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BioC 2.14: CHECK report for BiocGenerics on moscato2

This page was generated on 2014-10-08 08:54:25 -0700 (Wed, 08 Oct 2014).

Package 86/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.10.0
Bioconductor Package Maintainer
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/BiocGenerics
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: BiocGenerics
Version: 0.10.0
Command: rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.10.0.tar.gz >BiocGenerics-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.10.0.tar.gz
StartedAt: 2014-10-07 23:06:17 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:07:33 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 75.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.10.0.tar.gz >BiocGenerics-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '0.10.0'
* 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' 'utils' '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 'duplicated.Rd':
  '[IRanges]{duplicated,Ranges-method}'

Missing link or links in documentation object 'mapply.Rd':
  '[IRanges]{mapply,List-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' ... [10s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotMA 7.56   0.07     7.7
** running examples for arch 'x64' ... [11s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotMA 8.36   0.17    8.58
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'BiocGenerics_unit_tests.R' [1s]
 [2s] OK
** running tests for arch 'x64' ...
  Running 'BiocGenerics_unit_tests.R' [2s]
 [2s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

BiocGenerics.Rcheck/00install.out:


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 'do.call' 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, '2014-10-07 23:06:18', 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_0.10.0.zip
* DONE (BiocGenerics)

BiocGenerics.Rcheck/examples_i386/BiocGenerics-Ex.timings:

nameusersystemelapsed
BiocGenerics-package000
Extremes0.020.000.02
annotation0.370.000.37
append000
as.data.frame000
as.vector000
boxplot0.010.000.01
cbind000
clusterApply0.020.000.02
combine0.110.000.11
density000
do.call000
duplicated000
eval000
evalq000
funprog000
get0.010.000.01
image000
is.unsorted000
lapply000
mapply000
match0.020.000.02
normalize0.250.000.25
nrow000
order000
paste0.010.000.01
plotMA7.560.077.70
rank000
relist000
rep000
residuals000
row_colnames0.020.000.02
sets000
sort0.010.000.01
strand0.050.030.08
table0.010.000.02
tapply000
unique000
unlist0.020.000.01
updateObject0.230.000.24
weights000
xtabs000

BiocGenerics.Rcheck/examples_x64/BiocGenerics-Ex.timings:

nameusersystemelapsed
BiocGenerics-package000
Extremes0.020.000.02
annotation0.400.010.42
append0.010.000.01
as.data.frame000
as.vector000
boxplot000
cbind000
clusterApply0.020.000.01
combine0.140.000.14
density000
do.call0.010.000.02
duplicated000
eval000
evalq000
funprog0.020.000.01
get000
image000
is.unsorted000
lapply000
mapply000
match000
normalize0.210.020.22
nrow0.010.000.01
order000
paste000
plotMA8.360.178.58
rank000
relist000
rep0.000.010.01
residuals000
row_colnames000
sets0.020.000.02
sort000
strand0.080.020.09
table000
tapply0.010.000.02
unique000
unlist000
updateObject0.280.000.28
weights000
xtabs000