BioC 3.5: CHECK report for BioMedR on toluca2

Package: BioMedR

Version: 0.99.27

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioMedR_0.99.27.tar.gz

StartedAt: 2017-04-23 01:00:33 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:04:07 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 214.0 seconds

RetCode: 0

Status:  OK

CheckDir: BioMedR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioMedR_0.99.27.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BioMedR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioMedR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioMedR’ version ‘0.99.27’
* 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 ‘BioMedR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
extrDrugMannholdLogP 8.423  0.070   5.135
extrDrugKR           5.147  0.093   1.879
* checking for unstated dependencies in ‘tests’ ... OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘BioMedR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BioMedR)

name	user	system	elapsed
AA2DACOR	0.017	0.003	0.020
AA3DMoRSE	0.001	0.001	0.002
AAACF	0.002	0.000	0.002
AABLOSUM100	0.001	0.001	0.002
AABLOSUM45	0.001	0.001	0.002
AABLOSUM50	0.002	0.000	0.002
AABLOSUM62	0.002	0.001	0.002
AABLOSUM80	0.001	0.001	0.003
AABurden	0.001	0.000	0.002
AACPSA	0.001	0.001	0.002
AAConn	0.001	0.001	0.003
AAConst	0.001	0.001	0.003
AADescAll	0.001	0.000	0.003
AAEdgeAdj	0.001	0.000	0.002
AAEigIdx	0.001	0.001	0.002
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.001	0.001	0.003
AAGeom	0.001	0.000	0.002
AAInfo	0.002	0.000	0.002
AAMOE2D	0.002	0.001	0.002
AAMOE3D	0.002	0.001	0.002
AAMetaInfo	0.002	0.000	0.003
AAMolProp	0.002	0.000	0.002
AAPAM120	0.001	0.001	0.002
AAPAM250	0.001	0.001	0.002
AAPAM30	0.002	0.000	0.002
AAPAM40	0.002	0.001	0.002
AAPAM70	0.002	0.001	0.003
AARDF	0.001	0.001	0.002
AARandic	0.001	0.000	0.002
AATopo	0.002	0.001	0.003
AATopoChg	0.002	0.001	0.002
AAWHIM	0.002	0.001	0.002
AAWalk	0.002	0.001	0.002
AAindex	0.002	0.001	0.003
Autocorrelation	1.265	0.070	0.865
BMgetDNAGenBank	0	0	0
BioMedR-package	0.001	0.000	0.001
Constitutional	0.518	0.017	0.386
NNeighbors	0.994	0.049	1.045
OptAA3d	0	0	0
acc	0.015	0.003	0.018
apfp	0.001	0.000	0.002
atomprop	0.001	0.001	0.002
bcl	0.002	0.000	0.002
calcDrugFPSim	0.001	0.000	0.001
calcDrugMCSSim	0.707	0.040	0.759
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.277	0.058	1.144
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.185	0.020	0.205
checkDNA	0.001	0.000	0.001
checkProt	0.002	0.001	0.002
clusterCMP	1.422	0.091	1.514
clusterJP	1.660	0.089	1.755
clusterMDS	0.963	0.068	1.055
clusterStat	0.333	0.023	0.360
connectivity	2.054	0.104	0.907
convAPtoFP	0.147	0.002	0.150
convSDFtoAP	0.054	0.001	0.056
extrDNADAC	0.009	0.000	0.010
extrDNADACC	0.099	0.001	0.102
extrDNADCC	0.138	0.001	0.141
extrDNAIncDiv	0.130	0.002	0.131
extrDNAPseDNC	0.013	0.000	0.013
