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BioC 3.2: CHECK report for Rcpi on moscato1

This page was generated on 2016-04-23 10:20:05 -0700 (Sat, 23 Apr 2016).

Package 854/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.6.0
Nan Xiao
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rcpi
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rcpi
Version: 1.6.0
Command: rm -rf Rcpi.buildbin-libdir Rcpi.Rcheck && mkdir Rcpi.buildbin-libdir Rcpi.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rcpi.buildbin-libdir Rcpi_1.6.0.tar.gz >Rcpi.Rcheck\00install.out 2>&1 && cp Rcpi.Rcheck\00install.out Rcpi-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Rcpi.buildbin-libdir --install="check:Rcpi-install.out" --force-multiarch --no-vignettes --timings Rcpi_1.6.0.tar.gz
StartedAt: 2016-04-23 06:33:39 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:41:15 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 455.6 seconds
RetCode: 0
Status:  OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rcpi.buildbin-libdir Rcpi.Rcheck && mkdir Rcpi.buildbin-libdir Rcpi.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rcpi.buildbin-libdir Rcpi_1.6.0.tar.gz >Rcpi.Rcheck\00install.out 2>&1 && cp Rcpi.Rcheck\00install.out Rcpi-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Rcpi.buildbin-libdir --install="check:Rcpi-install.out" --force-multiarch --no-vignettes --timings Rcpi_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/Rcpi.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rcpi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rcpi' version '1.6.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [14s] OK
** running examples for arch 'x64' ... [16s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [9s]
 [9s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [9s]
 [9s] 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: OK

Rcpi.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'Rcpi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rcpi' as Rcpi_1.6.0.zip
* DONE (Rcpi)

Rcpi.Rcheck/examples_i386/Rcpi-Ex.timings:

nameusersystemelapsed
AA2DACOR0.010.000.02
AA3DMoRSE000
AAACF000
AABLOSUM1000.000.010.02
AABLOSUM45000
AABLOSUM50000
AABLOSUM620.010.000.02
AABLOSUM80000
AABurden000
AACPSA0.000.020.01
AAConn000
AAConst000
AADescAll0.000.010.02
AAEdgeAdj000
AAEigIdx000
AAFGC0.000.020.01
AAGETAWAY000
AAGeom000
AAInfo0.000.010.02
AAMOE2D000
AAMOE3D000
AAMetaInfo0.000.020.01
AAMolProp000
AAPAM120000
AAPAM2500.020.000.02
AAPAM30000
AAPAM40000
AAPAM70000
AARDF000
AARandic000
AATopo000
AATopoChg000
AAWHIM000
AAWalk000
AAindex000
OptAA3d000
Rcpi-package000
acc0.010.000.01
calcDrugFPSim000
calcDrugMCSSim000
calcParProtGOSim000
calcParProtSeqSim0.020.000.02
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt000
convMolFormat000
extractDrugAIO000
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability000
extractDrugBCUT000
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster000
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB000
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph000
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete000
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE000
extractDrugMannholdLogP000
extractDrugMomentOfInertia000
extractDrugOBFP2000
extractDrugOBFP3000
extractDrugOBFP4000
extractDrugOBMACCS000
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex000
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM0.000.020.02
extractPCMDescScales0.020.000.01
extractPCMFAScales0.030.000.03
extractPCMMDSScales0.010.000.02
extractPCMPropScales0.020.000.01
extractPCMScales0.030.000.04
extractProtAAC000
extractProtAPAAC2.780.002.77
extractProtCTDC0.010.000.02
extractProtCTDD000
extractProtCTDT0.020.000.01
extractProtCTriad0.110.010.13
extractProtDC0.010.000.01
extractProtGeary0.170.000.18
extractProtMoran0.180.000.17
extractProtMoreauBroto0.170.000.17
extractProtPAAC0.760.000.76
extractProtPSSM000
extractProtPSSMAcc000
extractProtPSSMFeature000
extractProtQSO1.270.001.27
extractProtSOCN1.260.001.26
extractProtTC0.050.030.08
getCPI000
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL0.010.000.01
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI000
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA000
readMolFromSDF000
readMolFromSmi000
readPDB2.230.002.23
searchDrug000
segProt000

Rcpi.Rcheck/examples_x64/Rcpi-Ex.timings:

nameusersystemelapsed
AA2DACOR0.010.000.25
AA3DMoRSE000
AAACF000
AABLOSUM100000
AABLOSUM450.000.000.05
AABLOSUM50000
AABLOSUM620.010.000.01
AABLOSUM80000
AABurden000
AACPSA000
AAConn0.020.000.02
AAConst000
AADescAll000
AAEdgeAdj0.010.000.02
AAEigIdx000
AAFGC000
AAGETAWAY000
AAGeom000
AAInfo000
AAMOE2D000
AAMOE3D0.000.010.02
AAMetaInfo000
AAMolProp000
AAPAM120000
AAPAM250000
AAPAM30000
AAPAM40000
AAPAM700.000.020.02
AARDF000
AARandic000
AATopo0.020.000.01
AATopoChg000
AAWHIM000
AAWalk000
AAindex0.020.000.02
OptAA3d000
Rcpi-package000
acc0.010.000.01
calcDrugFPSim000
calcDrugMCSSim000
calcParProtGOSim000
calcParProtSeqSim000
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt0.020.000.02
convMolFormat000
extractDrugAIO000
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass0.010.000.02
extractDrugAutocorrelationPolarizability000
extractDrugBCUT000
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster000
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB000
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity0.010.000.02
extractDrugGraph000
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete0.020.000.01
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE000
extractDrugMannholdLogP000
extractDrugMomentOfInertia0.010.000.02
extractDrugOBFP2000
extractDrugOBFP3000
extractDrugOBFP4000
extractDrugOBMACCS000
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex000
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM000
extractPCMDescScales000
extractPCMFAScales0.010.010.03
extractPCMMDSScales0.020.000.01
extractPCMPropScales0.010.000.02
extractPCMScales0.030.000.03
extractProtAAC000
extractProtAPAAC2.310.002.31
extractProtCTDC0.020.000.01
extractProtCTDD000
extractProtCTDT0.010.000.02
extractProtCTriad0.270.020.28
extractProtDC0.000.010.02
extractProtGeary0.300.000.29
extractProtMoran0.210.000.22
extractProtMoreauBroto0.190.000.19
extractProtPAAC0.920.000.92
extractProtPSSM000
extractProtPSSMAcc000
extractProtPSSMFeature000
extractProtQSO1.440.001.43
extractProtSOCN1.460.001.47
extractProtTC0.050.020.06
getCPI000
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI000
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA000
readMolFromSDF000
readMolFromSmi000
readPDB1.640.001.64
searchDrug000
segProt000