BioC 3.5: CHECK report for BioMedR on tokay2

Package: BioMedR

Version: 1.0.0

Command: rm -rf BioMedR.buildbin-libdir BioMedR.Rcheck && mkdir BioMedR.buildbin-libdir BioMedR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioMedR.buildbin-libdir BioMedR_1.0.0.tar.gz >BioMedR.Rcheck\00install.out 2>&1 && cp BioMedR.Rcheck\00install.out BioMedR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BioMedR.buildbin-libdir --install="check:BioMedR-install.out" --force-multiarch --no-vignettes --timings BioMedR_1.0.0.tar.gz

StartedAt: 2017-10-17 22:20:50 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:26:45 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 354.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: BioMedR.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BioMedR.buildbin-libdir BioMedR.Rcheck && mkdir BioMedR.buildbin-libdir BioMedR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioMedR.buildbin-libdir BioMedR_1.0.0.tar.gz >BioMedR.Rcheck\00install.out 2>&1 && cp BioMedR.Rcheck\00install.out BioMedR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BioMedR.buildbin-libdir --install="check:BioMedR-install.out" --force-multiarch --no-vignettes --timings BioMedR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BioMedR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
parSeqSim         0.72   0.05   12.72
calcParProtSeqSim 0.25   0.02    5.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
extrDrugKR           7.92   0.16    1.29
extrDrugMannholdLogP 6.12   0.09    3.26
parSeqSim            0.68   0.03   14.31
calcParProtSeqSim    0.29   0.00    9.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 1 
 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
** running tests for arch 'x64' ...
  Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 1 
 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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/BioMedR.Rcheck/00check.log'
for details.

R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 0.51 0.03 0.45
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779



RUNIT TEST PROTOCOL -- Tue Oct 17 22:26:21 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

R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 1.24 0.12 0.63
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779



RUNIT TEST PROTOCOL -- Tue Oct 17 22:26:31 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

install for i386

* 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

install for x64

* installing *source* package 'BioMedR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioMedR' as BioMedR_1.0.0.zip
* DONE (BioMedR)

