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BioC 3.5: CHECK report for BiocGenerics on veracruz2

This page was generated on 2017-08-16 13:30:03 -0400 (Wed, 16 Aug 2017).

Package 117/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.22.0
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/BiocGenerics
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocGenerics
Version: 0.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.22.0.tar.gz
StartedAt: 2017-08-16 00:14:14 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:15:17 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 63.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocGenerics_0.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.22.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'tapply':
tapply
  Code: function(X, INDEX, FUN = NULL, ..., default = NA, simplify =
                 TRUE)
  Docs: function(X, INDEX, FUN = NULL, ..., simplify = TRUE)
  Argument names in code not in docs:
    default
  Mismatches in argument names:
    Position: 5 Code: default Docs: simplify

Codoc mismatches from documentation object 'xtabs':
xtabs
  Code: function(formula = ˜., data = parent.frame(), subset, sparse =
                 FALSE, na.action, addNA = FALSE, exclude = if (!addNA)
                 c(NA, NaN), drop.unused.levels = FALSE)
  Docs: function(formula = ˜., data = parent.frame(), subset, sparse =
                 FALSE, na.action, exclude = c(NA, NaN),
                 drop.unused.levels = FALSE)
  Argument names in code not in docs:
    addNA
  Mismatches in argument names:
    Position: 6 Code: addNA Docs: exclude
    Position: 7 Code: exclude Docs: drop.unused.levels
  Mismatches in argument default values:
    Name: 'exclude' Code: if (!addNA) c(NA, NaN) Docs: c(NA, NaN)

* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
testPackage 8.811  0.033   9.074
plotMA      6.823  0.183   7.226
plotPCA     4.936  0.041   5.107
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.


BiocGenerics.Rcheck/00install.out:

* 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 ‘rowSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘colSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘rowMeans’ in package ‘BiocGenerics’
Creating a new generic function for ‘colMeans’ 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 ‘var’ in package ‘BiocGenerics’
Creating a new generic function for ‘sd’ 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
* DONE (BiocGenerics)

BiocGenerics.Rcheck/BiocGenerics-Ex.timings:

nameusersystemelapsed
BiocGenerics-package0.0020.0010.002
Extremes0.0130.0020.015
IQR0.0020.0000.002
annotation0.2010.0080.219
append0.0060.0000.006
as.data.frame0.0030.0010.002
as.vector0.0020.0000.002
boxplot0.0020.0000.002
cbind0.0030.0000.003
clusterApply0.0210.0030.024
combine0.1990.0020.203
dbconn1.9580.0492.068
density0.0030.0010.003
do.call0.0080.0000.008
duplicated0.0040.0010.005
eval0.0030.0000.004
evalq0.0010.0000.001
fileName2.0640.0632.504
funprog0.0120.0010.013
get0.0050.0010.009
grep0.0030.0000.003
image0.0020.0010.002
is.unsorted0.0020.0000.003
lapply0.0050.0010.005
lengths0.1640.0020.179
mad0.0020.0000.002
mapply0.0010.0000.002
match0.0030.0000.003
matrix-summary0.0030.0000.003
mean0.0030.0010.003
normalize0.0340.0010.035
nrow0.0100.0010.011
order0.0050.0010.005
organism_species0.2550.0170.282
paste0.0020.0000.002
plotMA6.8230.1837.226
plotPCA4.9360.0415.107
rank0.0050.0010.004
relist0.0040.0000.004
rep0.0040.0010.003
residuals0.0020.0000.003
row_colnames0.0100.0010.011
score0.0990.0030.103
sets0.0120.0010.012
sort0.0030.0000.004
start0.0890.0040.095
strand0.1130.0040.117
subset0.0380.0020.040
t0.0050.0000.006
table0.0030.0000.003
tapply0.0040.0000.005
testPackage8.8110.0339.074
unique0.0020.0000.004
unlist0.0040.0000.003
unsplit0.0020.0000.003
updateObject0.3020.0050.309
var0.0020.0000.003
weights0.0020.0000.002
which0.0080.0000.008
xtabs0.0040.0010.004