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BioC 3.4: CHECK report for BiocGenerics on moscato1

This page was generated on 2016-09-21 03:43:59 -0700 (Wed, 21 Sep 2016).

Package 109/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.19.2
Bioconductor Package Maintainer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocGenerics
Last Changed Rev: 119047 / Revision: 121152
Last Changed Date: 2016-06-30 01:14:40 -0700 (Thu, 30 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocGenerics
Version: 0.19.2
Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.19.2.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.19.2.tar.gz
StartedAt: 2016-09-20 04:39:50 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:41:38 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 108.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.19.2.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.19.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.19.2'
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'sets.Rd':
  '[GenomicRanges]{union,GRanges,GRanges-method}'

See section 'Cross-references' in 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 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' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 6.99   0.01    7.00
plotMA      5.25   0.05    5.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-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 '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 'grep' in package 'BiocGenerics'
Creating a new generic function for 'grepl' 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 'lengths' 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 '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 'unsplit' in package 'BiocGenerics'
Creating a new generic function for 'which' in package 'BiocGenerics'
Creating a new generic function for 'which.max' in package 'BiocGenerics'
Creating a new generic function for 'which.min' in package 'BiocGenerics'
Creating a new generic function for 'IQR' in package 'BiocGenerics'
Creating a new generic function for 'mad' 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'
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_0.19.2.zip
* DONE (BiocGenerics)

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

nameusersystemelapsed
BiocGenerics-package000
Extremes0.020.000.01
IQR000
annotation0.210.000.20
append000
as.data.frame000
as.vector0.020.000.01
boxplot000
cbind000
clusterApply0.010.000.02
combine0.100.000.09
dbconn1.740.011.77
density000
do.call000
duplicated000
eval000
evalq0.010.000.02
fileName1.910.102.06
funprog000
get000
grep0.020.000.02
image000
is.unsorted000
lapply000
lengths0.050.000.04
mad000
mapply000
match0.010.000.02
normalize0.020.000.02
nrow000
order000
organism_species0.250.010.27
paste000
plotMA4.770.054.90
plotPCA2.750.002.75
rank0.010.000.01
relist000
rep000
residuals000
row_colnames000
score0.080.010.09
sets0.010.000.02
sort000
start0.060.000.06
strand0.100.020.11
subset0.010.000.01
table0.020.000.02
tapply000
testPackage4.940.004.94
unique000
unlist000
unsplit0.020.000.02
updateObject0.170.000.17
weights000
which000
xtabs0.020.000.02

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

nameusersystemelapsed
BiocGenerics-package000
Extremes0.020.000.02
IQR000
annotation0.200.020.21
append000
as.data.frame000
as.vector000
boxplot000
cbind0.020.000.01
clusterApply0.020.000.02
combine0.060.000.06
dbconn1.920.041.97
density000
do.call000
duplicated000
eval000
evalq000
fileName2.290.052.37
funprog0.020.000.01
get000
grep000
image000
is.unsorted0.010.000.02
lapply000
lengths0.050.000.05
mad000
mapply000
match000
normalize0.030.000.03
nrow000
order0.020.000.02
organism_species0.280.010.29
paste000
plotMA5.250.055.31
plotPCA2.890.002.88
rank000
relist0.020.000.02
rep000
residuals000
row_colnames0.010.000.02
score0.080.000.07
sets0.010.000.02
sort000
start0.060.000.07
strand0.100.000.09
subset0.030.000.03
table000
tapply000
testPackage6.990.017.00
unique000
unlist000
unsplit000
updateObject0.20.00.2
weights000
which0.020.000.02
xtabs000