name	user	system	elapsed
AA2DACOR	0.03	0.00	0.03
AA3DMoRSE	0	0	0
AAACF	0	0	0
AABLOSUM100	0.00	0.02	0.02
AABLOSUM45	0	0	0
AABLOSUM50	0	0	0
AABLOSUM62	0.02	0.00	0.01
AABLOSUM80	0	0	0
AABurden	0	0	0
AACPSA	0	0	0
AAConn	0	0	0
AAConst	0	0	0
AADescAll	0	0	0
AAEdgeAdj	0	0	0
AAEigIdx	0	0	0
AAFGC	0	0	0
AAGETAWAY	0	0	0
AAGeom	0	0	0
AAInfo	0.02	0.00	0.02
AAMOE2D	0	0	0
AAMOE3D	0.00	0.02	0.01
AAMetaInfo	0	0	0
AAMolProp	0	0	0
AAPAM120	0	0	0
AAPAM250	0	0	0
AAPAM30	0	0	0
AAPAM40	0	0	0
AAPAM70	0.00	0.01	0.02
AARDF	0	0	0
AARandic	0.00	0.02	0.02
AATopo	0	0	0
AATopoChg	0.00	0.01	0.01
AAWHIM	0	0	0
AAWalk	0.01	0.00	0.02
AAindex	0	0	0
Autocorrelation	1.03	0.14	4.25
BMgetDNAGenBank	0	0	0
BioMedR-package	0	0	0
Constitutional	0.49	0.00	1.07
NNeighbors	1.11	0.00	1.11
OptAA3d	0	0	0
acc	0	0	0
apfp	0	0	0
atomprop	0	0	0
bcl	0	0	0
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.58	0.03	1.70
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.25	0.02	5.89
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.16	0.00	0.16
checkDNA	0	0	0
checkProt	0	0	0
clusterCMP	1.54	0.03	1.56
clusterJP	1.95	0.00	1.96
clusterMDS	0.53	0.00	0.53
clusterStat	0.27	0.00	0.26
connectivity	1.70	0.01	1.77
convAPtoFP	0.37	0.00	0.37
convSDFtoAP	0.07	0.00	0.07
extrDNADAC	0.01	0.00	0.01
extrDNADACC	0.08	0.00	0.08
extrDNADCC	0.09	0.00	0.09
extrDNAIncDiv	0.1	0.0	0.1
extrDNAPseDNC	0	0	0
extrDNAPseKNC	0.01	0.00	0.01
extrDNATAC	0	0	0
extrDNATACC	0.06	0.00	0.06
extrDNATCC	0.09	0.00	0.10
extrDNAkmer	0	0	0
extrDrugAIO	0	0	0
extrDrugAP	0.2	0.0	0.2
extrDrugBCUT	0.08	0.00	0.14
extrDrugCPSA	0.30	0.05	0.94
extrDrugEstate	0.31	0.00	0.47
extrDrugEstateComplete	0.06	0.00	0.05
extrDrugExtended	0.06	0.00	0.13
extrDrugExtendedComplete	0.03	0.00	0.01
extrDrugGraph	0.03	0.00	0.05
extrDrugGraphComplete	0.02	0.00	0.02
extrDrugHybridization	0.02	0.00	0.01
extrDrugHybridizationComplete	0.03	0.00	0.02
extrDrugHybridizationRatio	0.03	0.00	0.03
extrDrugIPMolecularLearning	0.00	0.00	0.04
extrDrugKR	2.39	0.00	2.25
extrDrugKRComplete	2.05	0.01	2.06
extrDrugKappaShapeIndices	0.08	0.02	0.14
extrDrugKierHallSmarts	0.08	0.00	0.11
extrDrugMACCS	0.13	0.00	0.12
extrDrugMACCSComplete	0.06	0.00	0.07
extrDrugMannholdLogP	3.02	0.01	2.95
extrDrugOBFP2	0.17	0.00	0.41
extrDrugOBFP3	0	0	0
extrDrugOBFP4	0.11	0.00	0.12
extrDrugPubChem	0.44	0.02	0.43
extrDrugPubChemComplete	0.39	0.00	0.40
extrDrugShortestPath	0	0	0
extrDrugShortestPathComplete	0	0	0
extrDrugStandard	0.02	0.00	0.01
extrDrugStandardComplete	0.01	0.00	0.02
extrDrugWHIM	0.11	0.00	0.11
extrPCMBLOSUM	0.08	0.00	0.10
extrPCMDescScales	0.01	0.00	0.01
extrPCMFAScales	0.05	0.00	0.05
extrPCMMDSScales	0.01	0.00	0.01
extrPCMPropScales	0.05	0.00	0.05
extrPCMScaleGap	0.03	0.00	0.03
extrPCMScales	0.05	0.00	0.05
extrProtAAC	0	0	0
extrProtAPAAC	1.23	0.00	1.23
extrProtCTDC	0.02	0.00	0.02
extrProtCTDCClass	0	0	0
extrProtCTDD	0	0	0
extrProtCTDDClass	0.01	0.00	0.01
extrProtCTDT	0	0	0
extrProtCTDTClass	0.00	0.01	0.02
extrProtCTriad	0.10	0.02	0.11
extrProtCTriadClass	0.09	0.00	0.09
extrProtDC	0	0	0
extrProtFPGap	0.03	0.00	0.03
extrProtGeary	0.14	0.02	0.16
extrProtMoran	0.14	0.00	0.14
extrProtMoreauBroto	0.14	0.00	0.14
extrProtPAAC	0.40	0.00	0.39
extrProtPSSM	0	0	0
extrProtPSSMAcc	0	0	0
extrProtPSSMFeature	0	0	0
extrProtQSO	0.65	0.00	0.66
extrProtSOCN	0.64	0.00	0.64
extrProtTC	0.05	0.01	0.06
geometric	0.05	0.00	0.10
getCPI	0	0	0
getDrug	0	0	0
getProt	0	0	0
make_kmer_index	0	0	0
parGOSim	0	0	0
parSeqSim	0.72	0.05	12.72
plotStructure	0.36	0.01	0.37
pls.cv	0.26	0.00	0.27
property	0.24	0.02	0.40
readFASTA	0	0	0
readMolFromSDF	0.03	0.00	0.03
readMolFromSmi	0	0	0
readPDB	1.90	0.03	1.94
revchars	0	0	0
rf.cv	0.71	0.02	0.72
rf.fs	0.69	0.00	0.68
sdfbcl	0	0	0
searchDrug	0	0	0
segProt	0	0	0
topology	0.37	0.03	0.49
twoGOSim	0	0	0
twoSeqSim	0.57	0.03	0.59

