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This page was generated on 2016-06-24 11:50:17 -0700 (Fri, 24 Jun 2016).
| Package 944/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| Rcpi 1.8.0 Nan Xiao
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | ERROR | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: Rcpi |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.8.0.tar.gz |
| StartedAt: 2016-06-24 05:51:40 -0700 (Fri, 24 Jun 2016) |
| EndedAt: 2016-06-24 05:54:24 -0700 (Fri, 24 Jun 2016) |
| EllapsedTime: 163.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Rcpi.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rcpi.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.8.0’
* 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 ‘Rcpi’ 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 ... NOTE
acc: no visible global function definition for ‘combn’
calcParProtGOSim: no visible global function definition for ‘combn’
calcParProtSeqSim: no visible global function definition for ‘combn’
extractPCMFAScales: no visible global function definition for
‘factanal’
extractPCMMDSScales: no visible global function definition for ‘dist’
extractPCMMDSScales: no visible global function definition for
‘cmdscale’
extractPCMPropScales: no visible global function definition for
‘na.omit’
extractPCMScales: no visible global function definition for ‘prcomp’
extractPCMScales: no visible global function definition for ‘predict’
extractProtAPAAC: no visible global function definition for ‘read.csv’
extractProtGeary: no visible global function definition for ‘read.csv’
extractProtGeary: no visible binding for global variable ‘sd’
extractProtMoran: no visible global function definition for ‘read.csv’
extractProtMoran: no visible binding for global variable ‘sd’
extractProtMoreauBroto: no visible global function definition for
‘read.csv’
extractProtMoreauBroto: no visible binding for global variable ‘sd’
extractProtPAAC: no visible global function definition for ‘read.csv’
extractProtPSSMAcc : accpssm: no visible global function definition for
‘combn’
extractProtQSO: no visible global function definition for ‘read.csv’
extractProtSOCN: no visible global function definition for ‘read.csv’
getDrug: no visible global function definition for ‘capture.output’
getProt: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
capture.output cmdscale combn dist factanal na.omit prcomp predict
read.csv sd
Consider adding
importFrom("stats", "cmdscale", "dist", "factanal", "na.omit",
"prcomp", "predict", "sd")
importFrom("utils", "capture.output", "combn", "read.csv")
to your NAMESPACE file.
* 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
* 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:
Rcpi RUnit Tests - 7 test functions, 1 error, 0 failures
ERROR in test_extractDrugALOGP: Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
RcallMethod: cannot determine object class
