dexus 1.16.0
Guenter Klambauer
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/dexus | | Branch: RELEASE_3_5 | | Last Commit: 64b2e66 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dexus_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/dexus.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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.
* installing *source* package ‘dexus’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -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)