name	user	system	elapsed
AA2DACOR	0.00	0.03	0.03
AA3DMoRSE	0	0	0
AAACF	0.02	0.00	0.01
AABLOSUM100	0	0	0
AABLOSUM45	0	0	0
AABLOSUM50	0	0	0
AABLOSUM62	0.02	0.00	0.02
AABLOSUM80	0	0	0
AABurden	0.00	0.02	0.01
AACPSA	0	0	0
AAConn	0	0	0
AAConst	0.00	0.01	0.02
AADescAll	0	0	0
AAEdgeAdj	0.01	0.00	0.01
AAEigIdx	0	0	0
AAFGC	0	0	0
AAGETAWAY	0.00	0.02	0.02
AAGeom	0	0	0
AAInfo	0.02	0.00	0.01
AAMOE2D	0	0	0
AAMOE3D	0	0	0
AAMetaInfo	0.00	0.01	0.02
AAMolProp	0	0	0
AAPAM120	0	0	0
AAPAM250	0.01	0.00	0.02
AAPAM30	0	0	0
AAPAM40	0	0	0
AAPAM70	0	0	0
AARDF	0	0	0
AARandic	0.00	0.02	0.02
AATopo	0	0	0
AATopoChg	0	0	0
AAWHIM	0	0	0
AAWalk	0.00	0.02	0.02
AAindex	0	0	0
Autocorrelation	1.94	0.17	1.03
BMgetDNAGenBank	0	0	0
BioMedR-package	0	0	0
Constitutional	0.72	0.01	0.44
NNeighbors	0.98	0.05	1.06
OptAA3d	0	0	0
acc	0	0	0
apfp	0.02	0.00	0.01
atomprop	0	0	0
bcl	0	0	0
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.53	0.03	1.08
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.29	0.00	9.19
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.16	0.00	0.15
checkDNA	0	0	0
checkProt	0	0	0
clusterCMP	1.57	0.02	1.59
clusterJP	2.14	0.03	2.20
clusterMDS	0.61	0.00	0.66
clusterStat	0.46	0.00	0.45
connectivity	2.77	0.06	0.94
convAPtoFP	0.47	0.00	0.33
convSDFtoAP	0.04	0.00	0.04
extrDNADAC	0	0	0
extrDNADACC	0.09	0.00	0.09
extrDNADCC	0.11	0.00	0.11
extrDNAIncDiv	0.11	0.00	0.11
extrDNAPseDNC	0	0	0
extrDNAPseKNC	0.02	0.00	0.02
extrDNATAC	0.01	0.00	0.01
extrDNATACC	0.1	0.0	0.1
extrDNATCC	0.10	0.00	0.09
extrDNAkmer	0.00	0.02	0.02
extrDrugAIO	0	0	0
extrDrugAP	0.18	0.00	0.19
extrDrugBCUT	0.10	0.00	0.04
extrDrugCPSA	0.59	0.01	0.24
extrDrugEstate	0.59	0.05	0.36
extrDrugEstateComplete	0.33	0.00	0.05
extrDrugExtended	0.19	0.00	0.07
extrDrugExtendedComplete	0.06	0.00	0.03
extrDrugGraph	0.08	0.00	0.02
extrDrugGraphComplete	0.02	0.01	0.03
extrDrugHybridization	0.07	0.00	0.02
extrDrugHybridizationComplete	0.07	0.00	0.02