Test files with failing tests
test_extractDrugALOGP.R
test_extractDrugALOGP
Error in BiocGenerics:::testPackage("Rcpi") :
unit tests failed for package Rcpi
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 NOTE
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/Rcpi.Rcheck/00check.log’
for details.
runTests.Rout.fail:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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('Rcpi')
Timing stopped at: 0.096 0.017 0.313
Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
RcallMethod: cannot determine object class
RUNIT TEST PROTOCOL -- Fri Jun 24 05:54:18 2016
***********************************************
Number of test functions: 7
Number of errors: 1
Number of failures: 0
1 Test Suite :
Rcpi RUnit Tests - 7 test functions, 1 error, 0 failures
ERROR in test_extractDrugALOGP: Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
RcallMethod: cannot determine object class
Test files with failing tests
test_extractDrugALOGP.R
test_extractDrugALOGP
Error in BiocGenerics:::testPackage("Rcpi") :
unit tests failed for package Rcpi
Execution halted
Rcpi.Rcheck/00install.out:
* installing *source* package ‘Rcpi’ ... ** 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 (Rcpi)
Rcpi.Rcheck/Rcpi-Ex.timings:
| name | user | system | elapsed | |
| AA2DACOR | 0.019 | 0.003 | 0.022 | |
| AA3DMoRSE | 0.001 | 0.001 | 0.002 | |
| AAACF | 0.001 | 0.001 | 0.002 | |
| AABLOSUM100 | 0.002 | 0.001 | 0.002 | |
| AABLOSUM45 | 0.002 | 0.001 | 0.002 | |
| AABLOSUM50 | 0.002 | 0.000 | 0.002 | |
| AABLOSUM62 | 0.002 | 0.000 | 0.002 | |
| AABLOSUM80 | 0.002 | 0.000 | 0.002 | |
| AABurden | 0.001 | 0.001 | 0.002 | |
| AACPSA | 0.001 | 0.000 | 0.001 | |
| AAConn | 0.001 | 0.001 | 0.002 | |
| AAConst | 0.002 | 0.001 | 0.002 | |
| AADescAll | 0.002 | 0.000 | 0.002 | |
| AAEdgeAdj | 0.002 | 0.000 | 0.002 | |
| AAEigIdx | 0.002 | 0.001 | 0.003 | |
| AAFGC | 0.002 | 0.001 | 0.003 | |
| AAGETAWAY | 0.002 | 0.000 | 0.003 | |
| AAGeom | 0.002 | 0.001 | 0.002 | |
| AAInfo | 0.002 | 0.001 | 0.003 | |
| AAMOE2D | 0.002 | 0.001 | 0.002 | |
| AAMOE3D | 0.001 | 0.000 | 0.002 | |
| AAMetaInfo | 0.001 | 0.000 | 0.001 | |
| AAMolProp | 0.002 | 0.001 | 0.003 | |
| AAPAM120 | 0.002 | 0.001 | 0.002 | |
| AAPAM250 | 0.002 | 0.001 | 0.002 | |
| AAPAM30 | 0.002 | 0.000 | 0.002 | |
| AAPAM40 | 0.002 | 0.000 | 0.002 | |
| AAPAM70 | 0.002 | 0.001 | 0.003 | |
| AARDF | 0.002 | 0.001 | 0.002 | |
| AARandic | 0.002 | 0.001 | 0.002 | |
| AATopo | 0.002 | 0.001 | 0.002 | |
| AATopoChg | 0.002 | 0.000 | 0.003 | |
| AAWHIM | 0.001 | 0.000 | 0.002 | |
| AAWalk | 0.001 | 0.001 | 0.002 | |
| AAindex | 0.001 | 0.000 | 0.002 | |
| OptAA3d | 0.001 | 0.000 | 0.000 | |
| Rcpi-package | 0.001 | 0.000 | 0.000 | |
| acc | 0.010 | 0.003 | 0.013 | |
| calcDrugFPSim | 0 | 0 | 0 | |
| calcDrugMCSSim | 0 | 0 | 0 | |
| calcParProtGOSim | 0 | 0 | 0 | |
| calcParProtSeqSim | 0 | 0 | 0 | |
