BioC 3.3: CHECK report for Rcpi on morelia

Package: Rcpi

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.7.0.tar.gz

StartedAt: 2016-04-21 06:40:37 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:42:54 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 136.7 seconds

RetCode: 0

Status:  OK

CheckDir: Rcpi.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 Rcpi_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rcpi.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.7.0’
* 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 ‘Rcpi’ can be installed ... [12s/13s] 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 ... NOTE
acc: no visible global function definition for ‘combn’
calcParProtGOSim: no visible global function definition for ‘combn’
calcParProtSeqSim: no visible global function definition for ‘combn’
extractPCMFAScales: no visible global function definition for
  ‘factanal’
extractPCMMDSScales: no visible global function definition for ‘dist’
extractPCMMDSScales: no visible global function definition for
  ‘cmdscale’
extractPCMPropScales: no visible global function definition for
  ‘na.omit’
extractPCMScales: no visible global function definition for ‘prcomp’
extractPCMScales: no visible global function definition for ‘predict’
extractProtAPAAC: no visible global function definition for ‘read.csv’
extractProtGeary: no visible global function definition for ‘read.csv’
extractProtGeary: no visible binding for global variable ‘sd’
extractProtMoran: no visible global function definition for ‘read.csv’
extractProtMoran: no visible binding for global variable ‘sd’
extractProtMoreauBroto: no visible global function definition for
  ‘read.csv’
extractProtMoreauBroto: no visible binding for global variable ‘sd’
extractProtPAAC: no visible global function definition for ‘read.csv’
extractProtPSSMAcc : accpssm: no visible global function definition for
  ‘combn’
extractProtQSO: no visible global function definition for ‘read.csv’
extractProtSOCN: no visible global function definition for ‘read.csv’
getDrug: no visible global function definition for ‘capture.output’
getProt: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output cmdscale combn dist factanal na.omit prcomp predict
  read.csv sd
Consider adding
  importFrom("stats", "cmdscale", "dist", "factanal", "na.omit",
             "prcomp", "predict", "sd")
  importFrom("utils", "capture.output", "combn", "read.csv")
to your NAMESPACE file.
* 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 ... [12s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rcpi.Rcheck/00check.log’
for details.

* installing *source* package ‘Rcpi’ ...
** 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 (Rcpi)

