BioC 3.6: CHECK report for BioMedR on veracruz1

Package: BioMedR

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioMedR_1.1.0.tar.gz

StartedAt: 2017-08-16 00:27:49 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:30:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 178.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: BioMedR.Rcheck

Warnings: NA

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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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.1.0’
* 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 ‘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 6.213  0.089   3.963
extrDrugKR           4.948  0.137   1.640
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  BioMedR RUnit Tests - 7 test functions, 0 errors, 1 failure
  FAILURE in test_extrDrugALOGP: Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
    Mean relative difference: 0.04145779
  
  
  Test files with failing tests
  
     test_extractDrugALOGP.R 
       test_extrDrugALOGP 
  
  
  Error in BiocGenerics:::testPackage("BioMedR") : 
    unit tests failed for package BioMedR
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck/00check.log’
for details.

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('BioMedR')


Timing stopped at: 1.021 0.049 0.498
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779



RUNIT TEST PROTOCOL -- Wed Aug 16 00:30:38 2017 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
BioMedR RUnit Tests - 7 test functions, 0 errors, 1 failure
FAILURE in test_extrDrugALOGP: Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779


Test files with failing tests

   test_extractDrugALOGP.R 
     test_extrDrugALOGP 


Error in BiocGenerics:::testPackage("BioMedR") : 
  unit tests failed for package BioMedR
Execution halted

