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BioC 3.6: CHECK report for BioMedR on malbec1

This page was generated on 2017-08-16 13:25:39 -0400 (Wed, 16 Aug 2017).

Package 128/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMedR 1.1.0
Min-feng Zhu
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BioMedR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ ERROR ]
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: BioMedR
Version: 1.1.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BioMedR_1.1.0.tar.gz
StartedAt: 2017-08-15 21:34:31 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:37:14 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 163.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: BioMedR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BioMedR_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
extrDrugKR           6.092  0.048   1.058
extrDrugMannholdLogP 5.352  0.024   3.102
* 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
  ‘/home/biocbuild/bbs-3.6-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-pc-linux-gnu (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: 1.1 0.036 0.471
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) : 
  Mean relative difference: 0.04145779



RUNIT TEST PROTOCOL -- Tue Aug 15 21:37:06 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
AA2DACOR0.0160.0040.021
AA3DMoRSE0.0000.0000.001
AAACF0.0000.0000.001
AABLOSUM1000.0040.0000.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0040.0000.001
AABLOSUM620.0000.0000.001
AABLOSUM800.0040.0000.001
AABurden0.0000.0000.001
AACPSA0.0000.0000.001
AAConn0.0000.0000.001
AAConst0.0000.0000.001
AADescAll0.0000.0000.001
AAEdgeAdj0.0000.0000.001
AAEigIdx0.0040.0000.001
AAFGC0.0000.0000.001
AAGETAWAY0.0040.0000.001
AAGeom0.0000.0000.001
AAInfo0.0040.0000.002
AAMOE2D0.0000.0000.001
AAMOE3D0.0000.0000.001
AAMetaInfo0.0000.0000.001
AAMolProp0.0000.0000.002
AAPAM1200.0040.0000.001
AAPAM2500.0000.0000.001
AAPAM300.0040.0000.001
AAPAM400.0000.0000.001
AAPAM700.0040.0000.001
AARDF0.0000.0000.001
AARandic0.0000.0000.001
AATopo0.0000.0000.001
AATopoChg0.0000.0000.002
AAWHIM0.0000.0000.001
AAWalk0.0000.0000.001
AAindex0.0000.0000.001
Autocorrelation1.3600.0481.247
BMgetDNAGenBank0.0000.0000.001
BioMedR-package0.0040.0000.001
Constitutional0.6160.0200.402
NNeighbors0.7280.0080.734
OptAA3d0.0000.0000.001
acc0.0080.0040.010
apfp0.0000.0000.001
atomprop0.0040.0000.001
bcl0.0000.0000.001
calcDrugFPSim0.0040.0000.000
calcDrugMCSSim0.480.021.36
calcParProtGOSim000
calcParProtSeqSim0.3960.0920.493
calcTwoProtGOSim000
calcTwoProtSeqSim0.1040.0040.108
checkDNA0.0000.0000.001
checkProt0.0040.0000.001
clusterCMP1.3400.0361.375
clusterJP1.7120.0001.714
clusterMDS0.6320.0000.632
clusterStat0.3120.0000.311
connectivity2.2000.0240.784
convAPtoFP0.1960.0000.169
convSDFtoAP0.0400.0000.041
extrDNADAC0.0120.0000.013
extrDNADACC0.0640.0000.064
extrDNADCC0.0920.0000.091
extrDNAIncDiv0.1080.0040.115
extrDNAPseDNC0.0080.0000.009
extrDNAPseKNC0.0040.0000.006
extrDNATAC0.0120.0000.011
extrDNATACC0.0800.0000.077
extrDNATCC0.1280.0000.127
extrDNAkmer0.0040.0000.002
extrDrugAIO0.0000.0000.001
extrDrugAP0.1720.0000.170
extrDrugBCUT0.0680.0040.070
extrDrugCPSA0.4280.0240.211
extrDrugEstate0.4360.0000.309
extrDrugEstateComplete0.2040.0080.044
extrDrugExtended0.1320.0000.040
extrDrugExtendedComplete0.0240.0040.019
extrDrugGraph0.0360.0080.025
extrDrugGraphComplete0.0160.0000.015
extrDrugHybridization0.0400.0040.020
extrDrugHybridizationComplete0.0480.0000.015
extrDrugHybridizationRatio0.0920.0000.027
extrDrugIPMolecularLearning0.0320.0000.012
extrDrugKR6.0920.0481.058
extrDrugKRComplete0.8920.0120.592
extrDrugKappaShapeIndices0.0600.0000.055
extrDrugKierHallSmarts0.0800.0000.076
extrDrugMACCS0.7320.0120.138
extrDrugMACCSComplete0.3040.0000.044
extrDrugMannholdLogP5.3520.0243.102
extrDrugOBFP20.1240.0000.146
extrDrugOBFP30.0040.0000.001
extrDrugOBFP40.0760.0000.086
extrDrugPubChem0.7320.0160.225
extrDrugPubChemComplete0.8680.0000.176
extrDrugShortestPath000
extrDrugShortestPathComplete000
extrDrugStandard0.0280.0040.012
extrDrugStandardComplete0.0440.0000.008
extrDrugWHIM0.1320.0000.046
extrPCMBLOSUM0.1000.0000.049
extrPCMDescScales0.0160.0000.009
extrPCMFAScales0.0280.0000.015
extrPCMMDSScales0.0280.0000.014
extrPCMPropScales0.0480.0000.023
extrPCMScaleGap0.0240.0000.012
extrPCMScales0.0280.0000.019
extrProtAAC0.0000.0000.002
extrProtAPAAC0.9080.0080.913
extrProtCTDC0.0040.0000.004
extrProtCTDCClass0.0040.0000.005
extrProtCTDD0.0040.0000.004
extrProtCTDDClass0.0040.0000.005
extrProtCTDT0.0040.0000.005
extrProtCTDTClass0.0040.0000.006
extrProtCTriad0.1240.0080.131
extrProtCTriadClass0.0760.0000.076
extrProtDC0.0000.0040.006
extrProtFPGap0.0320.0000.032
extrProtGeary0.180.000.18
extrProtMoran0.1760.0040.181
extrProtMoreauBroto0.1520.0000.155
extrProtPAAC0.5200.0040.523
extrProtPSSM0.0000.0000.001
extrProtPSSMAcc0.0000.0000.001
extrProtPSSMFeature000
extrProtQSO0.8720.0040.872
extrProtSOCN0.840.000.84
extrProtTC0.0320.0120.042
geometric0.0720.0080.055
getCPI0.0080.0000.009
getDrug0.0000.0000.001
getProt0.0000.0000.001
make_kmer_index0.0000.0000.002
parGOSim0.0000.0000.001
parSeqSim1.5760.3321.295
plotStructure0.2520.0160.270
pls.cv0.2280.0000.230
property0.3960.0000.185
readFASTA0.0040.0000.001
readMolFromSDF0.0600.0000.021
readMolFromSmi0.0120.0000.003
readPDB1.6880.0441.608
revchars0.0040.0000.001
rf.cv0.8880.0040.891
rf.fs0.5640.0000.564
sdfbcl0.0040.0000.002
searchDrug000
segProt0.0040.0000.004
topology0.4560.0080.324
twoGOSim0.0040.0000.001
twoSeqSim0.5360.0000.531