BioC 2.13: CHECK report for BiocGenerics on moscato1

Package: BiocGenerics

Version: 0.8.0

Command: rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.8.0.tar.gz >BiocGenerics-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.8.0.tar.gz && mv BiocGenerics.buildbin-libdir/* BiocGenerics.Rcheck/ && rmdir BiocGenerics.buildbin-libdir

StartedAt: 2014-04-05 02:30:22 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:31:55 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 92.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.8.0'
* 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 'BiocGenerics' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'graphics' 'stats' 'parallel'
A package should be listed in only one of these fields.
* 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 ... OK
* 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 ... WARNING
Missing link or links in documentation object 'D:/biocbld/bbs-2.13-bioc/tmpdir/RtmpEnsOvo/R.INSTALL241cc201d63/BiocGenerics/man/tapply.Rd':
  '[IRanges]{tapply,Vector-method}'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'rep':
  'rep.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ...
** running examples for arch 'i386' ... [13s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotMA 8.83   0.15    9.14
** running examples for arch 'x64' ... [12s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotMA 9.14   0.06    9.39
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'BiocGenerics_unit_tests.R' [2s]
 [2s] OK
** running tests for arch 'x64'
  Running 'BiocGenerics_unit_tests.R' [2s]
 [3s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'append' in package 'BiocGenerics'
Creating a new generic function for 'as.data.frame' in package 'BiocGenerics'
Creating a new generic function for 'as.vector' in package 'BiocGenerics'
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'is.unsorted' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rank' in package 'BiocGenerics'
Creating a new generic function for 'rep.int' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'sort' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'unlist' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Warning in getPackageName(environment(fdef)) :
  Created a package name, '2014-04-05 02:30:25', when none found
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' in package 'BiocGenerics'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'BiocGenerics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocGenerics' as BiocGenerics_0.8.0.zip
* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.01	0.00	0.02
annotation	0.59	0.01	0.61
append	0.01	0.00	0.02
as.data.frame	0	0	0
as.vector	0.01	0.00	0.02
boxplot	0.02	0.00	0.01
cbind	0.01	0.00	0.02
clusterApply	0.08	0.00	0.08
combine	0.22	0.00	0.22
density	0.01	0.00	0.02
duplicated	0.02	0.00	0.01
eval	0	0	0
evalq	0	0	0
funprog	0.02	0.00	0.01
get	0	0	0
image	0	0	0
is.unsorted	0	0	0
lapply	0.02	0.00	0.01
mapply	0.01	0.00	0.02
match	0.02	0.00	0.02
normalize	0.31	0.08	0.39
nrow	0.05	0.00	0.05
order	0.06	0.00	0.07
paste	0	0	0
plotMA	8.83	0.15	9.14
rank	0.01	0.00	0.01
rep	0	0	0
residuals	0	0	0
row_colnames	0.02	0.00	0.02
sets	0.01	0.00	0.01
sort	0	0	0
strand	0.12	0.00	0.12
table	0.02	0.00	0.02
tapply	0	0	0
unique	0	0	0
unlist	0.01	0.00	0.01
updateObject	0.28	0.02	0.30
weights	0.02	0.00	0.01
xtabs	0	0	0

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.03	0.00	0.03
annotation	0.45	0.01	0.47
append	0.02	0.00	0.01
as.data.frame	0	0	0
as.vector	0	0	0
boxplot	0	0	0
cbind	0.02	0.00	0.01
clusterApply	0.06	0.00	0.07
combine	0.15	0.00	0.15
density	0	0	0
duplicated	0.02	0.00	0.01
eval	0	0	0
evalq	0	0	0
funprog	0.02	0.00	0.02
get	0	0	0
image	0	0	0
is.unsorted	0.01	0.00	0.01
lapply	0	0	0
mapply	0.07	0.00	0.06
match	0	0	0
normalize	0.23	0.03	0.27
nrow	0.02	0.00	0.01
order	0	0	0
paste	0	0	0
plotMA	9.14	0.06	9.39
rank	0.02	0.00	0.02
rep	0	0	0
residuals	0	0	0
row_colnames	0.01	0.00	0.01
sets	0.03	0.00	0.03
sort	0.02	0.00	0.02
strand	0.12	0.00	0.12
table	0.02	0.00	0.02
tapply	0.02	0.00	0.01
unique	0.01	0.00	0.02
unlist	0	0	0
updateObject	0.55	0.01	0.56
weights	0.01	0.00	0.02
xtabs	0.00	0.02	0.01