OrganismDbi 1.14.1
Biocore Data Team
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/OrganismDbi | | Last Changed Rev: 117533 / Revision: 122332 | | Last Changed Date: 2016-05-16 07:30:03 -0700 (Mon, 16 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.14.1.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && E:\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_1.14.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/OrganismDbi.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.14.1'
* 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 ... NOTE
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
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 ... 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 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
makeOrganismDbFromBiomart 20.00 1.00 153.90
rangeBasedAccessors 14.86 0.12 15.55
makeOrganismDbFromUCSC 9.43 0.16 75.56
OrganismDb 9.04 0.15 12.34
makeOrganismDbFromTxDb 7.91 0.12 71.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeOrganismDbFromBiomart 23.73 0.69 58.65
OrganismDb 13.70 0.31 14.51
rangeBasedAccessors 12.38 0.04 12.43
makeOrganismDbFromUCSC 11.90 0.22 91.71
makeOrganismDbFromTxDb 9.83 0.25 72.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'OrganismDbi_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'OrganismDbi_unit_tests.R'
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: 1 NOTE
See
'E:/biocbld/bbs-3.3-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_1.14.1.zip
* DONE (OrganismDbi)