| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:17:04 -0400 (Thu, 12 Apr 2018).
| Package 134/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Min-feng Zhu
| 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 |
| Package: BioMedR |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BioMedR_1.2.0.tar.gz |
| StartedAt: 2018-04-11 21:49:21 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:52:06 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 164.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BioMedR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BioMedR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* 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 ‘/home/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 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 6.368 0.048 1.188
extrDrugMannholdLogP 5.240 0.032 2.982
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck/00check.log’
for details.
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)
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-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: 0.784 0.044 0.314
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 -- Wed Apr 11 21:51:59 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
BioMedR.Rcheck/BioMedR-Ex.timings
| name | user | system | elapsed | |
| AA2DACOR | 0.012 | 0.004 | 0.015 | |
| AA3DMoRSE | 0.004 | 0.000 | 0.001 | |
| AAACF | 0.000 | 0.000 | 0.002 | |
| AABLOSUM100 | 0.004 | 0.000 | 0.001 | |
| AABLOSUM45 | 0.000 | 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 | 0.000 | 0.000 | 0.001 | |
| AAConn | 0.004 | 0.000 | 0.001 | |
| AAConst | 0.000 | 0.000 | 0.001 | |
| AADescAll | 0.000 | 0.004 | 0.001 | |
| AAEdgeAdj | 0.000 | 0.000 | 0.001 | |
| AAEigIdx | 0.004 | 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 | 0.001 | |
| AAMOE2D | 0.000 | 0.000 | 0.001 | |
| AAMOE3D | 0.000 | 0.000 | 0.001 | |
| AAMetaInfo | 0.000 | 0.000 | 0.001 | |
| AAMolProp | 0.000 | 0.000 | 0.001 | |
| AAPAM120 | 0.004 | 0.000 | 0.001 | |
| AAPAM250 | 0.000 | 0.000 | 0.001 | |
| AAPAM30 | 0.004 | 0.000 | 0.001 | |
| AAPAM40 | 0.000 | 0.000 | 0.001 | |
| AAPAM70 | 0.004 | 0.000 | 0.001 | |
| AARDF | 0.000 | 0.000 | 0.001 | |
| AARandic | 0.000 | 0.000 | 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 | 0.004 | 0.000 | 0.001 | |
| Autocorrelation | 1.088 | 0.052 | 0.580 | |
| BMgetDNAGenBank | 0.000 | 0.000 | 0.001 | |
| BioMedR-package | 0.000 | 0.000 | 0.001 | |
| Constitutional | 0.616 | 0.028 | 0.370 | |
| NNeighbors | 0.816 | 0.004 | 0.818 | |
| OptAA3d | 0 | 0 | 0 | |
| acc | 0.012 | 0.004 | 0.014 | |
| apfp | 0.000 | 0.000 | 0.001 | |
| atomprop | 0.000 | 0.000 | 0.001 | |
| bcl | 0.000 | 0.000 | 0.001 | |
| calcDrugFPSim | 0 | 0 | 0 | |
| calcDrugMCSSim | 0.476 | 0.024 | 0.897 | |
| calcParProtGOSim | 0.000 | 0.000 | 0.001 | |
| calcParProtSeqSim | 0.452 | 0.104 | 0.618 | |
| calcTwoProtGOSim | 0.000 | 0.000 | 0.001 | |
| calcTwoProtSeqSim | 0.144 | 0.008 | 0.150 | |
| checkDNA | 0 | 0 | 0 | |
| checkProt | 0.004 | 0.000 | 0.002 | |
| clusterCMP | 1.404 | 0.040 | 1.443 | |
| clusterJP | 1.684 | 0.004 | 1.687 | |
| clusterMDS | 0.564 | 0.000 | 0.563 | |
| clusterStat | 0.280 | 0.008 | 0.284 | |
| connectivity | 2.144 | 0.112 | 0.874 | |
| convAPtoFP | 0.524 | 0.004 | 0.253 | |
| convSDFtoAP | 0.072 | 0.000 | 0.061 | |
| extrDNADAC | 0.008 | 0.000 | 0.009 | |
| extrDNADACC | 0.060 | 0.000 | 0.061 | |
| extrDNADCC | 0.080 | 0.000 | 0.082 | |
| extrDNAIncDiv | 0.076 | 0.000 | 0.076 | |
| extrDNAPseDNC | 0.012 | 0.000 | 0.008 | |
| extrDNAPseKNC | 0.004 | 0.000 | 0.006 | |
| extrDNATAC | 0.008 | 0.004 | 0.011 | |
| extrDNATACC | 0.080 | 0.004 | 0.080 | |
| extrDNATCC | 0.084 | 0.004 | 0.087 | |
