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This page was generated on 2017-08-16 13:18:21 -0400 (Wed, 16 Aug 2017).
| Package 127/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| BioMedR 1.0.0 Min-feng Zhu
| 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 |
| Package: BioMedR |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BioMedR_1.0.0.tar.gz |
| StartedAt: 2017-08-15 21:31:24 -0400 (Tue, 15 Aug 2017) |
| EndedAt: 2017-08-15 21:34:09 -0400 (Tue, 15 Aug 2017) |
| EllapsedTime: 165.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BioMedR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BioMedR_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.0.0’
* 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 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 5.864 0.068 1.028
extrDrugMannholdLogP 5.604 0.012 3.249
* 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-3.5-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-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: 1.124 0.04 0.511
Error in checkEqualsNumeric(sum(as.matrix(dat)), 328.1937635, tolerance = 1e-04) :
Mean relative difference: 0.04145779
RUNIT TEST PROTOCOL -- Tue Aug 15 21:34:00 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:
| name | user | system | elapsed | |
| AA2DACOR | 0.012 | 0.000 | 0.014 | |
| AA3DMoRSE | 0.004 | 0.000 | 0.001 | |
| AAACF | 0.004 | 0.000 | 0.002 | |
| AABLOSUM100 | 0.000 | 0.000 | 0.001 | |
| AABLOSUM45 | 0.004 | 0.000 | 0.001 | |
| AABLOSUM50 | 0.000 | 0.000 | 0.001 | |
| AABLOSUM62 | 0.000 | 0.000 | 0.001 | |
| AABLOSUM80 | 0.000 | 0.000 | 0.001 | |
| AABurden | 0.000 | 0.000 | 0.001 | |
| AACPSA | 0.004 | 0.000 | 0.001 | |
| AAConn | 0.000 | 0.000 | 0.001 | |
| AAConst | 0.004 | 0.000 | 0.001 | |
| AADescAll | 0.000 | 0.000 | 0.001 | |
| AAEdgeAdj | 0.000 | 0.000 | 0.001 | |
| AAEigIdx | 0.000 | 0.000 | 0.001 | |
| AAFGC | 0.000 | 0.000 | 0.001 | |
| AAGETAWAY | 0.000 | 0.000 | 0.001 | |
| AAGeom | 0.000 | 0.000 | 0.001 | |
| AAInfo | 0.004 | 0.000 | 0.002 | |
| AAMOE2D | 0.000 | 0.000 | 0.001 | |
| AAMOE3D | 0.004 | 0.000 | 0.001 | |
| AAMetaInfo | 0.000 | 0.000 | 0.001 | |
| AAMolProp | 0.004 | 0.000 | 0.001 | |
| AAPAM120 | 0.000 | 0.000 | 0.001 | |
| AAPAM250 | 0.004 | 0.000 | 0.001 | |
| AAPAM30 | 0.000 | 0.000 | 0.001 | |
| AAPAM40 | 0.000 | 0.000 | 0.001 | |
| AAPAM70 | 0.000 | 0.000 | 0.001 | |
| AARDF | 0.000 | 0.000 | 0.001 | |
| AARandic | 0.000 | 0.004 | 0.001 | |
| AATopo | 0.000 | 0.000 | 0.001 | |
| AATopoChg | 0.000 | 0.000 | 0.001 | |
| AAWHIM | 0.000 | 0.000 | 0.001 | |
