Guenter Klambauer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/dexus |
| Branch: RELEASE_3_6 |
| Last Commit: 8d67f5b |
| Last Changed Date: 2017-10-30 12:40:00 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:36:36 -0400 (Thu, 12 Apr 2018).
| Package 361/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dexus 1.18.0 Guenter Klambauer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: dexus |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dexus_1.18.0.tar.gz |
| StartedAt: 2018-04-12 02:50:42 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:51:30 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 48.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dexus.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dexus_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/dexus.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.18.0’
* 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-3.6-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 -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-3.6-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
| name | user | system | elapsed | |
| DEXUSResult-class | 0.003 | 0.000 | 0.003 | |
| DEXUSResult-subset | 1.523 | 0.060 | 1.633 | |
| INI | 1.159 | 0.020 | 1.193 | |
| INIThreshold-set | 0.669 | 0.015 | 0.695 | |
| accessors | 0.688 | 0.017 | 0.713 | |
| dexss | 1.128 | 0.016 | 1.165 | |
| dexus | 0.718 | 0.015 | 0.746 | |
| dexus.parallel | 0.728 | 0.015 | 0.744 | |
| getSizeNB | 0.001 | 0.000 | 0.002 | |
| normalizeData | 0.953 | 0.040 | 0.999 | |
| plot | 1.060 | 0.026 | 1.096 | |
| sort | 0.993 | 0.015 | 1.016 | |