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This page was generated on 2015-10-27 12:15:06 -0400 (Tue, 27 Oct 2015).
| Package 735/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| OrganismDbi 1.13.0 Biocore Data Team
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK |
| Package: OrganismDbi |
| Version: 1.13.0 |
| Command: rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.13.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.13.0.tar.gz |
| StartedAt: 2015-10-27 04:47:01 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 05:02:39 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 937.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OrganismDbi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.13.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/OrganismDbi.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OrganismDbi/DESCRIPTION' ... OK
* this is package 'OrganismDbi' version '1.13.0'
* 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 'OrganismDbi' 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 ... WARNING
'library' or 'require' call not declared from: 'AnnotationHub'
'library' or 'require' call to 'GenomicFeatures' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' call to 'AnnotationHub' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: 'GenomicFeatures:::.set.group.names'
Unexported objects imported by ':::' calls:
'AnnotationDbi:::.chooseCentralOrgPkgSymbol'
'AnnotationDbi:::.mapIds' 'AnnotationDbi:::.resort'
'AnnotationDbi:::.testForValidKeytype'
'AnnotationDbi:::.testSelectArgs' 'BiocGenerics:::testPackage'
'GenomicFeatures:::.makePackageName'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.biocAnnPackages' '.extractPkgsAndCols' '.gentlyExtractDbFiles'
'.lookupDbNameFromKeytype' '.mungeGraphData' '.taxIdToOrgDb'
'.taxIdToOrgDbName' '.testGraphData' '.testKeys' 'OrganismDb'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.selectByRanges: no visible global function definition for
'findOverlaps'
.selectByRanges: no visible global function definition for 'queryHits'
.selectByRanges: no visible global function definition for
'subjectHits'
.taxIdToOrgDb: no visible global function definition for
'AnnotationHub'
.taxIdToOrgDbName: no visible global function definition for
'AnnotationHub'
available.GTFsForTxDbs: no visible global function definition for
'AnnotationHub'
makeHubGTFIntoTxDb: no visible global function definition for
'makeTxDbFromGRanges'
makeOrganismDbFromBiomart: no visible binding for global variable
'DEFAULT_CIRC_SEQS'
makeOrganismDbFromBiomart: no visible global function definition for
'makeTxDbFromBiomart'
makeOrganismDbFromTxDb: no visible global function definition for
'isSingleStringOrNA'
makeOrganismDbFromUCSC: no visible binding for global variable
'DEFAULT_CIRC_SEQS'
makeOrganismDbFromUCSC: no visible global function definition for
'makeTxDbFromUCSC'
makeOuterMcolFromInnerMcol: no visible global function definition for
'elementLengths'
Undefined global functions or variables:
AnnotationHub DEFAULT_CIRC_SEQS elementLengths findOverlaps
isSingleStringOrNA makeTxDbFromBiomart makeTxDbFromGRanges
makeTxDbFromUCSC queryHits subjectHits
* 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 ... WARNING
'library' or 'require' calls not declared from:
'biomaRt' 'rtracklayer'
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [186s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 15.02 0.89 38.16
rangeBasedAccessors 9.35 0.08 9.71
OrganismDb 6.67 0.26 6.93
makeOrganismDbFromUCSC 6.81 0.08 62.22
makeOrganismDbFromTxDb 6.32 0.27 63.06
** running examples for arch 'x64' ... [181s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 13.68 0.70 32.64
makeOrganismDbFromUCSC 8.33 0.04 61.61
rangeBasedAccessors 8.03 0.06 8.10
OrganismDb 7.10 0.19 7.28
makeOrganismDbFromTxDb 6.44 0.16 62.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'OrganismDbi_unit_tests.R' [216s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-B/R/bin/i386/R" CMD BATCH --vanilla "OrganismDbi_unit_tests.R" "OrganismDbi_unit_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/OrganismDbi_unit_tests.R' failed.
Last 13 lines of output:
Test files with failing tests
test_wrappedFuns.R
test_extractTranscriptSeqs
Error in BiocGenerics:::testPackage("OrganismDbi") :
unit tests failed for package OrganismDbi
In addition: Warning messages:
1: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
Execution halted
** running tests for arch 'x64' ...
Running 'OrganismDbi_unit_tests.R' [198s]
Warning message:
running command '"c:/biocbld/BBS-3˜1.3-B/R/bin/x64/R" CMD BATCH --vanilla "OrganismDbi_unit_tests.R" "OrganismDbi_unit_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/OrganismDbi_unit_tests.R' failed.
Last 13 lines of output:
Test files with failing tests
test_wrappedFuns.R
test_extractTranscriptSeqs
Error in BiocGenerics:::testPackage("OrganismDbi") :
unit tests failed for package OrganismDbi
In addition: Warning messages:
1: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
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 WARNINGs, 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.