| AAWalk | 0.000 | 0.000 | 0.001 | |
| AAindex | 0.000 | 0.004 | 0.001 | |
| Autocorrelation | 1.288 | 0.080 | 1.254 | |
| BMgetDNAGenBank | 0.000 | 0.000 | 0.001 | |
| BioMedR-package | 0.000 | 0.000 | 0.001 | |
| Constitutional | 0.584 | 0.044 | 0.389 | |
| NNeighbors | 0.936 | 0.000 | 0.937 | |
| OptAA3d | 0.000 | 0.000 | 0.001 | |
| acc | 0.012 | 0.004 | 0.013 | |
| apfp | 0.000 | 0.000 | 0.001 | |
| atomprop | 0.000 | 0.004 | 0.001 | |
| bcl | 0.000 | 0.000 | 0.002 | |
| calcDrugFPSim | 0 | 0 | 0 | |
| calcDrugMCSSim | 0.512 | 0.016 | 0.876 | |
| calcParProtGOSim | 0 | 0 | 0 | |
| calcParProtSeqSim | 0.504 | 0.072 | 0.655 | |
| calcTwoProtGOSim | 0.000 | 0.000 | 0.001 | |
| calcTwoProtSeqSim | 0.164 | 0.004 | 0.170 | |
| checkDNA | 0.000 | 0.000 | 0.001 | |
| checkProt | 0.004 | 0.000 | 0.002 | |
| clusterCMP | 1.360 | 0.036 | 1.393 | |
| clusterJP | 1.564 | 0.000 | 1.563 | |
| clusterMDS | 0.596 | 0.004 | 0.602 | |
| clusterStat | 0.344 | 0.000 | 0.341 | |
| connectivity | 2.144 | 0.132 | 0.919 | |
| convAPtoFP | 0.176 | 0.000 | 0.178 | |
| convSDFtoAP | 0.040 | 0.000 | 0.038 | |
| extrDNADAC | 0.008 | 0.000 | 0.006 | |
| extrDNADACC | 0.072 | 0.000 | 0.072 | |
| extrDNADCC | 0.140 | 0.000 | 0.142 | |
| extrDNAIncDiv | 0.08 | 0.00 | 0.08 | |
| extrDNAPseDNC | 0.012 | 0.000 | 0.008 | |
| extrDNAPseKNC | 0.004 | 0.000 | 0.005 | |
| extrDNATAC | 0.008 | 0.004 | 0.010 | |
| extrDNATACC | 0.080 | 0.000 | 0.076 | |
| extrDNATCC | 0.088 | 0.000 | 0.088 | |
| extrDNAkmer | 0.000 | 0.000 | 0.002 | |
| extrDrugAIO | 0 | 0 | 0 | |
| extrDrugAP | 0.168 | 0.000 | 0.169 | |
| extrDrugBCUT | 0.112 | 0.000 | 0.307 | |
| extrDrugCPSA | 0.468 | 0.004 | 0.425 | |
| extrDrugEstate | 0.420 | 0.020 | 0.367 | |
| extrDrugEstateComplete | 0.240 | 0.000 | 0.073 | |
| extrDrugExtended | 0.096 | 0.000 | 0.049 | |
| extrDrugExtendedComplete | 0.024 | 0.000 | 0.012 | |
| extrDrugGraph | 0.020 | 0.000 | 0.012 | |
| extrDrugGraphComplete | 0.024 | 0.000 | 0.013 | |
| extrDrugHybridization | 0.048 | 0.000 | 0.019 | |
| extrDrugHybridizationComplete | 0.056 | 0.000 | 0.015 | |
| extrDrugHybridizationRatio | 0.088 | 0.000 | 0.023 | |
| extrDrugIPMolecularLearning | 0.068 | 0.000 | 0.028 | |
| extrDrugKR | 5.864 | 0.068 | 1.028 | |
| extrDrugKRComplete | 1.016 | 0.008 | 0.783 | |
| extrDrugKappaShapeIndices | 0.060 | 0.000 | 0.036 | |
| extrDrugKierHallSmarts | 0.060 | 0.000 | 0.044 | |
| extrDrugMACCS | 0.384 | 0.000 | 0.078 | |
| extrDrugMACCSComplete | 0.464 | 0.000 | 0.056 | |
| extrDrugMannholdLogP | 5.604 | 0.012 | 3.249 | |
| extrDrugOBFP2 | 0.076 | 0.000 | 0.087 | |
