Package: BioMedR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioMedR_1.2.0.tar.gz

StartedAt: 2018-04-12 00:58:09 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:01:22 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 192.3 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'BioMedR' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck/00install.out’ for details.
* 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 6.309  0.049   3.946
* 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, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck/00check.log’
for details.

* 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
Warning: Package 'BioMedR' is deprecated and will be removed from Bioconductor
  version 3.7
* DONE (BioMedR)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 0.881 0.039 0.451
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779

In addition: Warning message:
Package 'BioMedR' is deprecated and will be removed from Bioconductor
  version 3.7 


RUNIT TEST PROTOCOL -- Thu Apr 12 01:01:13 2018 
*********************************************** 
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

name	user	system	elapsed
AA2DACOR	0.018	0.003	0.023
AA3DMoRSE	0.001	0.001	0.002
AAACF	0.002	0.001	0.003
AABLOSUM100	0.001	0.001	0.003
AABLOSUM45	0.001	0.001	0.002
AABLOSUM50	0.001	0.001	0.003
AABLOSUM62	0.002	0.001	0.003
AABLOSUM80	0.002	0.001	0.003
AABurden	0.002	0.001	0.003
AACPSA	0.002	0.001	0.003
AAConn	0.002	0.001	0.003
AAConst	0.002	0.001	0.003
AADescAll	0.002	0.001	0.003
AAEdgeAdj	0.002	0.001	0.003
AAEigIdx	0.002	0.001	0.003
AAFGC	0.002	0.001	0.003
AAGETAWAY	0.002	0.001	0.002
AAGeom	0.001	0.000	0.002
AAInfo	0.001	0.000	0.002
AAMOE2D	0.002	0.000	0.002
AAMOE3D	0.002	0.001	0.002
AAMetaInfo	0.001	0.001	0.002
AAMolProp	0.002	0.001	0.003
AAPAM120	0.002	0.001	0.002
AAPAM250	0.001	0.001	0.002
AAPAM30	0.002	0.001	0.003
AAPAM40	0.001	0.001	0.001
AAPAM70	0.001	0.000	0.002
AARDF	0.001	0.001	0.002
AARandic	0.002	0.001	0.002
AATopo	0.001	0.001	0.002
AATopoChg	0.001	0.001	0.002
AAWHIM	0.002	0.000	0.002
AAWalk	0.002	0.000	0.003
AAindex	0.001	0.000	0.002
Autocorrelation	1.037	0.062	0.627
BMgetDNAGenBank	0.000	0.000	0.001
BioMedR-package	0.000	0.000	0.001
Constitutional	0.484	0.025	0.351
NNeighbors	0.895	0.055	0.963
OptAA3d	0.000	0.000	0.001
acc	0.016	0.004	0.021
apfp	0.002	0.001	0.002
atomprop	0.002	0.001	0.003
bcl	0.001	0.001	0.002
calcDrugFPSim	0.001	0.000	0.001
calcDrugMCSSim	0.718	0.052	0.940
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.212	0.048	0.755
calcTwoProtGOSim	0.001	0.000	0.000
calcTwoProtSeqSim	0.139	0.016	0.162
checkDNA	0.001	0.000	0.002
checkProt	0.001	0.000	0.001
clusterCMP	1.232	0.064	1.320
clusterJP	1.472	0.033	1.528
clusterMDS	0.923	0.052	0.996
clusterStat	0.294	0.021	0.325
connectivity	2.082	0.111	0.815
convAPtoFP	0.217	0.003	0.135
convSDFtoAP	0.043	0.001	0.044
extrDNADAC	0.009	0.001	0.009
