Leo Lahti
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/RPA |
| Branch: RELEASE_3_6 |
| Last Commit: f092cb1 |
| Last Changed Date: 2017-10-30 12:39:26 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:08:45 -0400 (Thu, 12 Apr 2018).
| Package 1207/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RPA 1.34.0 Leo Lahti
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: RPA |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RPA_1.34.0.tar.gz |
| StartedAt: 2018-04-12 02:34:02 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:36:23 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 140.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RPA.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RPA_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/RPA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RPA’ version ‘1.34.0’
* 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 ‘RPA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
RPA.iteration: no visible global function definition for ‘sd’
levelmap: no visible global function definition for ‘na.omit’
plot.rpa.list: no visible global function definition for ‘par’
probeplot: no visible global function definition for ‘plot’
probeplot: no visible global function definition for ‘lines’
rpa.fit : <anonymous>: no visible global function definition for
‘rnorm’
rpa.fit : <anonymous>: no visible global function definition for ‘sd’
rpa.impute : <anonymous>: no visible global function definition for
‘rnorm’
rpa.impute : <anonymous>: no visible global function definition for
‘sd’
rpa.online: no visible global function definition for ‘rnorm’
rpa.online: no visible global function definition for ‘sessionInfo’
rpaplot: no visible global function definition for ‘par’
rpaplot: no visible global function definition for ‘lines’
s2.neglogp: no visible global function definition for ‘dchisq’
s2.neglogp: no visible global function definition for ‘dgamma’
s2.update: no visible global function definition for ‘optim’
sample.probeset: no visible global function definition for ‘rgamma’
sample.probeset: no visible global function definition for ‘rnorm’
summarize_probedata: no visible global function definition for
‘read.csv’
Undefined global functions or variables:
dchisq dgamma lines na.omit optim par plot read.csv rgamma rnorm sd
sessionInfo
Consider adding
importFrom("graphics", "lines", "par", "plot")
importFrom("stats", "dchisq", "dgamma", "na.omit", "optim", "rgamma",
"rnorm", "sd")
importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘RPA.Rmd’, ‘RPA.md’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘rpa.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/RPA.Rcheck/00check.log’
for details.
RPA.Rcheck/00install.out
* installing *source* package ‘RPA’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RPA)
RPA.Rcheck/tests/rpa.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> library(affydata)
Package LibPath Item
[1,] "affydata" "/home/biocbuild/bbs-3.6-bioc/R/library" "Dilution"
Title
[1,] "AffyBatch instance Dilution"
> library(RPA)
Loading required package: phyloseq
Attaching package: 'phyloseq'
The following object is masked from 'package:affy':
sampleNames
The following object is masked from 'package:Biobase':
sampleNames
RPA Copyright (C) 2008-2016 Leo Lahti.
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under the FreeBSD open source license.
> data(Dilution)
> eset <- rpa(Dilution)
Preprocessing affybatch...
Background correcting...
Normalizing...
Logging PM values...
Retrieving probe positions..
...
Preprocessing completed.
Setting quantile basis
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf'
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf'
>
> proc.time()
user system elapsed
16.216 0.252 16.979
RPA.Rcheck/RPA-Ex.timings
| name | user | system | elapsed | |
| RPA-package | 0 | 0 | 0 | |
| RPA.iteration | 0 | 0 | 0 | |
| RPA.preprocess | 0 | 0 | 0 | |
| collect.hyperparameters | 0 | 0 | 0 | |
| d.update.fast | 0 | 0 | 0 | |
| estimate.affinities | 0 | 0 | 0 | |
| estimate.hyperparameters | 0 | 0 | 0 | |
| frpa | 0 | 0 | 0 | |
| get.batches | 0 | 0 | 0 | |
| get.probe.matrix | 0 | 0 | 0 | |
| get.probe.parameters | 0.000 | 0.000 | 0.001 | |
| get.probeset | 0.000 | 0.000 | 0.001 | |
| hyperparameter.update | 0.004 | 0.000 | 0.001 | |
| online.quantile | 0 | 0 | 0 | |
| probe.parameters.tolist | 0 | 0 | 0 | |
| probe.performance | 0 | 0 | 0 | |
| probeplot | 0.000 | 0.000 | 0.001 | |
| probetable | 0.000 | 0.000 | 0.001 | |
| retrieve.probesets | 0.000 | 0.004 | 0.001 | |
| rpa | 0.000 | 0.000 | 0.001 | |
| rpa.complete | 0 | 0 | 0 | |
| rpa.fit | 0 | 0 | 0 | |
| rpa.online | 0 | 0 | 0 | |
| rpa.plot | 0 | 0 | 0 | |
| rpa.summarize | 0.000 | 0.000 | 0.001 | |
| rpaplot | 0.004 | 0.000 | 0.001 | |
| sample.probeset | 0 | 0 | 0 | |
| summarize.batch | 0 | 0 | 0 | |
| summarize.batches | 0 | 0 | 0 | |
| summarize_probedata | 0 | 0 | 0 | |
| updating.hyperparameters | 0.000 | 0.000 | 0.001 | |