| extrDNAkmer | 0.000 | 0.000 | 0.002 | |
| extrDrugAIO | 0.000 | 0.000 | 0.001 | |
| extrDrugAP | 0.204 | 0.000 | 0.204 | |
| extrDrugBCUT | 0.068 | 0.000 | 0.057 | |
| extrDrugCPSA | 0.404 | 0.012 | 0.194 | |
| extrDrugEstate | 0.388 | 0.020 | 0.286 | |
| extrDrugEstateComplete | 0.164 | 0.004 | 0.048 | |
| extrDrugExtended | 0.120 | 0.008 | 0.032 | |
| extrDrugExtendedComplete | 0.024 | 0.000 | 0.018 | |
| extrDrugGraph | 0.040 | 0.000 | 0.019 | |
| extrDrugGraphComplete | 0.016 | 0.000 | 0.015 | |
| extrDrugHybridization | 0.036 | 0.000 | 0.015 | |
| extrDrugHybridizationComplete | 0.044 | 0.004 | 0.013 | |
| extrDrugHybridizationRatio | 0.068 | 0.000 | 0.018 | |
| extrDrugIPMolecularLearning | 0.028 | 0.000 | 0.009 | |
| extrDrugKR | 6.368 | 0.048 | 1.188 | |
| extrDrugKRComplete | 1.704 | 0.008 | 0.949 | |
| extrDrugKappaShapeIndices | 0.048 | 0.008 | 0.026 | |
| extrDrugKierHallSmarts | 0.116 | 0.000 | 0.056 | |
| extrDrugMACCS | 0.608 | 0.008 | 0.125 | |
| extrDrugMACCSComplete | 0.312 | 0.004 | 0.043 | |
| extrDrugMannholdLogP | 5.240 | 0.032 | 2.982 | |
| extrDrugOBFP2 | 0.104 | 0.000 | 0.121 | |
| extrDrugOBFP3 | 0 | 0 | 0 | |
| extrDrugOBFP4 | 0.052 | 0.000 | 0.064 | |
| extrDrugPubChem | 0.968 | 0.000 | 0.206 | |
| extrDrugPubChemComplete | 0.820 | 0.004 | 0.179 | |
| extrDrugShortestPath | 0.000 | 0.000 | 0.001 | |
| extrDrugShortestPathComplete | 0.004 | 0.000 | 0.000 | |
| extrDrugStandard | 0.064 | 0.000 | 0.012 | |
| extrDrugStandardComplete | 0.072 | 0.004 | 0.017 | |
| extrDrugWHIM | 0.216 | 0.000 | 0.089 | |
| extrPCMBLOSUM | 0.112 | 0.000 | 0.057 | |
| extrPCMDescScales | 0.032 | 0.000 | 0.014 | |
| extrPCMFAScales | 0.048 | 0.004 | 0.025 | |
| extrPCMMDSScales | 0.016 | 0.000 | 0.015 | |
| extrPCMPropScales | 0.024 | 0.000 | 0.024 | |
| extrPCMScaleGap | 0.008 | 0.004 | 0.012 | |
| extrPCMScales | 0.02 | 0.00 | 0.02 | |
| extrProtAAC | 0.000 | 0.000 | 0.002 | |
| extrProtAPAAC | 1.080 | 0.008 | 1.093 | |
| extrProtCTDC | 0.004 | 0.000 | 0.004 | |
| extrProtCTDCClass | 0.004 | 0.000 | 0.004 | |
| extrProtCTDD | 0.004 | 0.000 | 0.005 | |
| extrProtCTDDClass | 0.004 | 0.000 | 0.004 | |
| extrProtCTDT | 0.004 | 0.000 | 0.006 | |
| extrProtCTDTClass | 0.000 | 0.004 | 0.006 | |
| extrProtCTriad | 0.108 | 0.008 | 0.114 | |
| extrProtCTriadClass | 0.080 | 0.000 | 0.081 | |
| extrProtDC | 0.004 | 0.000 | 0.005 | |
| extrProtFPGap | 0.024 | 0.000 | 0.025 | |
| extrProtGeary | 0.176 | 0.004 | 0.177 | |
| extrProtMoran | 0.172 | 0.004 | 0.177 | |
| extrProtMoreauBroto | 0.164 | 0.000 | 0.165 | |
| extrProtPAAC | 0.520 | 0.000 | 0.522 | |
| extrProtPSSM | 0 | 0 | 0 | |
| extrProtPSSMAcc | 0.000 | 0.000 | 0.001 | |
| extrProtPSSMFeature | 0 | 0 | 0 | |
| extrProtQSO | 1.076 | 0.000 | 1.075 | |
| extrProtSOCN | 0.792 | 0.000 | 0.792 | |
| extrProtTC | 0.024 | 0.024 | 0.048 | |
| geometric | 0.052 | 0.000 | 0.039 | |
| getCPI | 0.004 | 0.000 | 0.006 | |
| getDrug | 0 | 0 | 0 | |
| getProt | 0.000 | 0.000 | 0.001 | |
| make_kmer_index | 0.000 | 0.000 | 0.001 | |
| parGOSim | 0.000 | 0.000 | 0.001 | |
| parSeqSim | 1.540 | 0.388 | 1.253 | |
| plotStructure | 0.268 | 0.036 | 0.303 | |
| pls.cv | 0.212 | 0.008 | 0.221 | |
| property | 0.548 | 0.024 | 0.279 | |
| readFASTA | 0.008 | 0.000 | 0.002 | |
| readMolFromSDF | 0.108 | 0.000 | 0.031 | |
| readMolFromSmi | 0.008 | 0.000 | 0.005 | |
| readPDB | 1.428 | 0.004 | 1.396 | |
| revchars | 0.000 | 0.000 | 0.001 | |
| rf.cv | 0.812 | 0.004 | 0.819 | |
| rf.fs | 0.56 | 0.00 | 0.56 | |
| sdfbcl | 0.000 | 0.000 | 0.002 | |
| searchDrug | 0.004 | 0.000 | 0.001 | |
| segProt | 0.000 | 0.000 | 0.002 | |
| topology | 0.336 | 0.016 | 0.225 | |
| twoGOSim | 0.000 | 0.000 | 0.001 | |
| twoSeqSim | 0.636 | 0.004 | 0.613 | |