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BioC 3.5: CHECK report for dexus on oaxaca

This page was generated on 2017-03-04 16:45:16 -0500 (Sat, 04 Mar 2017).

Package 329/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dexus 1.15.0
Guenter Klambauer
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/dexus
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: dexus
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dexus_1.15.0.tar.gz
StartedAt: 2017-03-04 01:50:12 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 01:51:01 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 49.6 seconds
RetCode: 0
Status:  OK 
CheckDir: dexus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dexus_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/dexus.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dexus’ version ‘1.15.0’
* 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 ‘dexus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘DESeq’ ‘parallel’ ‘statmod’ ‘stats’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dexss : <anonymous>: no visible global function definition for ‘hist’
dexss: no visible global function definition for ‘runif’
dexss: no visible global function definition for ‘new’
dexus : <anonymous>: no visible global function definition for ‘hist’
dexus: no visible global function definition for ‘runif’
dexus: no visible global function definition for ‘new’
dexus.parallel: no visible global function definition for ‘mclapply’
dexus.parallel: no visible global function definition for ‘new’
getSizeNB: no visible global function definition for ‘var’
initialize.clusters.kmeans: no visible global function definition for
  ‘kmeans’
initialize.clusters.kmeans: no visible global function definition for
  ‘median’
initialize.clusters.kmeans: no visible global function definition for
  ‘rnorm’
initialize.clusters.quantiles: no visible global function definition
  for ‘rnorm’
initialize.clusters.quantiles: no visible global function definition
  for ‘quantile’
initialize.clusters.quantiles : <anonymous>: no visible global function
  definition for ‘rnorm’
nbinomTestForMatrices : <anonymous>: no visible global function
  definition for ‘dnbinom’
normalize.rle : <anonymous>: no visible global function definition for
  ‘median’
normalize.uq : <anonymous>: no visible global function definition for
  ‘quantile’
testMulticlass : <anonymous>: no visible global function definition for
  ‘deviance’
testMulticlass : <anonymous>: no visible global function definition for
  ‘pchisq’
INIThreshold<-,DEXUSResult: no visible global function definition for
  ‘slot<-’
[,DEXUSResult-character: no visible global function definition for
  ‘new’
[,DEXUSResult-logical: no visible global function definition for ‘new’
[,DEXUSResult-numeric: no visible global function definition for ‘new’
plot,DEXUSResult-missing: no visible global function definition for
  ‘par’
plot,DEXUSResult-missing: no visible global function definition for
  ‘colorRampPalette’
plot,DEXUSResult-missing: no visible global function definition for
  ‘image’
plot,DEXUSResult-missing: no visible global function definition for
  ‘rect’
plot,DEXUSResult-missing: no visible global function definition for
  ‘points’
plot,DEXUSResult-missing: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  axis colorRampPalette deviance dnbinom hist image kmeans mclapply
  median new par pchisq points quantile rect rnorm runif slot<- var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "hist", "image", "par", "points",
             "rect")
  importFrom("methods", "new", "slot<-")
  importFrom("stats", "deviance", "dnbinom", "kmeans", "median",
             "pchisq", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/dexus.Rcheck/00check.log’
for details.


dexus.Rcheck/00install.out:

* installing *source* package ‘dexus’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c dexus.cpp -o dexus.o
dexus.cpp:136:15: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((innerCyc==maxInnerCyc))
             ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
dexus.cpp:136:15: note: remove extraneous parentheses around the comparison to silence this warning
        if ((innerCyc==maxInnerCyc))
            ˜        ^            ˜
dexus.cpp:136:15: note: use '=' to turn this equality comparison into an assignment
        if ((innerCyc==maxInnerCyc))
                     ^˜
                     =
dexus.cpp:193:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
dexus.cpp:575:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
3 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o dexus.so dexus.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/dexus.Rcheck/dexus/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dexus)

dexus.Rcheck/dexus-Ex.timings:

nameusersystemelapsed
DEXUSResult-class0.0030.0010.004
DEXUSResult-subset1.6370.0601.697
INI1.3720.0221.396
INIThreshold-set0.6920.0150.707
accessors0.7340.0190.753
dexss1.2860.0191.306
dexus0.8230.0200.842
dexus.parallel0.7120.0130.726
getSizeNB0.0010.0000.000
normalizeData1.0130.0431.057
plot1.2770.0331.311
sort1.1150.0161.132