| calcTwoProtGOSim | 0.000 | 0.000 | 0.001 | |
| calcTwoProtSeqSim | 0.000 | 0.000 | 0.001 | |
| checkProt | 0.002 | 0.000 | 0.002 | |
| convMolFormat | 0 | 0 | 0 | |
| extractDrugAIO | 0 | 0 | 0 | |
| extractDrugALOGP | 0 | 0 | 0 | |
| extractDrugAminoAcidCount | 0.000 | 0.000 | 0.001 | |
| extractDrugApol | 0.000 | 0.000 | 0.001 | |
| extractDrugAromaticAtomsCount | 0 | 0 | 0 | |
| extractDrugAromaticBondsCount | 0 | 0 | 0 | |
| extractDrugAtomCount | 0 | 0 | 0 | |
| extractDrugAutocorrelationCharge | 0 | 0 | 0 | |
| extractDrugAutocorrelationMass | 0 | 0 | 0 | |
| extractDrugAutocorrelationPolarizability | 0 | 0 | 0 | |
| extractDrugBCUT | 0.000 | 0.000 | 0.001 | |
| extractDrugBPol | 0.000 | 0.000 | 0.001 | |
| extractDrugBondCount | 0 | 0 | 0 | |
| extractDrugCPSA | 0 | 0 | 0 | |
| extractDrugCarbonTypes | 0 | 0 | 0 | |
| extractDrugChiChain | 0 | 0 | 0 | |
| extractDrugChiCluster | 0.000 | 0.000 | 0.001 | |
| extractDrugChiPath | 0.000 | 0.000 | 0.001 | |
| extractDrugChiPathCluster | 0.001 | 0.000 | 0.001 | |
| extractDrugDescOB | 0.000 | 0.000 | 0.001 | |
| extractDrugECI | 0.000 | 0.001 | 0.001 | |
| extractDrugEstate | 0.001 | 0.000 | 0.001 | |
| extractDrugEstateComplete | 0.001 | 0.000 | 0.000 | |
| extractDrugExtended | 0 | 0 | 0 | |
| extractDrugExtendedComplete | 0 | 0 | 0 | |
| extractDrugFMF | 0.001 | 0.000 | 0.000 | |
| extractDrugFragmentComplexity | 0 | 0 | 0 | |
| extractDrugGraph | 0 | 0 | 0 | |
| extractDrugGraphComplete | 0.001 | 0.000 | 0.000 | |
| extractDrugGravitationalIndex | 0.001 | 0.000 | 0.000 | |
| extractDrugHBondAcceptorCount | 0 | 0 | 0 | |
| extractDrugHBondDonorCount | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridization | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridizationComplete | 0.000 | 0.000 | 0.001 | |
| extractDrugHybridizationRatio | 0.000 | 0.000 | 0.001 | |
| extractDrugIPMolecularLearning | 0 | 0 | 0 | |
| extractDrugKR | 0.001 | 0.000 | 0.000 | |
| extractDrugKRComplete | 0.000 | 0.000 | 0.001 | |
| extractDrugKappaShapeIndices | 0.000 | 0.000 | 0.001 | |
| extractDrugKierHallSmarts | 0.001 | 0.000 | 0.001 | |
| extractDrugLargestChain | 0.000 | 0.000 | 0.001 | |
| extractDrugLargestPiSystem | 0.000 | 0.000 | 0.001 | |
| extractDrugLengthOverBreadth | 0.001 | 0.000 | 0.001 | |
| extractDrugLongestAliphaticChain | 0.001 | 0.000 | 0.001 | |
| extractDrugMACCS | 0.000 | 0.000 | 0.001 | |
| extractDrugMACCSComplete | 0.000 | 0.000 | 0.001 | |
| extractDrugMDE | 0.001 | 0.000 | 0.001 | |
| extractDrugMannholdLogP | 0.001 | 0.000 | 0.001 | |
| extractDrugMomentOfInertia | 0.000 | 0.000 | 0.001 | |
| extractDrugOBFP2 | 0.000 | 0.000 | 0.001 | |
| extractDrugOBFP3 | 0 | 0 | 0 | |
| extractDrugOBFP4 | 0 | 0 | 0 | |
| extractDrugOBMACCS | 0.001 | 0.000 | 0.001 | |
| extractDrugPetitjeanNumber | 0.001 | 0.001 | 0.001 | |
| extractDrugPetitjeanShapeIndex | 0.001 | 0.000 | 0.000 | |
