OrganismDbi 1.11.42
Biocore Data Team
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OrganismDbi | | Last Changed Rev: 105883 / Revision: 107696 | | Last Changed Date: 2015-07-07 11:35:41 -0700 (Tue, 07 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.11.42.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/OrganismDbi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.11.42’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OrganismDbi’ can be installed ... [15s/15s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/158s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 14.405 0.188 51.277
rangeBasedAccessors 8.788 0.024 8.831
OrganismDb 7.504 0.043 7.621
makeOrganismDbFromUCSC 5.899 0.032 41.359
makeOrganismDbFromTxDb 5.843 0.076 40.916
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘OrganismDbi_unit_tests.R’ [227s/231s]
[227s/232s] 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
‘/home/biocbuild/bbs-3.2-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.