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BioC 3.0: CHECK report for BiocGenerics on moscato1

This page was generated on 2015-04-10 09:47:37 -0700 (Fri, 10 Apr 2015).

Package 89/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.12.1
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BiocGenerics
Last Changed Rev: 96708 / Revision: 102249
Last Changed Date: 2014-11-12 18:24:18 -0800 (Wed, 12 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: BiocGenerics
Version: 0.12.1
Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.12.1.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.12.1.tar.gz
StartedAt: 2015-04-09 23:00:21 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:01:43 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 82.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.12.1.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '0.12.1'
* 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 ... NOTE
'library' or 'require' call to 'RUnit' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
testPackage: no visible global function definition for
  'defineTestSuite'
testPackage: no visible global function definition for 'runTestSuite'
testPackage: no visible global function definition for
  'printTextProtocol'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'unsplit':
unsplit
  Code: function(value, f, drop = FALSE)
  Docs: function(x, recursive = TRUE, use.names = TRUE)
  Argument names in code not in docs:
    value f drop
  Argument names in docs not in code:
    x recursive use.names
  Mismatches in argument names:
    Position: 1 Code: value Docs: x
    Position: 2 Code: f Docs: recursive
    Position: 3 Code: drop Docs: use.names

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'unsplit'
  'x' 'recursive' 'use.names'
Documented arguments not in \usage in documentation object 'unsplit':
  'value' 'f' 'drop'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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 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' ... [14s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotMA 9.83   0.25   10.51
** running examples for arch 'x64' ... [16s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotMA 11.66   0.29   12.33
* 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]
 [3s] OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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 'unsplit' 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, '2015-04-09 23:00:24', 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_0.12.1.zip
* DONE (BiocGenerics)

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

nameusersystemelapsed
BiocGenerics-package000
Extremes0.010.000.01
annotation0.550.020.57
append000
as.data.frame000
as.vector000
boxplot000
cbind0.020.000.02
clusterApply0.030.000.03
combine0.150.000.16
density0.020.000.01
do.call000
duplicated000
eval0.010.000.02
evalq000
funprog0.020.000.01
get000
image000
is.unsorted0.020.000.02
lapply000
mapply000
match000
normalize0.310.020.33
nrow0.020.000.02
order000
paste000
plotMA 9.83 0.2510.51
rank0.010.000.02
relist000
rep000
residuals000
row_colnames000
sets0.010.000.02
sort000
start0.100.000.09
strand0.110.030.14
table0.020.000.01
tapply000
unique000
unlist000
unsplit000
updateObject0.410.000.41
weights0.010.000.01
xtabs000

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

nameusersystemelapsed
BiocGenerics-package000
Extremes0.020.000.02
annotation0.650.000.65
append0.020.000.02
as.data.frame000
as.vector000
boxplot000
cbind0.010.000.01
clusterApply0.020.000.02
combine0.170.000.17
density000
do.call000
duplicated0.010.000.02
eval000
evalq000
funprog0.020.000.01
get0.020.000.02
image000
is.unsorted000
lapply0.010.000.01
mapply000
match0.020.000.02
normalize0.370.000.37
nrow000
order0.010.000.01
paste000
plotMA11.66 0.2912.33
rank0.010.000.01
relist000
rep000
residuals0.020.000.02
row_colnames000
sets000
sort000
start0.160.000.16
strand0.170.020.19
table000
tapply000
unique0.010.000.02
unlist000
unsplit000
updateObject0.310.000.31
weights0.020.000.02
xtabs000