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: 2017-10-18 01:02:00 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:05:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 195.3 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 3.4.2 (2017-09-28)
* 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 7.019  0.064   4.160
extrDrugKR           5.233  0.102   1.529
* 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 3.4.2 (2017-09-28) -- "Short Summer"
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: 1.074 0.062 0.603
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779



RUNIT TEST PROTOCOL -- Wed Oct 18 01:05:03 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	0.018	0.003	0.022
AA3DMoRSE	0.001	0.001	0.002
AAACF	0.001	0.000	0.002
AABLOSUM100	0.002	0.000	0.002
AABLOSUM45	0.001	0.001	0.002
AABLOSUM50	0.002	0.001	0.003
AABLOSUM62	0.001	0.001	0.002
AABLOSUM80	0.001	0.000	0.001
AABurden	0.002	0.001	0.003
AACPSA	0.002	0.001	0.003
AAConn	0.001	0.001	0.002
AAConst	0.002	0.001	0.002
AADescAll	0.002	0.001	0.002
AAEdgeAdj	0.002	0.000	0.002
AAEigIdx	0.002	0.000	0.002
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.002	0.000	0.002
AAInfo	0.001	0.000	0.002
AAMOE2D	0.002	0.001	0.001
AAMOE3D	0.001	0.000	0.001
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.001	0.001	0.001
AAPAM250	0.002	0.000	0.002
AAPAM30	0.001	0.000	0.001
AAPAM40	0.001	0.001	0.002
AAPAM70	0.001	0.000	0.002
AARDF	0.001	0.000	0.002
AARandic	0.002	0.001	0.001
AATopo	0.001	0.001	0.002
AATopoChg	0.002	0.000	0.002
AAWHIM	0.001	0.000	0.002
AAWalk	0.001	0.001	0.002
AAindex	0.002	0.001	0.002
Autocorrelation	1.164	0.069	0.763
BMgetDNAGenBank	0.000	0.001	0.001
BioMedR-package	0.001	0.000	0.001
Constitutional	0.450	0.017	0.343
NNeighbors	0.925	0.035	0.981
OptAA3d	0	0	0
acc	0.014	0.003	0.017
apfp	0.001	0.001	0.001
atomprop	0.002	0.000	0.002
bcl	0.002	0.001	0.002
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.539	0.044	0.657
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.443	0.161	0.621
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.112	0.012	0.124
checkDNA	0	0	0
checkProt	0.002	0.001	0.001
clusterCMP	1.190	0.039	1.266
clusterJP	1.402	0.021	1.481
clusterMDS	0.853	0.032	0.946
clusterStat	0.298	0.005	0.310
connectivity	1.974	0.093	0.774
convAPtoFP	0.369	0.007	0.157
convSDFtoAP	0.041	0.001	0.042
extrDNADAC	0.016	0.001	0.016
extrDNADACC	0.078	0.001	0.082
extrDNADCC	0.114	0.001	0.119
extrDNAIncDiv	0.120	0.002	0.128
extrDNAPseDNC	0.008	0.000	0.013
extrDNAPseKNC	0.006	0.001	0.007
extrDNATAC	0.013	0.000	0.014
extrDNATACC	0.093	0.001	0.097
extrDNATCC	0.122	0.001	0.124
extrDNAkmer	0.002	0.000	0.002
extrDrugAIO	0.001	0.000	0.001
extrDrugAP	0.126	0.002	0.156
extrDrugBCUT	0.108	0.004	0.078
extrDrugCPSA	0.379	0.012	0.178
extrDrugEstate	0.327	0.013	0.214
extrDrugEstateComplete	0.184	0.006	0.050
extrDrugExtended	0.151	0.006	0.047
extrDrugExtendedComplete	0.032	0.001	0.017
extrDrugGraph	0.031	0.001	0.018
extrDrugGraphComplete	0.012	0.000	0.012
extrDrugHybridization	0.040	0.002	0.020
extrDrugHybridizationComplete	0.037	0.001	0.015
extrDrugHybridizationRatio	0.084	0.001	0.025
extrDrugIPMolecularLearning	0.036	0.001	0.014
extrDrugKR	5.233	0.102	1.529
extrDrugKRComplete	1.499	0.029	0.884
extrDrugKappaShapeIndices	0.049	0.001	0.032
extrDrugKierHallSmarts	0.241	0.006	0.092
extrDrugMACCS	0.365	0.012	0.100
extrDrugMACCSComplete	0.237	0.003	0.058
extrDrugMannholdLogP	7.019	0.064	4.160
extrDrugOBFP2	0.082	0.000	0.085
extrDrugOBFP3	0.000	0.000	0.001
extrDrugOBFP4	0.057	0.001	0.063
extrDrugPubChem	1.050	0.013	0.318
extrDrugPubChemComplete	0.425	0.012	0.181
extrDrugShortestPath	0	0	0
extrDrugShortestPathComplete	0.001	0.000	0.000
extrDrugStandard	0.039	0.002	0.013
extrDrugStandardComplete	0.053	0.001	0.019
extrDrugWHIM	0.109	0.001	0.071
extrPCMBLOSUM	0.062	0.000	0.064
extrPCMDescScales	0.012	0.000	0.012
extrPCMFAScales	0.030	0.002	0.031
extrPCMMDSScales	0.012	0.001	0.013
extrPCMPropScales	0.027	0.000	0.027
extrPCMScaleGap	0.015	0.001	0.017
extrPCMScales	0.028	0.001	0.029
extrProtAAC	0.002	0.000	0.002
extrProtAPAAC	1.285	0.013	1.326
extrProtCTDC	0.005	0.000	0.005
extrProtCTDCClass	0.006	0.001	0.007
extrProtCTDD	0.006	0.001	0.008
extrProtCTDDClass	0.007	0.001	0.008
extrProtCTDT	0.015	0.001	0.017
extrProtCTDTClass	0.009	0.001	0.010
extrProtCTriad	0.156	0.007	0.164
extrProtCTriadClass	0.099	0.002	0.103
extrProtDC	0.005	0.003	0.007
extrProtFPGap	0.031	0.001	0.031
extrProtGeary	0.252	0.005	0.265
extrProtMoran	0.234	0.005	0.245
extrProtMoreauBroto	0.234	0.005	0.244
extrProtPAAC	0.718	0.004	0.754
extrProtPSSM	0.000	0.000	0.001
extrProtPSSMAcc	0	0	0
extrProtPSSMFeature	0.000	0.000	0.001
extrProtQSO	1.146	0.012	1.227
extrProtSOCN	1.348	0.015	1.435
extrProtTC	0.051	0.046	0.098
geometric	0.066	0.002	0.054
getCPI	0.007	0.002	0.009
getDrug	0.001	0.000	0.000
getProt	0	0	0
make_kmer_index	0.001	0.000	0.002
parGOSim	0.001	0.000	0.001
parSeqSim	1.454	0.541	1.540
plotStructure	0.329	0.037	0.371
pls.cv	0.325	0.004	0.338
property	0.416	0.014	0.250
readFASTA	0.005	0.000	0.002
readMolFromSDF	0.070	0.003	0.023
readMolFromSmi	0.009	0.001	0.005
readPDB	1.549	0.015	1.523
revchars	0.001	0.001	0.001
rf.cv	1.029	0.010	1.063
rf.fs	0.628	0.004	0.660
sdfbcl	0.002	0.001	0.002
searchDrug	0.000	0.000	0.001
segProt	0.003	0.001	0.003
topology	0.530	0.016	0.361
twoGOSim	0	0	0
twoSeqSim	0.807	0.013	0.845