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BioC 3.4: CHECK report for Rcpi on zin1

This page was generated on 2016-09-21 03:38:52 -0700 (Wed, 21 Sep 2016).

Package 987/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.9.0
Nan Xiao
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rcpi
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: Rcpi
Version: 1.9.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.9.0.tar.gz
StartedAt: 2016-09-20 11:21:11 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:23:02 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 110.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Rcpi.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.9.0’
* 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’
calcDrugMCSSim: no visible global function definition for ‘as’
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:
  as capture.output cmdscale combn dist factanal na.omit prcomp predict
  read.csv sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "cmdscale", "dist", "factanal", "na.omit",
             "prcomp", "predict", "sd")
  importFrom("utils", "capture.output", "combn", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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’
 OK
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Rcpi.Rcheck/00check.log’
for details.


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:

nameusersystemelapsed
AA2DACOR0.0120.0000.013
AA3DMoRSE0.0040.0000.001
AAACF0.0000.0000.001
AABLOSUM1000.0040.0000.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0040.0000.001
AABLOSUM620.0000.0000.001
AABLOSUM800.0000.0000.002
AABurden0.0000.0000.001
AACPSA0.0000.0000.001
AAConn0.0000.0000.001
AAConst0.0000.0000.001
AADescAll0.0000.0000.001
AAEdgeAdj0.0000.0000.001
AAEigIdx0.0000.0000.001
AAFGC0.0000.0000.001
AAGETAWAY0.0000.0000.001
AAGeom0.0000.0000.001
AAInfo0.0040.0000.001
AAMOE2D0.0000.0000.002
AAMOE3D0.0040.0000.002
AAMetaInfo0.0000.0000.001
AAMolProp0.0040.0000.001
AAPAM1200.0000.0000.001
AAPAM2500.0040.0000.001
AAPAM300.0000.0000.001
AAPAM400.0040.0000.001
AAPAM700.0000.0000.001
AARDF0.0040.0000.001
AARandic0.0000.0000.001
AATopo0.0040.0000.001
AATopoChg0.0000.0000.002
AAWHIM0.0000.0000.002
AAWalk0.0000.0000.001
AAindex0.0000.0000.001
OptAA3d0.0000.0000.001
Rcpi-package0.0000.0000.001
acc0.0080.0040.011
calcDrugFPSim0.0000.0000.001
calcDrugMCSSim0.0000.0000.001
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim000
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt0.0040.0000.002
convMolFormat000
extractDrugAIO0.0000.0000.001
extractDrugALOGP0.0040.0000.001
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability0.0000.0000.001
extractDrugBCUT0.0000.0000.001
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster0.0000.0000.001
extractDrugChiPath0.0000.0000.001
extractDrugChiPathCluster0.0000.0000.001
extractDrugDescOB0.0040.0000.001
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph0.0000.0000.001
extractDrugGraphComplete0.0000.0000.001
extractDrugGravitationalIndex0.0000.0000.001
extractDrugHBondAcceptorCount0.0000.0040.001
extractDrugHBondDonorCount000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete0.0040.0000.001
extractDrugKappaShapeIndices0.0000.0000.001
extractDrugKierHallSmarts0.0000.0000.001
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP0.0000.0000.001
extractDrugMomentOfInertia0.0040.0000.001
extractDrugOBFP2000
extractDrugOBFP3000
extractDrugOBFP4000
extractDrugOBMACCS000
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex000
extractDrugPubChem000
extractDrugPubChemComplete0.0000.0000.001
extractDrugRotatableBondsCount0.0000.0000.001
extractDrugRuleOfFive0.0000.0000.001
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa0.0000.0000.001
extractDrugWHIM0.0040.0000.001
extractDrugWeight0.0000.0000.001
extractDrugWeightedPath000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM0.0120.0000.010
extractPCMDescScales0.0120.0000.011
extractPCMFAScales0.0160.0000.018
extractPCMMDSScales0.0080.0000.009
extractPCMPropScales0.0120.0040.014
extractPCMScales0.0160.0000.016
extractProtAAC0.0040.0000.002
extractProtAPAAC1.8440.0041.847
extractProtCTDC0.0040.0000.005
extractProtCTDD0.0040.0000.004
extractProtCTDT0.0080.0000.006
extractProtCTriad0.0760.0200.097
extractProtDC0.0000.0040.005
extractProtGeary0.1400.0000.142
extractProtMoran0.1400.0040.143
extractProtMoreauBroto0.140.000.14
extractProtPAAC0.6680.0000.668
extractProtPSSM000
extractProtPSSMAcc000
extractProtPSSMFeature000
extractProtQSO1.1040.0041.104
extractProtSOCN1.1160.0001.117
extractProtTC0.0360.0280.061
getCPI0.0040.0000.003
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt0.0040.0000.000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank0.0000.0000.001
getMolFromKEGG0.0000.0000.001
getMolFromPubChem0.0000.0000.001
getPDBFromRCSBPDB0.0000.0000.001
getPPI0.0040.0000.003
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0000.001
readFASTA0.0000.0000.002
readMolFromSDF0.0000.0000.001
readMolFromSmi000
readPDB1.2360.0081.245
searchDrug0.0000.0000.001
segProt0.0000.0000.002