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CHECK report for BioMedR on veracruz1

This page was generated on 2018-04-12 13:46:15 -0400 (Thu, 12 Apr 2018).

Package 134/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMedR 1.2.0
Min-feng Zhu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BioMedR
Branch: RELEASE_3_6
Last Commit: c53e5bd
Last Changed Date: 2017-10-30 12:41:27 -0400 (Mon, 30 Oct 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: 1.2.0
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

Command output

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


* 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.


Installation output

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

Tests output

BioMedR.Rcheck/tests/runTests.Rout.fail


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

Example timings

BioMedR.Rcheck/BioMedR-Ex.timings

nameusersystemelapsed
AA2DACOR0.0180.0030.023
AA3DMoRSE0.0010.0010.002
AAACF0.0020.0010.003
AABLOSUM1000.0010.0010.003
AABLOSUM450.0010.0010.002
AABLOSUM500.0010.0010.003
AABLOSUM620.0020.0010.003
AABLOSUM800.0020.0010.003
AABurden0.0020.0010.003
AACPSA0.0020.0010.003
AAConn0.0020.0010.003
AAConst0.0020.0010.003
AADescAll0.0020.0010.003
AAEdgeAdj0.0020.0010.003
AAEigIdx0.0020.0010.003
AAFGC0.0020.0010.003
AAGETAWAY0.0020.0010.002
AAGeom0.0010.0000.002
AAInfo0.0010.0000.002
AAMOE2D0.0020.0000.002
AAMOE3D0.0020.0010.002
AAMetaInfo0.0010.0010.002
AAMolProp0.0020.0010.003
AAPAM1200.0020.0010.002
AAPAM2500.0010.0010.002
AAPAM300.0020.0010.003
AAPAM400.0010.0010.001
AAPAM700.0010.0000.002
AARDF0.0010.0010.002
AARandic0.0020.0010.002
AATopo0.0010.0010.002
AATopoChg0.0010.0010.002
AAWHIM0.0020.0000.002
AAWalk0.0020.0000.003
AAindex0.0010.0000.002
Autocorrelation1.0370.0620.627
BMgetDNAGenBank0.0000.0000.001
BioMedR-package0.0000.0000.001
Constitutional0.4840.0250.351
NNeighbors0.8950.0550.963
OptAA3d0.0000.0000.001
acc0.0160.0040.021
apfp0.0020.0010.002
atomprop0.0020.0010.003
bcl0.0010.0010.002
calcDrugFPSim0.0010.0000.001
calcDrugMCSSim0.7180.0520.940
calcParProtGOSim0.0010.0000.001
calcParProtSeqSim0.2120.0480.755
calcTwoProtGOSim0.0010.0000.000
calcTwoProtSeqSim0.1390.0160.162
checkDNA0.0010.0000.002
checkProt0.0010.0000.001
clusterCMP1.2320.0641.320
clusterJP1.4720.0331.528
clusterMDS0.9230.0520.996
clusterStat0.2940.0210.325
connectivity2.0820.1110.815
convAPtoFP0.2170.0030.135
convSDFtoAP0.0430.0010.044
extrDNADAC0.0090.0010.009
extrDNADACC0.0880.0010.089
extrDNADCC0.1180.0010.120
extrDNAIncDiv0.1050.0010.106
extrDNAPseDNC0.0110.0010.012
extrDNAPseKNC0.0080.0010.009
extrDNATAC0.0160.0000.016
extrDNATACC0.0990.0010.101
extrDNATCC0.1340.0010.136
extrDNAkmer0.0010.0000.001
extrDrugAIO000
extrDrugAP0.1250.0020.133
extrDrugBCUT0.1070.0030.078
extrDrugCPSA0.4110.0340.228
extrDrugEstate0.3330.0140.239
extrDrugEstateComplete0.1710.0070.060
extrDrugExtended0.1430.0050.043
extrDrugExtendedComplete0.0360.0010.019
extrDrugGraph0.0260.0010.018
extrDrugGraphComplete0.0230.0010.012
extrDrugHybridization0.0280.0010.017
extrDrugHybridizationComplete0.0390.0010.013
extrDrugHybridizationRatio0.0830.0020.026
extrDrugIPMolecularLearning0.0280.0010.016
extrDrugKR4.7850.1251.565
extrDrugKRComplete1.2900.0190.849
extrDrugKappaShapeIndices0.0660.0010.036
extrDrugKierHallSmarts0.1530.0030.077
extrDrugMACCS0.3130.0110.109
extrDrugMACCSComplete0.2050.0040.056
extrDrugMannholdLogP6.3090.0493.946
extrDrugOBFP20.0770.0010.083
extrDrugOBFP3000
extrDrugOBFP40.0570.0010.060
extrDrugPubChem0.7990.0150.256
extrDrugPubChemComplete0.6080.0050.200
extrDrugShortestPath0.0010.0000.000
extrDrugShortestPathComplete0.0020.0010.001
extrDrugStandard0.0710.0010.023
extrDrugStandardComplete0.0500.0010.014
extrDrugWHIM0.2360.0050.080
extrPCMBLOSUM0.1280.0020.070
extrPCMDescScales0.0260.0010.013
extrPCMFAScales0.0190.0010.018
extrPCMMDSScales0.0110.0010.012
extrPCMPropScales0.0400.0000.041
extrPCMScaleGap0.0180.0010.019
extrPCMScales0.0190.0010.020
extrProtAAC0.0030.0010.003
extrProtAPAAC1.2170.0081.254
extrProtCTDC0.0060.0000.006
extrProtCTDCClass0.0200.0010.021
extrProtCTDD0.0070.0010.008
extrProtCTDDClass0.0080.0010.009
extrProtCTDT0.0070.0010.008
extrProtCTDTClass0.0070.0010.007
extrProtCTriad0.1580.0120.176
extrProtCTriadClass0.1010.0070.108
extrProtDC0.0050.0030.008
extrProtFPGap0.0340.0010.036
extrProtGeary0.2250.0060.246
extrProtMoran0.2260.0040.238
extrProtMoreauBroto0.2230.0060.238
extrProtPAAC0.7320.0030.751
extrProtPSSM000
extrProtPSSMAcc0.0000.0000.001
extrProtPSSMFeature000
extrProtQSO1.2640.0071.292
extrProtSOCN1.3410.0151.409
extrProtTC0.0680.0550.123
geometric0.0800.0020.052
getCPI0.0070.0020.009
getDrug0.0000.0000.001
getProt0.0000.0000.001
make_kmer_index0.0010.0000.001
parGOSim000
parSeqSim1.8780.7171.609
plotStructure0.3370.0390.376
pls.cv0.2670.0040.276
property0.4780.0240.221
readFASTA0.0040.0010.002
readMolFromSDF0.0810.0020.024
readMolFromSmi0.0100.0000.004
readPDB1.8760.0211.477
revchars0.0010.0010.001
rf.cv0.9480.0070.967
rf.fs0.6240.0020.636
sdfbcl0.0020.0010.007
searchDrug0.0010.0000.000
segProt0.0020.0010.003
topology0.4350.0130.327
twoGOSim0.0000.0010.001
twoSeqSim0.7600.0090.783