream0.0160.0000.016
sdfid0.0360.0000.035
sdfsample0.0600.0040.066
sdfstr2list0.9280.1601.094
searchSim000
searchString0.0000.0000.001
smiles2sdf000
validSDF0.0360.0040.038
view2.4000.0002.611
write.SDF0.3720.0040.442
write.SDFsplit0.0160.0000.029