GenomeInfoDb 1.13.4
Bioconductor Package Maintainer
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomeInfoDb | | Last Changed Rev: 130114 / Revision: 131943 | | Last Changed Date: 2017-06-05 12:56:44 -0400 (Mon, 05 Jun 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && mkdir GenomeInfoDb.buildbin-libdir GenomeInfoDb.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.13.4.tar.gz >GenomeInfoDb.Rcheck\00install.out 2>&1 && cp GenomeInfoDb.Rcheck\00install.out GenomeInfoDb-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomeInfoDb.buildbin-libdir --install="check:GenomeInfoDb-install.out" --force-multiarch --no-vignettes --timings GenomeInfoDb_1.13.4.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomeInfoDb/DESCRIPTION' ... OK
* this is package 'GenomeInfoDb' version '1.13.4'
* package encoding: UTF-8
* 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 'GenomeInfoDb' 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: 'utils:::.roman2numeric'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getTaxonomyId: no visible binding for global variable 'speciesMap'
.lookupSpeciesFromTaxId: no visible binding for global variable
'specData'
available.species: no visible binding for global variable 'speciesMap'
Undefined global functions or variables:
specData speciesMap
* 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
seqinfo 14.86 0.13 21.32
seqlevels-wrappers 13.41 0.11 13.52
available.species 8.71 0.21 8.91
GenomeDescription-class 5.33 0.27 5.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
seqinfo 16.99 0.11 17.12
seqlevels-wrappers 15.97 0.12 16.10
available.species 8.19 0.12 8.31
GenomeDescription-class 6.05 0.06 6.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomeInfoDb.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GenomeInfoDb' ...
** 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 'GenomeInfoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.13.4.zip
* DONE (GenomeInfoDb)