| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O [P] Q R S T U V W X Y Z |
This page was generated on 2017-10-18 14:23:04 -0400 (Wed, 18 Oct 2017).
| Package 1026/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PSICQUIC 1.14.0 Paul Shannon
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: PSICQUIC |
| Version: 1.14.0 |
| Command: rm -rf PSICQUIC.buildbin-libdir PSICQUIC.Rcheck && mkdir PSICQUIC.buildbin-libdir PSICQUIC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PSICQUIC.buildbin-libdir PSICQUIC_1.14.0.tar.gz >PSICQUIC.Rcheck\00install.out 2>&1 && cp PSICQUIC.Rcheck\00install.out PSICQUIC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PSICQUIC.buildbin-libdir --install="check:PSICQUIC-install.out" --force-multiarch --no-vignettes --timings PSICQUIC_1.14.0.tar.gz |
| StartedAt: 2017-10-18 02:12:02 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 02:17:05 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 302.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PSICQUIC.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf PSICQUIC.buildbin-libdir PSICQUIC.Rcheck && mkdir PSICQUIC.buildbin-libdir PSICQUIC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PSICQUIC.buildbin-libdir PSICQUIC_1.14.0.tar.gz >PSICQUIC.Rcheck\00install.out 2>&1 && cp PSICQUIC.Rcheck\00install.out PSICQUIC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PSICQUIC.buildbin-libdir --install="check:PSICQUIC-install.out" --force-multiarch --no-vignettes --timings PSICQUIC_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/PSICQUIC.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PSICQUIC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PSICQUIC' version '1.14.0'
* 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 'PSICQUIC' 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
'httr' 'plyr'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.loadRegistry: no visible global function definition for 'DataFrame'
.loadRegistry : <anonymous>: no visible global function definition for
'str'
.retrieveData: no visible global function definition for 'read.table'
.retrieveData : <anonymous>: no visible global function definition for
'str'
.translate.uniprotkb: no visible binding for global variable 'id'
detectionMethods: no visible global function definition for 'browseURL'
interactionTypes: no visible global function definition for 'browseURL'
speciesIDs: no visible global function definition for 'browseURL'
Undefined global functions or variables:
DataFrame browseURL id read.table str
Consider adding
importFrom("utils", "browseURL", "read.table", "str")
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 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
PSICQUIC-class 2.36 0.05 22.52
IDMapper-class 0.89 0.12 5.08
interactions 0.46 0.03 7.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PSICQUIC-class 2.34 0.08 21.84
IDMapper-class 1.14 0.06 5.61
interactions 0.87 0.03 9.36
* 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˜1.5-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 :
PSICQUIC RUnit Tests - 31 test functions, 0 errors, 1 failure
FAILURE in test_.loadRegistry: Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (22, 24) differ
Test files with failing tests
test_PSICQUIC.R
test_.loadRegistry
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
PSICQUIC RUnit Tests - 31 test functions, 0 errors, 1 failure
FAILURE in test_.loadRegistry: Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (22, 24) differ
Test files with failing tests
test_PSICQUIC.R
test_.loadRegistry
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/PSICQUIC.Rcheck/00check.log'
for details.
runTests.Rout.fail:
R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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("PSICQUIC")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:httr':
content
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.categorize"
[1] "--- test_.translate.ensemblGene"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.translate.ensemblProt"
[1] "--- test_.translate.locuslink"
[1] "--- test_.translate.refseq"
[1] "--- test_.translate.string"
[1] "--- test_.translate.uniprotkb"
[1] "--- test_translateAll"
[1] "--- test_addGeneInfo"
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_addStandardNames"
[1] "--- test_ctor"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_preserveKnownGeneIdentifiers"
Loading required package: bitops
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.loadRegistry"
Timing stopped at: 0.12 0 0.48
Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (22, 24) differ
[1] "--- test_.restrictBySpecies"
[1] "--- test_.retrieveData"
List of 2
$ message: chr "Could not resolve host: intentionally.bogus"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_RESOLVE_HOST" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://intentionally.bogus"
[1] "--- test_ctor"
[1] test providers: MINT,Reactome,IntAct
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: I2D-IMEx,InnateDB-IMEx,MPIDB
[1] "--- test_initialConditions"
[1] "--- test_interactions"
[1] "--- test_interactionsFourGenes"
[1] "expected psicquic sources not available, test_interactionFourGenes"
[1] "--- test_interactionsTwoGenes"
[1] "--- test_rawQuery"
[1] test providers: HPIDb,MatrixDB,EBI-GOA-nonIntAct
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: BAR,ChEMBL,BioGrid
[1] "--- test_retrieveByOmimId"
[1] test providers: BioGrid,EBI-GOA-miRNA,InnateDB-IMEx
[1] "--- test_retrieveByPubmedID"
[1] test providers: ZINC,MBInfo,BAR
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: MINT,MBInfo,VirHostNet
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: Reactome-FIs,MBInfo,MatrixDB
[1] "--- test_smallMoleculeWithoutSpeciesDesignation"
[1] retrieving from ChEMBL
[1] PSICQUIC:::.runQuery: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] final query.url: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] --- http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib result: 141 15
RUNIT TEST PROTOCOL -- Wed Oct 18 02:16:00 2017
***********************************************
Number of test functions: 31
Number of errors: 0
Number of failures: 1
1 Test Suite :
PSICQUIC RUnit Tests - 31 test functions, 0 errors, 1 failure
FAILURE in test_.loadRegistry: Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (22, 24) differ
Test files with failing tests
test_PSICQUIC.R
test_.loadRegistry
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
runTests.Rout.fail:
R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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("PSICQUIC")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:httr':
content
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.categorize"
[1] "--- test_.translate.ensemblGene"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.translate.ensemblProt"
[1] "--- test_.translate.locuslink"
[1] "--- test_.translate.refseq"
[1] "--- test_.translate.string"
[1] "--- test_.translate.uniprotkb"
[1] "--- test_translateAll"
[1] "--- test_addGeneInfo"
[1] "--- test_addGeneInfoMinimalTable"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_addStandardNames"
[1] "--- test_ctor"
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_preserveKnownGeneIdentifiers"
Loading required package: bitops
[1] "--- test_.enumerateSearchPairs"
[1] "--- test_.loadRegistry"
Timing stopped at: 0.14 0 0.67
Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (22, 24) differ
[1] "--- test_.restrictBySpecies"
[1] "--- test_.retrieveData"
List of 2
$ message: chr "Could not resolve host: intentionally.bogus"
$ call : language function (type, msg, asError = TRUE) { ...
