destiny 1.2.1
Philipp Angerer
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/destiny | | Last Changed Rev: 117305 / Revision: 122332 | | Last Changed Date: 2016-05-11 07:31:54 -0700 (Wed, 11 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings destiny_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/destiny.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘1.2.1’
* package encoding: UTF-8
* 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 ‘destiny’ 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DiffusionMap: no visible global function definition for
‘txtProgressBar’
DiffusionMap : cb: no visible global function definition for
‘setTxtProgressBar’
centered.cosine.dist: no visible global function definition for ‘cor’
colorlegend: no visible global function definition for ‘palette’
colorlegend: no visible global function definition for
‘colorRampPalette’
continuous.colors: no visible global function definition for ‘palette’
continuous.colors: no visible global function definition for
‘colorRamp’
continuous.colors: no visible global function definition for ‘rgb’
cube.helix : <anonymous>: no visible global function definition for
‘rgb’
find.sigmas: no visible global function definition for ‘txtProgressBar’
find.sigmas: no visible global function definition for
‘setTxtProgressBar’
plot.DiffusionMap: no visible global function definition for ‘palette’
plot.DiffusionMap: no visible global function definition for ‘axis’
plot.DiffusionMap: no visible global function definition for ‘plot.new’
read.ExpressionSet: no visible global function definition for
‘read.table’
plot,Sigmas-missing: no visible global function definition for
‘dotchart’
plot,Sigmas-missing: no visible global function definition for ‘layout’
print,DiffusionMap: no visible global function definition for ‘str’
updateObject,DiffusionMap: no visible global function definition for
‘.hasSlot’
updateObject,DiffusionMap: no visible global function definition for
‘slot<-’
Undefined global functions or variables:
.hasSlot axis colorRamp colorRampPalette cor dotchart layout palette
plot.new read.table rgb setTxtProgressBar slot<- str txtProgressBar
Consider adding
importFrom("grDevices", "colorRamp", "colorRampPalette", "palette",
"rgb")
importFrom("graphics", "axis", "dotchart", "layout", "plot.new")
importFrom("methods", ".hasSlot", "slot<-")
importFrom("stats", "cor")
importFrom("utils", "read.table", "setTxtProgressBar", "str",
"txtProgressBar")
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 ... WARNING
Data with usage in documentation object 'guo' but not in code:
guo.norm
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'plot.DiffusionMap':
‘plot.DiffusionMap’
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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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
Examples with CPU or elapsed time > 5s
user system elapsed
destiny 9.477 0.016 9.599
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
‘IRdisplay’ ‘IRkernel’ ‘base64enc’ ‘repr’ ‘xlsx’
* 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/destiny.Rcheck/00check.log’
for details.
* installing *source* package ‘destiny’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppEigen/include" -g -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppEigen/include" -g -fpic -g -O2 -c censoring.cpp -o censoring.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppEigen/include" -g -fpic -g -O2 -c no_censoring.cpp -o no_censoring.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o no_censoring.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/destiny.Rcheck/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘destiny’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (destiny)