| Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:30:57 -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: rm -rf BioMedR.buildbin-libdir BioMedR.Rcheck && mkdir BioMedR.buildbin-libdir BioMedR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioMedR.buildbin-libdir BioMedR_1.2.0.tar.gz >BioMedR.Rcheck\00install.out 2>&1 && cp BioMedR.Rcheck\00install.out BioMedR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BioMedR.buildbin-libdir --install="check:BioMedR-install.out" --force-multiarch --no-vignettes --timings BioMedR_1.2.0.tar.gz |
| StartedAt: 2018-04-11 22:31:14 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:38:32 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 437.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BioMedR.Rcheck |
| Warnings: NA |
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### Running command:
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### rm -rf BioMedR.buildbin-libdir BioMedR.Rcheck && mkdir BioMedR.buildbin-libdir BioMedR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioMedR.buildbin-libdir BioMedR_1.2.0.tar.gz >BioMedR.Rcheck\00install.out 2>&1 && cp BioMedR.Rcheck\00install.out BioMedR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BioMedR.buildbin-libdir --install="check:BioMedR-install.out" --force-multiarch --no-vignettes --timings BioMedR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'BioMedR' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'BioMedR' is deprecated and will be removed from Bioconductor
See 'C:/Users/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
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Autocorrelation 0.64 0.06 26.27
calcDrugMCSSim 0.55 0.01 7.54
parSeqSim 0.40 0.03 13.14
calcParProtSeqSim 0.24 0.00 7.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
extrDrugKR 6.61 0.13 1.08
parSeqSim 0.67 0.02 13.61
calcParProtSeqSim 0.19 0.02 6.84
extrDrugOBFP2 0.11 0.00 5.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
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
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
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: 2 ERRORs, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioMedR.Rcheck/00check.log'
for details.
BioMedR.Rcheck/00install.out
install for i386
* installing *source* package 'BioMedR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'BioMedR'
finding HTML links ... done
AA2DACOR html
AA3DMoRSE html
AAACF html
AABLOSUM100 html
AABLOSUM45 html
AABLOSUM50 html
AABLOSUM62 html
AABLOSUM80 html
AABurden html
AACPSA html
AAConn html
AAConst html
AADescAll html
AAEdgeAdj html
AAEigIdx html
AAFGC html
AAGETAWAY html
AAGeom html
AAInfo html
AAMOE2D html
AAMOE3D html
AAMetaInfo html
AAMolProp html
AAPAM120 html
AAPAM250 html
AAPAM30 html
AAPAM40 html
AAPAM70 html
AARDF html
AARandic html
AATopo html
AATopoChg html
AAWHIM html
AAWalk html
AAindex html
Autocorrelation html
BMgetDNAGenBank html
BioMedR-package html
Constitutional html
NNeighbors html
finding level-2 HTML links ... done
OptAA3d html
acc html
apfp html
atomprop html
bcl html
calcDrugFPSim html
calcDrugMCSSim html
calcParProtGOSim html
calcParProtSeqSim html
calcTwoProtGOSim html
calcTwoProtSeqSim html
checkDNA html
checkProt html
clusterCMP html
clusterJP html
clusterMDS html
clusterStat html
connectivity html
convAPtoFP html
convSDFtoAP html
diversity html
extrDNADAC html
extrDNADACC html
extrDNADCC html
extrDNAIncDiv html
extrDNAPseDNC html
extrDNAPseKNC html
extrDNATAC html
extrDNATACC html
extrDNATCC html
extrDNAkmer html
extrDrugAIO html
extrDrugAP html
extrDrugBCUT html
extrDrugCPSA html
extrDrugEstate html
extrDrugEstateComplete html
extrDrugExtended html
extrDrugExtendedComplete html
extrDrugGraph html
extrDrugGraphComplete html
extrDrugHybridization html
extrDrugHybridizationComplete html
extrDrugHybridizationRatio html
extrDrugIPMolecularLearning html
extrDrugKR html
extrDrugKRComplete html
extrDrugKappaShapeIndices html
extrDrugKierHallSmarts html
extrDrugMACCS html
extrDrugMACCSComplete html
extrDrugMannholdLogP html
extrDrugOBFP2 html
extrDrugOBFP3 html
extrDrugOBFP4 html
extrDrugPubChem html
extrDrugPubChemComplete html
extrDrugShortestPath html
extrDrugShortestPathComplete html
extrDrugStandard html
extrDrugStandardComplete html
extrDrugWHIM html
extrPCMBLOSUM html
extrPCMDescScales html
extrPCMFAScales html
extrPCMMDSScales html
extrPCMPropScales html
extrPCMScaleGap html
extrPCMScales html
extrProtAAC html
extrProtAPAAC html
extrProtCTDC html
extrProtCTDCClass html
extrProtCTDD html
extrProtCTDDClass html
extrProtCTDT html
extrProtCTDTClass html
extrProtCTriad html
extrProtCTriadClass html
extrProtDC html
extrProtFPGap html
extrProtGeary html
extrProtMoran html
extrProtMoreauBroto html
extrProtPAAC html
extrProtPSSM html
extrProtPSSMAcc html
extrProtPSSMFeature html
extrProtQSO html
extrProtSOCN html
extrProtTC html
geometric html
getCPI html
getDrug html
getProt html
id_x_s html
make_kmer_index html
parGOSim html
parSeqSim html
plotStructure html
pls.cv html
property html
readFASTA html
readMolFromSDF html
readMolFromSmi html
readPDB html
revchars html
rf.cv html
rf.fs html
sdfbcl html
searchDrug html
segProt html
topology html
twoGOSim html
twoSeqSim html
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'BioMedR' ...
** testing if installed package can be loaded
Warning: Package 'BioMedR' is deprecated and will be removed from Bioconductor
version 3.7
* MD5 sums
packaged installation of 'BioMedR' as BioMedR_1.2.0.zip
* DONE (BioMedR)
In R CMD INSTALL
In R CMD INSTALL
|
BioMedR.Rcheck/tests_i386/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: i386-w64-mingw32/i386 (32-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: 0.36 0 0.28
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 22:38:15 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/tests_x64/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-w64-mingw32/x64 (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: 0.52 0.03 0.26
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 22:38:22 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
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BioMedR.Rcheck/examples_i386/BioMedR-Ex.timings
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BioMedR.Rcheck/examples_x64/BioMedR-Ex.timings
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