BioC 3.5: CHECK report for BioMedR on veracruz2

Package: BioMedR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioMedR_1.0.0.tar.gz

StartedAt: 2017-08-16 00:16:57 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:20:10 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 192.4 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.0.0’
* 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 6.940  0.064   3.971
extrDrugKR           5.007  0.109   1.654
* 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-3.5-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: 1.025 0.05 0.51
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779



RUNIT TEST PROTOCOL -- Wed Aug 16 00:19:59 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	0.019	0.003	0.021
AA3DMoRSE	0.001	0.000	0.002
AAACF	0.002	0.000	0.003
AABLOSUM100	0.001	0.000	0.002
AABLOSUM45	0.001	0.001	0.002
AABLOSUM50	0.002	0.001	0.002
AABLOSUM62	0.001	0.000	0.002
AABLOSUM80	0.001	0.000	0.003
AABurden	0.002	0.000	0.002
AACPSA	0.002	0.001	0.002
AAConn	0.002	0.001	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.001	0.000	0.002
AAEdgeAdj	0.001	0.000	0.003
AAEigIdx	0.002	0.001	0.005
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.001	0.000	0.001
AAGeom	0.002	0.001	0.002
AAInfo	0.001	0.001	0.002
AAMOE2D	0.001	0.000	0.002
AAMOE3D	0.001	0.000	0.003
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.001	0.001	0.002
AAPAM250	0.001	0.000	0.002
AAPAM30	0.002	0.000	0.003
AAPAM40	0.002	0.000	0.002
AAPAM70	0.001	0.001	0.002
AARDF	0.002	0.001	0.002
AARandic	0.002	0.001	0.002
AATopo	0.002	0.001	0.003
AATopoChg	0.001	0.000	0.001
AAWHIM	0.001	0.001	0.003
AAWalk	0.001	0.001	0.003
AAindex	0.001	0.001	0.002
Autocorrelation	1.179	0.072	0.871
BMgetDNAGenBank	0.001	0.000	0.001
BioMedR-package	0.001	0.000	0.001
Constitutional	0.469	0.018	0.374
NNeighbors	0.956	0.062	1.047
OptAA3d	0	0	0
acc	0.013	0.003	0.015
apfp	0.002	0.001	0.002
atomprop	0.002	0.001	0.002
bcl	0.002	0.000	0.003
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.577	0.040	0.689
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.218	0.049	0.700
calcTwoProtGOSim	0.001	0.000	0.000
calcTwoProtSeqSim	0.143	0.016	0.159
checkDNA	0.001	0.001	0.002
checkProt	0.002	0.000	0.002
clusterCMP	1.248	0.053	1.320
clusterJP	1.446	0.040	1.527
clusterMDS	0.887	0.054	0.964
clusterStat	0.311	0.020	0.345
connectivity	1.974	0.094	0.781
convAPtoFP	0.307	0.004	0.146
convSDFtoAP	0.044	0.002	0.050
extrDNADAC	0.009	0.000	0.009
extrDNADACC	0.080	0.000	0.088
extrDNADCC	0.095	0.001	0.096
extrDNAIncDiv	0.116	0.002	0.118
extrDNAPseDNC	0.012	0.000	0.012
extrDNAPseKNC	0.008	0.001	0.008
extrDNATAC	0.016	0.000	0.016
extrDNATACC	0.099	0.000	0.104
extrDNATCC	0.113	0.000	0.115