extrDNAPseKNC	0.009	0.001	0.009
extrDNATAC	0.017	0.000	0.017
extrDNATACC	0.130	0.001	0.134
extrDNATCC	0.162	0.001	0.164
extrDNAkmer	0.002	0.000	0.002
extrDrugAIO	0	0	0
extrDrugAP	0.153	0.002	0.157
extrDrugBCUT	0.113	0.003	0.072
extrDrugCPSA	0.429	0.018	0.233
extrDrugEstate	0.357	0.013	0.254
extrDrugEstateComplete	0.169	0.006	0.061
extrDrugExtended	0.127	0.009	0.065
extrDrugExtendedComplete	0.111	0.002	0.034
extrDrugGraph	0.061	0.001	0.032
extrDrugGraphComplete	0.056	0.000	0.023
extrDrugHybridization	0.044	0.001	0.030
extrDrugHybridizationComplete	0.063	0.002	0.028
extrDrugHybridizationRatio	0.024	0.000	0.025
extrDrugIPMolecularLearning	0.011	0.001	0.012
extrDrugKR	5.147	0.093	1.879
extrDrugKRComplete	1.857	0.034	1.007
extrDrugKappaShapeIndices	0.062	0.001	0.042
extrDrugKierHallSmarts	0.168	0.003	0.095
extrDrugMACCS	0.482	0.022	0.202
extrDrugMACCSComplete	0.196	0.007	0.073
extrDrugMannholdLogP	8.423	0.070	5.135
extrDrugOBFP2	0.107	0.000	0.109
extrDrugOBFP3	0.001	0.000	0.000
extrDrugOBFP4	0.070	0.001	0.072
extrDrugPubChem	0.577	0.012	0.229
extrDrugPubChemComplete	0.495	0.011	0.210
extrDrugShortestPath	0.000	0.000	0.001
extrDrugShortestPathComplete	0.000	0.000	0.001
extrDrugStandard	0.035	0.001	0.021
extrDrugStandardComplete	0.028	0.001	0.020
extrDrugWHIM	0.110	0.002	0.085
extrPCMBLOSUM	0.072	0.000	0.073
extrPCMDescScales	0.014	0.001	0.014
extrPCMFAScales	0.023	0.003	0.026
extrPCMMDSScales	0.021	0.001	0.023
extrPCMPropScales	0.039	0.000	0.039
extrPCMScaleGap	0.019	0.001	0.020
extrPCMScales	0.030	0.001	0.031
extrProtAAC	0.002	0.000	0.003
extrProtAPAAC	1.613	0.015	1.648
extrProtCTDC	0.007	0.000	0.006
extrProtCTDCClass	0.007	0.000	0.007
extrProtCTDD	0.007	0.001	0.007
extrProtCTDDClass	0.007	0.001	0.007
extrProtCTDT	0.008	0.001	0.008
extrProtCTDTClass	0.008	0.000	0.009
extrProtCTriad	0.182	0.008	0.192
extrProtCTriadClass	0.124	0.013	0.137
extrProtDC	0.006	0.003	0.007
extrProtFPGap	0.038	0.000	0.038
extrProtGeary	0.313	0.005	0.324
extrProtMoran	0.303	0.006	0.347
extrProtMoreauBroto	0.291	0.007	0.315
extrProtPAAC	0.964	0.006	0.978
extrProtPSSM	0.001	0.000	0.000
extrProtPSSMAcc	0.000	0.000	0.001
extrProtPSSMFeature	0.001	0.000	0.001
extrProtQSO	1.655	0.011	1.674
extrProtSOCN	1.658	0.009	1.678
extrProtTC	0.056	0.042	0.099
geometric	0.074	0.002	0.066
getCPI	0.008	0.002	0.010
getDrug	0.001	0.000	0.001
getProt	0.001	0.000	0.001
make_kmer_index	0.001	0.000	0.002
parGOSim	0.000	0.000	0.001
parSeqSim	2.885	0.975	2.335
plotStructure	0.380	0.041	0.423
pls.cv	0.381	0.005	0.386
property	0.390	0.014	0.256
readFASTA	0.005	0.000	0.002
readMolFromSDF	0.054	0.002	0.026
readMolFromSmi	0.006	0.000	0.004
readPDB	1.702	0.014	1.724
revchars	0.000	0.000	0.001
rf.cv	1.210	0.009	1.246
rf.fs	0.670	0.003	0.674
sdfbcl	0.002	0.001	0.002
searchDrug	0	0	0
segProt	0.003	0.000	0.003
topology	0.499	0.015	0.368
twoGOSim	0	0	0
twoSeqSim	0.888	0.010	0.899