| extrDrugOBFP3 | 0.000 | 0.000 | 0.001 | |
| extrDrugOBFP4 | 0.048 | 0.004 | 0.193 | |
| extrDrugPubChem | 1.012 | 0.004 | 0.247 | |
| extrDrugPubChemComplete | 0.772 | 0.000 | 0.169 | |
| extrDrugShortestPath | 0.004 | 0.000 | 0.000 | |
| extrDrugShortestPathComplete | 0 | 0 | 0 | |
| extrDrugStandard | 0.052 | 0.000 | 0.015 | |
| extrDrugStandardComplete | 0.048 | 0.000 | 0.015 | |
| extrDrugWHIM | 0.192 | 0.004 | 0.081 | |
| extrPCMBLOSUM | 0.100 | 0.000 | 0.085 | |
| extrPCMDescScales | 0.012 | 0.000 | 0.014 | |
| extrPCMFAScales | 0.016 | 0.008 | 0.024 | |
| extrPCMMDSScales | 0.020 | 0.000 | 0.022 | |
| extrPCMPropScales | 0.040 | 0.000 | 0.043 | |
| extrPCMScaleGap | 0.020 | 0.000 | 0.021 | |
| extrPCMScales | 0.032 | 0.000 | 0.029 | |
| extrProtAAC | 0.004 | 0.000 | 0.003 | |
| extrProtAPAAC | 0.984 | 0.020 | 1.002 | |
| extrProtCTDC | 0.004 | 0.000 | 0.005 | |
| extrProtCTDCClass | 0.004 | 0.000 | 0.004 | |
| extrProtCTDD | 0.004 | 0.000 | 0.004 | |
| extrProtCTDDClass | 0.004 | 0.000 | 0.004 | |
| extrProtCTDT | 0.008 | 0.000 | 0.005 | |
| extrProtCTDTClass | 0.004 | 0.000 | 0.006 | |
| extrProtCTriad | 0.116 | 0.008 | 0.122 | |
| extrProtCTriadClass | 0.072 | 0.000 | 0.072 | |
| extrProtDC | 0.004 | 0.004 | 0.004 | |
| extrProtFPGap | 0.020 | 0.000 | 0.023 | |
| extrProtGeary | 0.172 | 0.000 | 0.175 | |
| extrProtMoran | 0.164 | 0.004 | 0.170 | |
| extrProtMoreauBroto | 0.140 | 0.012 | 0.151 | |
| extrProtPAAC | 0.572 | 0.000 | 0.570 | |
| extrProtPSSM | 0.000 | 0.000 | 0.001 | |
| extrProtPSSMAcc | 0.000 | 0.000 | 0.001 | |
| extrProtPSSMFeature | 0.004 | 0.000 | 0.001 | |
| extrProtQSO | 0.832 | 0.000 | 0.835 | |
| extrProtSOCN | 0.848 | 0.000 | 0.848 | |
| extrProtTC | 0.028 | 0.016 | 0.043 | |
| geometric | 0.128 | 0.004 | 0.071 | |
| getCPI | 0.012 | 0.000 | 0.010 | |
| getDrug | 0.000 | 0.000 | 0.001 | |
| getProt | 0.000 | 0.000 | 0.001 | |
| make_kmer_index | 0.000 | 0.000 | 0.002 | |
| parGOSim | 0 | 0 | 0 | |
| parSeqSim | 1.520 | 0.312 | 1.176 | |
| plotStructure | 0.252 | 0.028 | 0.283 | |
| pls.cv | 0.244 | 0.000 | 0.241 | |
| property | 0.452 | 0.012 | 0.261 | |
| readFASTA | 0.004 | 0.000 | 0.001 | |
| readMolFromSDF | 0.140 | 0.008 | 0.044 | |
| readMolFromSmi | 0.016 | 0.000 | 0.004 | |
| readPDB | 1.400 | 0.004 | 1.374 | |
| revchars | 0 | 0 | 0 | |
| rf.cv | 1.060 | 0.024 | 1.083 | |
| rf.fs | 0.508 | 0.000 | 0.504 | |
| sdfbcl | 0.000 | 0.000 | 0.001 | |
| searchDrug | 0 | 0 | 0 | |
| segProt | 0.004 | 0.000 | 0.002 | |
| topology | 0.356 | 0.012 | 0.278 | |
| twoGOSim | 0.004 | 0.000 | 0.000 | |
| twoSeqSim | 0.600 | 0.000 | 0.574 | |