OrganismDbi.Rcheck/tests_i386/OrganismDbi_unit_tests.Rout.fail:
R Under development (unstable) (2015-09-22 r69418) -- "Unsuffered Consequences"
Copyright (C) 2015 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("OrganismDbi")
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: Homo.sapiens
Loading required package: GO.db
Loading required package: DBI
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Loading required package: Rattus.norvegicus
Loading required package: org.Rn.eg.db
Loading required package: TxDb.Rnorvegicus.UCSC.rn5.refGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Timing stopped at: 2.42 0 2.42
Error in .local(x, transcripts, ...) :
failed to extract the exon ranges from 'transcripts' with
exonsBy(transcripts, by="tx", use.names=TRUE)
In addition: Warning messages:
1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
Loading required package: mirbase.db
Loading required package: FDb.UCSC.tRNAs
RUNIT TEST PROTOCOL -- Tue Oct 27 04:59:17 2015
***********************************************
Number of test functions: 42
Number of errors: 1
Number of failures: 0
1 Test Suite :
OrganismDbi RUnit Tests - 42 test functions, 1 error, 0 failures
ERROR in test_extractTranscriptSeqs: Error in .local(x, transcripts, ...) :
failed to extract the exon ranges from 'transcripts' with
exonsBy(transcripts, by="tx", use.names=TRUE)
Test files with failing tests
test_wrappedFuns.R
test_extractTranscriptSeqs
Error in BiocGenerics:::testPackage("OrganismDbi") :
unit tests failed for package OrganismDbi
In addition: Warning messages:
1: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
Execution halted
OrganismDbi.Rcheck/tests_x64/OrganismDbi_unit_tests.Rout.fail:
R Under development (unstable) (2015-09-22 r69418) -- "Unsuffered Consequences"
Copyright (C) 2015 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("OrganismDbi")
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: Homo.sapiens
Loading required package: GO.db
Loading required package: DBI
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Loading required package: Rattus.norvegicus
Loading required package: org.Rn.eg.db
Loading required package: TxDb.Rnorvegicus.UCSC.rn5.refGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Timing stopped at: 2.02 0 2.01
Error in .local(x, transcripts, ...) :
failed to extract the exon ranges from 'transcripts' with
exonsBy(transcripts, by="tx", use.names=TRUE)
In addition: Warning messages:
1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels in factors are deprecated
Loading required package: mirbase.db
Loading required package: FDb.UCSC.tRNAs
RUNIT TEST PROTOCOL -- Tue Oct 27 05:02:36 2015
***********************************************
Number of test functions: 42
Number of errors: 1
Number of failures: 0
1 Test Suite :
OrganismDbi RUnit Tests - 42 test functions, 1 error, 0 failures
ERROR in test_extractTranscriptSeqs: Error in .local(x, transcripts, ...) :
failed to extract the exon ranges from 'transcripts' with
exonsBy(transcripts, by="tx", use.names=TRUE)
Test files with failing tests
test_wrappedFuns.R
test_extractTranscriptSeqs
Error in BiocGenerics:::testPackage("OrganismDbi") :
unit tests failed for package OrganismDbi
In addition: Warning messages:
1: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(txdb) : is.na() applied to non-(list or vector) of type 'S4'
Execution halted
OrganismDbi.Rcheck/00install.out:
install for i386 * installing *source* package 'OrganismDbi' ... ** 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 'OrganismDbi' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'OrganismDbi' as OrganismDbi_1.13.0.zip * DONE (OrganismDbi)
OrganismDbi.Rcheck/examples_i386/OrganismDbi-Ex.timings:
| name | user | system | elapsed | |
| OrganismDb | 6.67 | 0.26 | 6.93 | |
| coordinate-mapping-method | 0.95 | 0.00 | 0.95 | |
| makeOrganismDbFromBiomart | 15.02 | 0.89 | 38.16 | |
| makeOrganismDbFromTxDb | 6.32 | 0.27 | 63.06 | |
| makeOrganismDbFromUCSC | 6.81 | 0.08 | 62.22 | |
| makeOrganismPackage | 0 | 0 | 0 | |
| rangeBasedAccessors | 9.35 | 0.08 | 9.71 | |
OrganismDbi.Rcheck/examples_x64/OrganismDbi-Ex.timings:
| name | user | system | elapsed | |
| OrganismDb | 7.10 | 0.19 | 7.28 | |
| coordinate-mapping-method | 1.02 | 0.02 | 1.04 | |
| makeOrganismDbFromBiomart | 13.68 | 0.70 | 32.64 | |
| makeOrganismDbFromTxDb | 6.44 | 0.16 | 62.77 | |
| makeOrganismDbFromUCSC | 8.33 | 0.04 | 61.61 | |
| makeOrganismPackage | 0.00 | 0.02 | 0.00 | |
| rangeBasedAccessors | 8.03 | 0.06 | 8.10 | |