| extractDrugPubChem | 0.001 | 0.000 | 0.000 | |
| extractDrugPubChemComplete | 0.001 | 0.000 | 0.000 | |
| extractDrugRotatableBondsCount | 0.001 | 0.000 | 0.000 | |
| extractDrugRuleOfFive | 0.001 | 0.000 | 0.001 | |
| extractDrugShortestPath | 0.001 | 0.000 | 0.001 | |
| extractDrugShortestPathComplete | 0.001 | 0.000 | 0.000 | |
| extractDrugStandard | 0.001 | 0.000 | 0.000 | |
| extractDrugStandardComplete | 0.001 | 0.000 | 0.000 | |
| extractDrugTPSA | 0 | 0 | 0 | |
| extractDrugVABC | 0 | 0 | 0 | |
| extractDrugVAdjMa | 0.001 | 0.000 | 0.000 | |
| extractDrugWHIM | 0.001 | 0.000 | 0.000 | |
| extractDrugWeight | 0 | 0 | 0 | |
| extractDrugWeightedPath | 0.001 | 0.000 | 0.000 | |
| extractDrugWienerNumbers | 0.001 | 0.000 | 0.000 | |
| extractDrugXLogP | 0.001 | 0.000 | 0.000 | |
| extractDrugZagrebIndex | 0 | 0 | 0 | |
| extractPCMBLOSUM | 0.014 | 0.002 | 0.014 | |
| extractPCMDescScales | 0.010 | 0.000 | 0.009 | |
| extractPCMFAScales | 0.023 | 0.002 | 0.025 | |
| extractPCMMDSScales | 0.019 | 0.002 | 0.020 | |
| extractPCMPropScales | 0.014 | 0.001 | 0.015 | |
| extractPCMScales | 0.017 | 0.001 | 0.017 | |
| extractProtAAC | 0.002 | 0.000 | 0.002 | |
| extractProtAPAAC | 2.220 | 0.028 | 2.248 | |
| extractProtCTDC | 0.004 | 0.001 | 0.004 | |
| extractProtCTDD | 0.006 | 0.001 | 0.007 | |
| extractProtCTDT | 0.005 | 0.000 | 0.006 | |
| extractProtCTriad | 0.085 | 0.002 | 0.087 | |
| extractProtDC | 0.003 | 0.002 | 0.005 | |
| extractProtGeary | 0.196 | 0.003 | 0.198 | |
| extractProtMoran | 0.135 | 0.002 | 0.138 | |
| extractProtMoreauBroto | 0.143 | 0.003 | 0.146 | |
| extractProtPAAC | 0.747 | 0.002 | 0.749 | |
| extractProtPSSM | 0.001 | 0.000 | 0.001 | |
| extractProtPSSMAcc | 0.000 | 0.000 | 0.001 | |
| extractProtPSSMFeature | 0.000 | 0.000 | 0.001 | |
| extractProtQSO | 1.516 | 0.008 | 1.518 | |
| extractProtSOCN | 1.512 | 0.007 | 1.518 | |
| extractProtTC | 0.053 | 0.043 | 0.096 | |
| getCPI | 0.003 | 0.000 | 0.003 | |
| getDrug | 0.001 | 0.000 | 0.001 | |
| getFASTAFromKEGG | 0.000 | 0.000 | 0.001 | |
| getFASTAFromUniProt | 0.001 | 0.000 | 0.001 | |
| getMolFromCAS | 0.001 | 0.000 | 0.001 | |
| getMolFromChEMBL | 0 | 0 | 0 | |
| getMolFromDrugBank | 0 | 0 | 0 | |
| getMolFromKEGG | 0 | 0 | 0 | |
| getMolFromPubChem | 0 | 0 | 0 | |
| getPDBFromRCSBPDB | 0.001 | 0.000 | 0.000 | |
| getPPI | 0.004 | 0.001 | 0.005 | |
| getProt | 0.000 | 0.000 | 0.001 | |
| getSeqFromKEGG | 0.001 | 0.000 | 0.000 | |
| getSeqFromRCSBPDB | 0.001 | 0.000 | 0.000 | |
| getSeqFromUniProt | 0.001 | 0.000 | 0.000 | |
| getSmiFromChEMBL | 0 | 0 | 0 | |
| getSmiFromDrugBank | 0 | 0 | 0 | |
| getSmiFromKEGG | 0.001 | 0.000 | 0.001 | |
| getSmiFromPubChem | 0.000 | 0.000 | 0.001 | |
| readFASTA | 0.001 | 0.000 | 0.002 | |
| readMolFromSDF | 0 | 0 | 0 | |
| readMolFromSmi | 0.000 | 0.000 | 0.001 | |
| readPDB | 1.220 | 0.014 | 1.234 | |
| searchDrug | 0 | 0 | 0 | |
| segProt | 0.002 | 0.001 | 0.003 | |