* 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	0.013	0.002	0.015
AA3DMoRSE	0.001	0.000	0.002
AAACF	0.002	0.000	0.003
AABLOSUM100	0.002	0.000	0.003
AABLOSUM45	0.002	0.000	0.002
AABLOSUM50	0.001	0.001	0.002
AABLOSUM62	0.001	0.001	0.003
AABLOSUM80	0.002	0.001	0.002
AABurden	0.002	0.001	0.002
AACPSA	0.002	0.001	0.003
AAConn	0.002	0.000	0.003
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.001	0.001	0.002
AAEigIdx	0.001	0.001	0.003
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.002	0.001	0.002
AAInfo	0.002	0.000	0.002
AAMOE2D	0.002	0.000	0.003
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.001	0.002
AAMolProp	0.001	0.001	0.002
AAPAM120	0.001	0.001	0.002
AAPAM250	0.001	0.001	0.003
AAPAM30	0.002	0.001	0.003
AAPAM40	0.002	0.001	0.002
AAPAM70	0.002	0.001	0.002
AARDF	0.001	0.000	0.003
AARandic	0.001	0.000	0.002
AATopo	0.002	0.000	0.002
AATopoChg	0.002	0.001	0.002
AAWHIM	0.002	0.001	0.002
AAWalk	0.002	0.001	0.003
AAindex	0.001	0.001	0.003
Autocorrelation	1.200	0.070	0.816
BMgetDNAGenBank	0	0	0
BioMedR-package	0.001	0.000	0.000
Constitutional	0.493	0.016	0.390
NNeighbors	0.854	0.057	0.922
OptAA3d	0.000	0.000	0.001
acc	0.012	0.003	0.014
apfp	0.002	0.000	0.004
atomprop	0.001	0.000	0.002
bcl	0.002	0.001	0.002
calcDrugFPSim	0.001	0.000	0.000
calcDrugMCSSim	0.695	0.049	0.825
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.211	0.047	0.715
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.145	0.015	0.164
checkDNA	0.001	0.001	0.001
checkProt	0.002	0.000	0.003
clusterCMP	1.208	0.070	1.307
clusterJP	1.438	0.066	1.538
clusterMDS	0.855	0.048	0.921
clusterStat	0.263	0.015	0.285
connectivity	1.924	0.099	0.775
convAPtoFP	0.247	0.004	0.137
convSDFtoAP	0.041	0.001	0.041
extrDNADAC	0.009	0.000	0.009
extrDNADACC	0.075	0.001	0.075
extrDNADCC	0.111	0.001	0.122
extrDNAIncDiv	0.121	0.002	0.126
extrDNAPseDNC	0.012	0.000	0.012
extrDNAPseKNC	0.008	0.000	0.008
extrDNATAC	0.016	0.000	0.016
extrDNATACC	0.097	0.000	0.104
extrDNATCC	0.124	0.001	0.135
extrDNAkmer	0.002	0.000	0.002
extrDrugAIO	0.001	0.000	0.000
extrDrugAP	0.116	0.001	0.121
extrDrugBCUT	0.089	0.005	0.067
extrDrugCPSA	0.381	0.021	0.210
extrDrugEstate	0.323	0.011	0.237
extrDrugEstateComplete	0.104	0.009	0.053
extrDrugExtended	0.140	0.014	0.075
extrDrugExtendedComplete	0.036	0.005	0.020
extrDrugGraph	0.058	0.002	0.019
extrDrugGraphComplete	0.037	0.000	0.013
extrDrugHybridization	0.043	0.002	0.019
extrDrugHybridizationComplete	0.038	0.000	0.013
extrDrugHybridizationRatio	0.054	0.003	0.026
extrDrugIPMolecularLearning	0.033	0.001	0.011
extrDrugKR	4.948	0.137	1.640
extrDrugKRComplete	1.625	0.025	0.904
extrDrugKappaShapeIndices	0.075	0.002	0.045
extrDrugKierHallSmarts	0.219	0.003	0.085
extrDrugMACCS	0.309	0.009	0.091
extrDrugMACCSComplete	0.115	0.011	0.054
extrDrugMannholdLogP	6.213	0.089	3.963
extrDrugOBFP2	0.087	0.001	0.090
extrDrugOBFP3	0	0	0
extrDrugOBFP4	0.059	0.001	0.064
extrDrugPubChem	0.677	0.024	0.252
extrDrugPubChemComplete	0.657	0.006	0.204
extrDrugShortestPath	0.000	0.000	0.001
extrDrugShortestPathComplete	0.001	0.000	0.001
extrDrugStandard	0.050	0.002	0.015
extrDrugStandardComplete	0.054	0.002	0.017
extrDrugWHIM	0.227	0.006	0.104
extrPCMBLOSUM	0.054	0.000	0.055
extrPCMDescScales	0.009	0.001	0.011
extrPCMFAScales	0.016	0.003	0.019
extrPCMMDSScales	0.019	0.001	0.020
extrPCMPropScales	0.032	0.000	0.041
extrPCMScaleGap	0.016	0.001	0.017
extrPCMScales	0.024	0.002	0.025
extrProtAAC	0.003	0.000	0.003
extrProtAPAAC	1.266	0.007	1.295
extrProtCTDC	0.005	0.001	0.005
extrProtCTDCClass	0.006	0.000	0.006
extrProtCTDD	0.012	0.001	0.014
extrProtCTDDClass	0.006	0.001	0.008
extrProtCTDT	0.006	0.001	0.007
extrProtCTDTClass	0.007	0.000	0.008
extrProtCTriad	0.147	0.007	0.160
extrProtCTriadClass	0.093	0.005	0.105
extrProtDC	0.005	0.003	0.008
extrProtFPGap	0.034	0.001	0.034
extrProtGeary	0.224	0.004	0.228
extrProtMoran	0.226	0.003	0.231
extrProtMoreauBroto	0.202	0.008	0.214
extrProtPAAC	0.692	0.002	0.733
extrProtPSSM	0.001	0.000	0.000
extrProtPSSMAcc	0	0	0
extrProtPSSMFeature	0.000	0.000	0.001
extrProtQSO	1.253	0.007	1.305
extrProtSOCN	1.265	0.009	1.309
extrProtTC	0.050	0.042	0.097
geometric	0.074	0.001	0.054
getCPI	0.007	0.002	0.008
getDrug	0.000	0.001	0.001
getProt	0	0	0
make_kmer_index	0.001	0.000	0.001
parGOSim	0	0	0
parSeqSim	1.840	0.689	1.540
plotStructure	0.276	0.030	0.309
pls.cv	0.297	0.003	0.300
property	0.576	0.021	0.244
readFASTA	0.012	0.000	0.002
readMolFromSDF	0.075	0.002	0.022
readMolFromSmi	0.012	0.000	0.004
readPDB	1.590	0.013	1.544
revchars	0.001	0.000	0.000
rf.cv	0.989	0.007	1.026
rf.fs	0.581	0.001	0.595
sdfbcl	0.002	0.000	0.002
searchDrug	0.001	0.000	0.000
segProt	0.003	0.001	0.003
topology	0.451	0.020	0.318
twoGOSim	0.000	0.001	0.001
twoSeqSim	0.745	0.010	0.778