extrDNAkmer	0.002	0.000	0.002
extrDrugAIO	0.000	0.000	0.001
extrDrugAP	0.127	0.002	0.136
extrDrugBCUT	0.106	0.003	0.061
extrDrugCPSA	0.434	0.017	0.229
extrDrugEstate	0.320	0.015	0.242
extrDrugEstateComplete	0.159	0.006	0.056
extrDrugExtended	0.148	0.005	0.056
extrDrugExtendedComplete	0.027	0.000	0.018
extrDrugGraph	0.033	0.001	0.018
extrDrugGraphComplete	0.014	0.000	0.013
extrDrugHybridization	0.028	0.002	0.017
extrDrugHybridizationComplete	0.030	0.000	0.015
extrDrugHybridizationRatio	0.087	0.001	0.026
extrDrugIPMolecularLearning	0.047	0.002	0.018
extrDrugKR	5.007	0.109	1.654
extrDrugKRComplete	1.737	0.022	0.943
extrDrugKappaShapeIndices	0.054	0.001	0.035
extrDrugKierHallSmarts	0.114	0.002	0.067
extrDrugMACCS	0.282	0.017	0.109
extrDrugMACCSComplete	0.206	0.006	0.063
extrDrugMannholdLogP	6.940	0.064	3.971
extrDrugOBFP2	0.078	0.000	0.082
extrDrugOBFP3	0.001	0.000	0.000
extrDrugOBFP4	0.063	0.001	0.069
extrDrugPubChem	0.749	0.008	0.241
extrDrugPubChemComplete	0.657	0.009	0.204
extrDrugShortestPath	0.004	0.000	0.000
extrDrugShortestPathComplete	0.001	0.000	0.000
extrDrugStandard	0.055	0.001	0.017
extrDrugStandardComplete	0.050	0.001	0.019
extrDrugWHIM	0.147	0.003	0.077
extrPCMBLOSUM	0.062	0.000	0.065
extrPCMDescScales	0.013	0.001	0.014
extrPCMFAScales	0.021	0.001	0.022
extrPCMMDSScales	0.012	0.001	0.014
extrPCMPropScales	0.049	0.001	0.050
extrPCMScaleGap	0.015	0.001	0.015
extrPCMScales	0.012	0.001	0.013
extrProtAAC	0.002	0.000	0.003
extrProtAPAAC	1.327	0.007	1.394
extrProtCTDC	0.006	0.001	0.006
extrProtCTDCClass	0.006	0.000	0.006
extrProtCTDD	0.006	0.001	0.006
extrProtCTDDClass	0.006	0.000	0.006
extrProtCTDT	0.013	0.000	0.016
extrProtCTDTClass	0.007	0.000	0.006
extrProtCTriad	0.156	0.004	0.161
extrProtCTriadClass	0.094	0.004	0.100
extrProtDC	0.004	0.003	0.007
extrProtFPGap	0.030	0.000	0.036
extrProtGeary	0.243	0.007	0.263
extrProtMoran	0.260	0.004	0.279
extrProtMoreauBroto	0.210	0.004	0.216
extrProtPAAC	0.807	0.003	0.832
extrProtPSSM	0.000	0.000	0.001
extrProtPSSMAcc	0.001	0.000	0.001
extrProtPSSMFeature	0	0	0
extrProtQSO	1.361	0.008	1.400
extrProtSOCN	1.317	0.009	1.388
extrProtTC	0.046	0.035	0.088
geometric	0.073	0.002	0.059
getCPI	0.007	0.002	0.009
getDrug	0.000	0.000	0.001
getProt	0.000	0.000	0.001
make_kmer_index	0.001	0.001	0.001
parGOSim	0	0	0
parSeqSim	1.739	0.589	1.463
plotStructure	0.273	0.034	0.312
pls.cv	0.296	0.004	0.308
property	0.563	0.023	0.241
readFASTA	0.007	0.000	0.002
readMolFromSDF	0.075	0.004	0.023
readMolFromSmi	0.008	0.000	0.004
readPDB	1.767	0.016	1.520
revchars	0.001	0.000	0.001
rf.cv	0.996	0.007	1.021
rf.fs	0.583	0.002	0.606
sdfbcl	0.002	0.001	0.002
searchDrug	0	0	0
segProt	0.003	0.001	0.003
topology	0.448	0.013	0.327
twoGOSim	0	0	0
twoSeqSim	0.688	0.009	0.710