OrganismDbi 1.12.0
Biocore Data Team
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/OrganismDbi | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.12.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.12.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/OrganismDbi.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.12.0'
* 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.
Unexported objects imported by ':::' calls:
'AnnotationDbi:::.chooseCentralOrgPkgSymbol'
'AnnotationDbi:::.mapIds' 'AnnotationDbi:::.resort'
'AnnotationDbi:::.testForValidKeytype'
'AnnotationDbi:::.testSelectArgs' 'BiocGenerics:::testPackage'
'GenomicFeatures:::.makePackageName'
'GenomicFeatures:::.set.group.names'
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'
* 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' ... [483s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 16.45 0.91 36.70
rangeBasedAccessors 7.97 0.20 8.17
OrganismDb 6.81 0.18 6.99
makeOrganismDbFromTxDb 6.18 0.17 277.02
makeOrganismDbFromUCSC 5.89 0.19 147.42
** running examples for arch 'x64' ... [272s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 16.99 0.64 36.75
rangeBasedAccessors 7.91 0.14 8.05
OrganismDb 7.33 0.22 7.55
makeOrganismDbFromUCSC 5.95 0.11 116.72
makeOrganismDbFromTxDb 5.87 0.16 94.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'OrganismDbi_unit_tests.R' [221s]
[222s] OK
** running tests for arch 'x64' ...
Running 'OrganismDbi_unit_tests.R' [225s]
[225s] 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: 2 WARNINGs, 1 NOTE
See
'C:/biocbld/bbs-3.2-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.
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_1.12.0.zip
* DONE (OrganismDbi)