BioC 2.12: CHECK report for GenomicFeatures on moscato2

Package: GenomicFeatures

Version: 1.12.4

Command: rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.12.4.tar.gz >GenomicFeatures-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.12.4.tar.gz && mv GenomicFeatures.buildbin-libdir/* GenomicFeatures.Rcheck/ && rmdir GenomicFeatures.buildbin-libdir

StartedAt: 2013-10-09 02:17:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:34:58 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 1042.9 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.12.4'
* 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 'GenomicFeatures' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.setseqnameStyle: no visible binding for global variable 'txdb'
* 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 examples ...
** running examples for arch 'i386' ... [269s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 117.74   8.68  128.86
makeFeatureDbFromUCSC          9.04   0.24   66.24
makeTranscriptDbFromUCSC       5.41   0.06   28.06
getPromoterSeq-methods         3.41   0.24    5.36
makeTranscriptDbFromBiomart    2.89   0.08   21.50
** running examples for arch 'x64' ... [259s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 107.25   8.16  115.48
makeFeatureDbFromUCSC         10.05   0.17   69.43
makeTranscriptDbFromUCSC       5.70   0.03   28.16
makeTranscriptDbFromBiomart    2.94   0.04   19.65
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'GenomicFeatures_unit_tests.R' [113s]
 [114s] OK
** running tests for arch 'x64'
  Running 'GenomicFeatures_unit_tests.R' [120s]
 [120s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GenomicFeatures' ...
** 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 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.12.4.zip
* DONE (GenomicFeatures)