name	user	system	elapsed
AA2DACOR	0.012	0.002	0.014
AA3DMoRSE	0.001	0.001	0.002
AAACF	0.001	0.000	0.001
AABLOSUM100	0.002	0.001	0.002
AABLOSUM45	0.002	0.001	0.003
AABLOSUM50	0.002	0.001	0.002
AABLOSUM62	0.002	0.001	0.002
AABLOSUM80	0.001	0.000	0.001
AABurden	0.001	0.001	0.001
AACPSA	0.001	0.000	0.002
AAConn	0.001	0.001	0.001
AAConst	0.001	0.000	0.002
AADescAll	0.001	0.001	0.003
AAEdgeAdj	0.001	0.001	0.003
AAEigIdx	0.001	0.001	0.002
AAFGC	0.001	0.000	0.002
AAGETAWAY	0.001	0.000	0.001
AAGeom	0.001	0.000	0.001
AAInfo	0.001	0.001	0.001
AAMOE2D	0.001	0.000	0.002
AAMOE3D	0.001	0.001	0.002
AAMetaInfo	0.001	0.000	0.001
AAMolProp	0.001	0.001	0.001
AAPAM120	0.001	0.000	0.001
AAPAM250	0.001	0.001	0.001
AAPAM30	0.001	0.000	0.002
AAPAM40	0.001	0.000	0.002
AAPAM70	0.001	0.000	0.001
AARDF	0.001	0.000	0.001
AARandic	0.001	0.000	0.001
AATopo	0.001	0.000	0.001
AATopoChg	0.001	0.001	0.003
AAWHIM	0.002	0.001	0.002
AAWalk	0.002	0.001	0.003
AAindex	0.001	0.000	0.001
OptAA3d	0.001	0.000	0.000
Rcpi-package	0.000	0.000	0.001
acc	0.018	0.004	0.023
calcDrugFPSim	0.001	0.000	0.000
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.001	0.000	0.001
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0	0	0
checkProt	0.002	0.000	0.002
convMolFormat	0.001	0.000	0.000
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.000
extractDrugApol	0.001	0.000	0.000
extractDrugAromaticAtomsCount	0.001	0.000	0.000
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.001	0.000	0.000
extractDrugAutocorrelationCharge	0.001	0.000	0.000
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.000
extractDrugBCUT	0	0	0
extractDrugBPol	0.001	0.000	0.000
extractDrugBondCount	0	0	0
extractDrugCPSA	0.000	0.000	0.001
extractDrugCarbonTypes	0	0	0
extractDrugChiChain	0	0	0
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0	0	0
extractDrugDescOB	0	0	0
extractDrugECI	0	0	0
extractDrugEstate	0.000	0.001	0.000
extractDrugEstateComplete	0	0	0
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0.000	0.000	0.001
extractDrugFragmentComplexity	0	0	0
extractDrugGraph	0	0	0
extractDrugGraphComplete	0	0	0
extractDrugGravitationalIndex	0	0	0
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.001	0.001	0.001
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.001	0.001	0.001
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0	0	0
extractDrugLargestChain	0	0	0
extractDrugLargestPiSystem	0.001	0.000	0.000
extractDrugLengthOverBreadth	0.000	0.000	0.001
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.000	0.001	0.000
extractDrugMDE	0.001	0.000	0.000
extractDrugMannholdLogP	0.001	0.000	0.000
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0.001	0.000	0.000
extractDrugOBFP3	0.000	0.000	0.001
extractDrugOBFP4	0	0	0
extractDrugOBMACCS	0	0	0
extractDrugPetitjeanNumber	0	0	0
extractDrugPetitjeanShapeIndex	0	0	0
extractDrugPubChem	0	0	0
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.000	0.000	0.001
extractDrugRuleOfFive	0	0	0
extractDrugShortestPath	0	0	0
extractDrugShortestPathComplete	0	0	0
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0	0	0
extractDrugTPSA	0.000	0.001	0.000
extractDrugVABC	0	0	0
extractDrugVAdjMa	0	0	0
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0	0	0
extractDrugWienerNumbers	0	0	0
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.013	0.001	0.016
extractPCMDescScales	0.013	0.001	0.014
extractPCMFAScales	0.023	0.003	0.027
extractPCMMDSScales	0.020	0.003	0.022
extractPCMPropScales	0.017	0.002	0.020
extractPCMScales	0.029	0.002	0.032
extractProtAAC	0.003	0.001	0.004
extractProtAPAAC	1.878	0.016	1.894
extractProtCTDC	0.006	0.000	0.007
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.008	0.001	0.009
extractProtCTriad	0.119	0.003	0.122
extractProtDC	0.004	0.003	0.007
extractProtGeary	0.196	0.004	0.202
extractProtMoran	0.202	0.003	0.206
extractProtMoreauBroto	0.135	0.003	0.137
extractProtPAAC	0.622	0.004	0.627
extractProtPSSM	0	0	0
extractProtPSSMAcc	0	0	0
extractProtPSSMFeature	0	0	0
extractProtQSO	1.408	0.011	1.414
extractProtSOCN	1.225	0.007	1.231
extractProtTC	0.046	0.036	0.081
getCPI	0.003	0.001	0.003
getDrug	0.001	0.000	0.001
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0.001	0.001	0.001
getMolFromChEMBL	0.001	0.000	0.001
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0.001	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.004	0.001	0.005
getProt	0.001	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.000
getSeqFromUniProt	0.001	0.000	0.000
getSmiFromChEMBL	0.001	0.000	0.000
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.002	0.001	0.002
readMolFromSDF	0.001	0.000	0.000
readMolFromSmi	0.001	0.000	0.000
readPDB	1.349	0.019	1.367
searchDrug	0.001	0.000	0.000
segProt	0.003	0.000	0.004