- attr(*, "class")= chr [1:4] "COULDNT_RESOLVE_HOST" "GenericCurlError" "error" "condition"
character(0)
[1] "failed url: http://intentionally.bogus"
[1] "--- test_ctor"
[1] test providers: EBI-GOA-miRNA,MPIDB,HPIDb
[1] "--- test_handleEmbeddedSingleQuote"
[1] test providers: Reactome,ChEMBL,EBI-GOA-miRNA
[1] "--- test_initialConditions"
[1] "--- test_interactions"
[1] "--- test_interactionsFourGenes"
[1] "expected psicquic sources not available, test_interactionFourGenes"
[1] "--- test_interactionsTwoGenes"
[1] "--- test_rawQuery"
[1] test providers: I2D,EBI-GOA-miRNA,InnateDB-IMEx
[1] "expected psicquic sources not available, skipping test_.retrieveData"
[1] "expected psicquic sources not available, test_retrieveByDetectionMethod"
[1] "--- test_retrieveByInteractionType"
[1] test providers: I2D,mentha,MBInfo
[1] "--- test_retrieveByOmimId"
[1] test providers: ChEMBL,mentha,MBInfo
[1] "--- test_retrieveByPubmedID"
[1] test providers: I2D,UniProt,InnateDB-All
[1] "--- test_retrieveByPubmedIdOnly"
[1] test providers: InnateDB-IMEx,HPIDb,InnateDB
[1] IntAct not available, skipping test_retrieveByPubmedIdOnly
[1] "--- test_retrieveBySpeciesId"
[1] test providers: I2D-IMEx,UniProt,EBI-GOA-miRNA
[1] "--- test_smallMoleculeWithoutSpeciesDesignation"
[1] retrieving from ChEMBL
[1] PSICQUIC:::.runQuery: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] final query.url: http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib
[1] --- http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/identifier:imatinib result: 141 15
RUNIT TEST PROTOCOL -- Wed Oct 18 02:16:53 2017
***********************************************
Number of test functions: 31
Number of errors: 0
Number of failures: 1
1 Test Suite :
PSICQUIC RUnit Tests - 31 test functions, 0 errors, 1 failure
FAILURE in test_.loadRegistry: Error in checkEquals(grep("^http://", tbl$url), 1:nrow(tbl)) :
Numeric: lengths (22, 24) differ
Test files with failing tests
test_PSICQUIC.R
test_.loadRegistry
Error in BiocGenerics:::testPackage("PSICQUIC") :
unit tests failed for package PSICQUIC
Execution halted
PSICQUIC.Rcheck/00install.out:
install for i386 * installing *source* package 'PSICQUIC' ... ** R ** 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 'PSICQUIC' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'PSICQUIC' as PSICQUIC_1.14.0.zip * DONE (PSICQUIC)
PSICQUIC.Rcheck/examples_i386/PSICQUIC-Ex.timings:
| name | user | system | elapsed | |
| IDMapper-class | 0.89 | 0.12 | 5.08 | |
| PSICQUIC-class | 2.36 | 0.05 | 22.52 | |
| interactions | 0.46 | 0.03 | 7.57 | |
| providers | 0.05 | 0.00 | 0.75 | |
| rawQuery | 0.11 | 0.00 | 1.03 | |
| webBrowser-functions | 0 | 0 | 0 | |
PSICQUIC.Rcheck/examples_x64/PSICQUIC-Ex.timings:
| name | user | system | elapsed | |
| IDMapper-class | 1.14 | 0.06 | 5.61 | |
| PSICQUIC-class | 2.34 | 0.08 | 21.84 | |
| interactions | 0.87 | 0.03 | 9.36 | |
| providers | 0.08 | 0.00 | 0.77 | |
| rawQuery | 0.03 | 0.00 | 1.05 | |
| webBrowser-functions | 0 | 0 | 0 | |