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BioC 3.5: CHECK report for BioMedR on veracruz2

This page was generated on 2017-08-16 13:35:40 -0400 (Wed, 16 Aug 2017).

Package 127/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMedR 1.0.0
Min-feng Zhu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/BioMedR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

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

Command output

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


* 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.

runTests.Rout.fail:


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

BioMedR.Rcheck/00install.out:

* 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)

BioMedR.Rcheck/BioMedR-Ex.timings:

nameusersystemelapsed
AA2DACOR0.0190.0030.021
AA3DMoRSE0.0010.0000.002
AAACF0.0020.0000.003
AABLOSUM1000.0010.0000.002
AABLOSUM450.0010.0010.002
AABLOSUM500.0020.0010.002
AABLOSUM620.0010.0000.002
AABLOSUM800.0010.0000.003
AABurden0.0020.0000.002
AACPSA0.0020.0010.002
AAConn0.0020.0010.002
AAConst0.0020.0000.002
AADescAll0.0010.0000.002
AAEdgeAdj0.0010.0000.003
AAEigIdx0.0020.0010.005
AAFGC0.0010.0010.002
AAGETAWAY0.0010.0000.001
AAGeom0.0020.0010.002
AAInfo0.0010.0010.002
AAMOE2D0.0010.0000.002
AAMOE3D0.0010.0000.003
AAMetaInfo0.0020.0000.002
AAMolProp0.0020.0010.002
AAPAM1200.0010.0010.002
AAPAM2500.0010.0000.002
AAPAM300.0020.0000.003
AAPAM400.0020.0000.002
AAPAM700.0010.0010.002
AARDF0.0020.0010.002
AARandic0.0020.0010.002
AATopo0.0020.0010.003
AATopoChg0.0010.0000.001
AAWHIM0.0010.0010.003
AAWalk0.0010.0010.003
AAindex0.0010.0010.002
Autocorrelation1.1790.0720.871
BMgetDNAGenBank0.0010.0000.001
BioMedR-package0.0010.0000.001
Constitutional0.4690.0180.374
NNeighbors0.9560.0621.047
OptAA3d000
acc0.0130.0030.015
apfp0.0020.0010.002
atomprop0.0020.0010.002
bcl0.0020.0000.003
calcDrugFPSim0.0000.0000.001
calcDrugMCSSim0.5770.0400.689
calcParProtGOSim000
calcParProtSeqSim0.2180.0490.700
calcTwoProtGOSim0.0010.0000.000
calcTwoProtSeqSim0.1430.0160.159
checkDNA0.0010.0010.002
checkProt0.0020.0000.002
clusterCMP1.2480.0531.320
clusterJP1.4460.0401.527
clusterMDS0.8870.0540.964
clusterStat0.3110.0200.345
connectivity1.9740.0940.781
convAPtoFP0.3070.0040.146
convSDFtoAP0.0440.0020.050
extrDNADAC0.0090.0000.009
extrDNADACC0.0800.0000.088
extrDNADCC0.0950.0010.096
extrDNAIncDiv0.1160.0020.118
extrDNAPseDNC0.0120.0000.012
extrDNAPseKNC0.0080.0010.008
extrDNATAC0.0160.0000.016
extrDNATACC0.0990.0000.104
extrDNATCC0.1130.0000.115
extrDNAkmer0.0020.0000.002
extrDrugAIO0.0000.0000.001
extrDrugAP0.1270.0020.136
extrDrugBCUT0.1060.0030.061
extrDrugCPSA0.4340.0170.229
extrDrugEstate0.3200.0150.242
extrDrugEstateComplete0.1590.0060.056
extrDrugExtended0.1480.0050.056
extrDrugExtendedComplete0.0270.0000.018
extrDrugGraph0.0330.0010.018
extrDrugGraphComplete0.0140.0000.013
extrDrugHybridization0.0280.0020.017
extrDrugHybridizationComplete0.0300.0000.015
extrDrugHybridizationRatio0.0870.0010.026
extrDrugIPMolecularLearning0.0470.0020.018
extrDrugKR5.0070.1091.654
extrDrugKRComplete1.7370.0220.943
extrDrugKappaShapeIndices0.0540.0010.035
extrDrugKierHallSmarts0.1140.0020.067
extrDrugMACCS0.2820.0170.109
extrDrugMACCSComplete0.2060.0060.063
extrDrugMannholdLogP6.9400.0643.971
extrDrugOBFP20.0780.0000.082
extrDrugOBFP30.0010.0000.000
extrDrugOBFP40.0630.0010.069
extrDrugPubChem0.7490.0080.241
extrDrugPubChemComplete0.6570.0090.204
extrDrugShortestPath0.0040.0000.000
extrDrugShortestPathComplete0.0010.0000.000
extrDrugStandard0.0550.0010.017
extrDrugStandardComplete0.0500.0010.019
extrDrugWHIM0.1470.0030.077
extrPCMBLOSUM0.0620.0000.065
extrPCMDescScales0.0130.0010.014
extrPCMFAScales0.0210.0010.022
extrPCMMDSScales0.0120.0010.014
extrPCMPropScales0.0490.0010.050
extrPCMScaleGap0.0150.0010.015
extrPCMScales0.0120.0010.013
extrProtAAC0.0020.0000.003
extrProtAPAAC1.3270.0071.394
extrProtCTDC0.0060.0010.006
extrProtCTDCClass0.0060.0000.006
extrProtCTDD0.0060.0010.006
extrProtCTDDClass0.0060.0000.006
extrProtCTDT0.0130.0000.016
extrProtCTDTClass0.0070.0000.006
extrProtCTriad0.1560.0040.161
extrProtCTriadClass0.0940.0040.100
extrProtDC0.0040.0030.007
extrProtFPGap0.0300.0000.036
extrProtGeary0.2430.0070.263
extrProtMoran0.2600.0040.279
extrProtMoreauBroto0.2100.0040.216
extrProtPAAC0.8070.0030.832
extrProtPSSM0.0000.0000.001
extrProtPSSMAcc0.0010.0000.001
extrProtPSSMFeature000
extrProtQSO1.3610.0081.400
extrProtSOCN1.3170.0091.388
extrProtTC0.0460.0350.088
geometric0.0730.0020.059
getCPI0.0070.0020.009
getDrug0.0000.0000.001
getProt0.0000.0000.001
make_kmer_index0.0010.0010.001
parGOSim000
parSeqSim1.7390.5891.463
plotStructure0.2730.0340.312
pls.cv0.2960.0040.308
property0.5630.0230.241
readFASTA0.0070.0000.002
readMolFromSDF0.0750.0040.023
readMolFromSmi0.0080.0000.004
readPDB1.7670.0161.520
revchars0.0010.0000.001
rf.cv0.9960.0071.021
rf.fs0.5830.0020.606
sdfbcl0.0020.0010.002
searchDrug000
segProt0.0030.0010.003
topology0.4480.0130.327
twoGOSim000
twoSeqSim0.6880.0090.710