extrDrugHybridizationRatio	0.14	0.00	0.05
extrDrugIPMolecularLearning	0.05	0.00	0.02
extrDrugKR	7.92	0.16	1.29
extrDrugKRComplete	1.18	0.00	0.99
extrDrugKappaShapeIndices	0.10	0.00	0.09
extrDrugKierHallSmarts	0.09	0.00	0.08
extrDrugMACCS	0.99	0.00	0.11
extrDrugMACCSComplete	0.31	0.00	0.05
extrDrugMannholdLogP	6.12	0.09	3.26
extrDrugOBFP2	0.16	0.00	0.31
extrDrugOBFP3	0	0	0
extrDrugOBFP4	0.09	0.00	0.09
extrDrugPubChem	1.41	0.05	0.25
extrDrugPubChemComplete	0.95	0.02	0.14
extrDrugShortestPath	0	0	0
extrDrugShortestPathComplete	0	0	0
extrDrugStandard	0	0	0
extrDrugStandardComplete	0.09	0.00	0.02
extrDrugWHIM	0.30	0.01	0.12
extrPCMBLOSUM	0.12	0.00	0.11
extrPCMDescScales	0.01	0.00	0.01
extrPCMFAScales	0.03	0.00	0.03
extrPCMMDSScales	0.02	0.00	0.02
extrPCMPropScales	0.06	0.00	0.06
extrPCMScaleGap	0.02	0.00	0.02
extrPCMScales	0.01	0.02	0.03
extrProtAAC	0	0	0
extrProtAPAAC	1.13	0.01	1.14
extrProtCTDC	0.00	0.02	0.01
extrProtCTDCClass	0	0	0
extrProtCTDD	0.01	0.00	0.02
extrProtCTDDClass	0	0	0
extrProtCTDT	0	0	0
extrProtCTDTClass	0	0	0
extrProtCTriad	0.19	0.00	0.19
extrProtCTriadClass	0.09	0.00	0.10
extrProtDC	0.02	0.00	0.01
extrProtFPGap	0.01	0.00	0.02
extrProtGeary	0.21	0.02	0.20
extrProtMoran	0.18	0.00	0.19
extrProtMoreauBroto	0.19	0.00	0.19
extrProtPAAC	0.66	0.00	0.65
extrProtPSSM	0	0	0
extrProtPSSMAcc	0	0	0
extrProtPSSMFeature	0	0	0
extrProtQSO	1.32	0.00	1.33
extrProtSOCN	0.96	0.00	0.95
extrProtTC	0.03	0.01	0.05
geometric	0.03	0.02	0.05
getCPI	0.02	0.00	0.01
getDrug	0	0	0
getProt	0	0	0
make_kmer_index	0	0	0
parGOSim	0	0	0
parSeqSim	0.68	0.03	14.31
plotStructure	0.42	0.00	0.42
pls.cv	0.38	0.00	0.38
property	0.48	0.03	0.22
readFASTA	0	0	0
readMolFromSDF	0.02	0.01	0.01
readMolFromSmi	0	0	0
readPDB	1.76	0.00	1.68
revchars	0	0	0
rf.cv	1.38	0.00	2.29
rf.fs	0.53	0.00	0.53
sdfbcl	0	0	0
searchDrug	0	0	0
segProt	0	0	0
topology	0.47	0.00	0.31
twoGOSim	0	0	0
twoSeqSim	0.83	0.02	0.84