extrDNADACC	0.088	0.001	0.089
extrDNADCC	0.118	0.001	0.120
extrDNAIncDiv	0.105	0.001	0.106
extrDNAPseDNC	0.011	0.001	0.012
extrDNAPseKNC	0.008	0.001	0.009
extrDNATAC	0.016	0.000	0.016
extrDNATACC	0.099	0.001	0.101
extrDNATCC	0.134	0.001	0.136
extrDNAkmer	0.001	0.000	0.001
extrDrugAIO	0	0	0
extrDrugAP	0.125	0.002	0.133
extrDrugBCUT	0.107	0.003	0.078
extrDrugCPSA	0.411	0.034	0.228
extrDrugEstate	0.333	0.014	0.239
extrDrugEstateComplete	0.171	0.007	0.060
extrDrugExtended	0.143	0.005	0.043
extrDrugExtendedComplete	0.036	0.001	0.019
extrDrugGraph	0.026	0.001	0.018
extrDrugGraphComplete	0.023	0.001	0.012
extrDrugHybridization	0.028	0.001	0.017
extrDrugHybridizationComplete	0.039	0.001	0.013
extrDrugHybridizationRatio	0.083	0.002	0.026
extrDrugIPMolecularLearning	0.028	0.001	0.016
extrDrugKR	4.785	0.125	1.565
extrDrugKRComplete	1.290	0.019	0.849
extrDrugKappaShapeIndices	0.066	0.001	0.036
extrDrugKierHallSmarts	0.153	0.003	0.077
extrDrugMACCS	0.313	0.011	0.109
extrDrugMACCSComplete	0.205	0.004	0.056
extrDrugMannholdLogP	6.309	0.049	3.946
extrDrugOBFP2	0.077	0.001	0.083
extrDrugOBFP3	0	0	0
extrDrugOBFP4	0.057	0.001	0.060
extrDrugPubChem	0.799	0.015	0.256
extrDrugPubChemComplete	0.608	0.005	0.200
extrDrugShortestPath	0.001	0.000	0.000
extrDrugShortestPathComplete	0.002	0.001	0.001
extrDrugStandard	0.071	0.001	0.023
extrDrugStandardComplete	0.050	0.001	0.014
extrDrugWHIM	0.236	0.005	0.080
extrPCMBLOSUM	0.128	0.002	0.070
extrPCMDescScales	0.026	0.001	0.013
extrPCMFAScales	0.019	0.001	0.018
extrPCMMDSScales	0.011	0.001	0.012
extrPCMPropScales	0.040	0.000	0.041
extrPCMScaleGap	0.018	0.001	0.019
extrPCMScales	0.019	0.001	0.020
extrProtAAC	0.003	0.001	0.003
extrProtAPAAC	1.217	0.008	1.254
extrProtCTDC	0.006	0.000	0.006
extrProtCTDCClass	0.020	0.001	0.021
extrProtCTDD	0.007	0.001	0.008
extrProtCTDDClass	0.008	0.001	0.009
extrProtCTDT	0.007	0.001	0.008
extrProtCTDTClass	0.007	0.001	0.007
extrProtCTriad	0.158	0.012	0.176
extrProtCTriadClass	0.101	0.007	0.108
extrProtDC	0.005	0.003	0.008
extrProtFPGap	0.034	0.001	0.036
extrProtGeary	0.225	0.006	0.246
extrProtMoran	0.226	0.004	0.238
extrProtMoreauBroto	0.223	0.006	0.238
extrProtPAAC	0.732	0.003	0.751
extrProtPSSM	0	0	0
extrProtPSSMAcc	0.000	0.000	0.001
extrProtPSSMFeature	0	0	0
extrProtQSO	1.264	0.007	1.292
extrProtSOCN	1.341	0.015	1.409
extrProtTC	0.068	0.055	0.123
geometric	0.080	0.002	0.052
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	0.000	0.001
parGOSim	0	0	0
parSeqSim	1.878	0.717	1.609
plotStructure	0.337	0.039	0.376
pls.cv	0.267	0.004	0.276
property	0.478	0.024	0.221
readFASTA	0.004	0.001	0.002
readMolFromSDF	0.081	0.002	0.024
readMolFromSmi	0.010	0.000	0.004
readPDB	1.876	0.021	1.477
revchars	0.001	0.001	0.001
rf.cv	0.948	0.007	0.967
rf.fs	0.624	0.002	0.636
sdfbcl	0.002	0.001	0.007
searchDrug	0.001	0.000	0.000
segProt	0.002	0.001	0.003
topology	0.435	0.013	0.327
twoGOSim	0.000	0.001	0.001
twoSeqSim	0.760	0.009	0.783