ensemblVEP 1.9.3
Valerie Obenchain
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ensemblVEP | | Last Changed Rev: 107236 / Revision: 107602 | | Last Changed Date: 2015-08-07 16:20:09 -0700 (Fri, 07 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | TIMEOUT | skipped | skipped | |
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### Running command:
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### rm -rf ensemblVEP.buildbin-libdir ensemblVEP.Rcheck && mkdir ensemblVEP.buildbin-libdir ensemblVEP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensemblVEP.buildbin-libdir ensemblVEP_1.9.3.tar.gz >ensemblVEP.Rcheck\00install.out 2>&1 && cp ensemblVEP.Rcheck\00install.out ensemblVEP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ensemblVEP.buildbin-libdir --install="check:ensemblVEP-install.out" --force-multiarch --no-vignettes --timings ensemblVEP_1.9.3.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ensemblVEP.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ensemblVEP/DESCRIPTION' ... OK
* this is package 'ensemblVEP' version '1.9.3'
* 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 'ensemblVEP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'S4Vectors'
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'S4Vectors:::selectSome'
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
parseCSQToGRanges,VCF : .local: no visible global function definition
for 'elementLengths'
parseCSQToGRanges,VCF : .local: no visible global function definition
for 'DataFrame'
parseCSQToGRanges,VCF : .local: no visible global function definition
for 'genome<-'
show,VEPParam: 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [253s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ensemblVEP 1.27 0.02 161.08
parseCSQToGRanges 0.64 0.01 78.08
** running examples for arch 'x64' ... [249s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ensemblVEP 1.33 0.03 154.92
parseCSQToGRanges 0.80 0.05 78.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [154s]
[154s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [158s]
[159s] 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 WARNING, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/ensemblVEP.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ensemblVEP' ...
** 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 'ensemblVEP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ensemblVEP' as ensemblVEP_1.9.3.zip
* DONE (ensemblVEP)