Dorothee Childs
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/TPP |
| Branch: RELEASE_3_6 |
| Last Commit: ce607f8 |
| Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:40:48 -0400 (Thu, 12 Apr 2018).
| Package 1410/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TPP 3.6.0 Dorothee Childs
| 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: TPP |
| Version: 3.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TPP_3.6.0.tar.gz |
| StartedAt: 2018-04-12 10:23:25 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 10:27:57 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 271.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TPP.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TPP_3.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TPP.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 ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.6.0’
* 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 ‘TPP’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 13.2Mb
sub-directories of 1Mb or more:
data 1.9Mb
example_data 8.0Mb
test_data 1.9Mb
* 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
Unexported objects imported by ':::' calls:
‘doParallel:::.options’ ‘mefa:::rep.data.frame’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘TPP/R/TPP.R’:
.onLoad calls:
packageStartupMessage(msgText, "\n")
See section ‘Good practice’ in '?.onAttach'.
plot_fSta_distribution: no visible binding for global variable
‘..density..’
plot_pVal_distribution: no visible binding for global variable
‘..density..’
Undefined global functions or variables:
..density..
* 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 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
analyzeTPPTR 28.235 0.201 28.730
tpptrSplineFitAndTest 24.833 0.160 25.182
tppQCPlotsCorrelateExperiments 15.339 0.109 15.692
tpptrFTest 14.999 0.304 14.836
tpptrPlotSplines 15.106 0.107 15.239
tpp2dSplineFitAndTest 14.341 0.082 14.651
tpp2dCreateDRplots 11.162 0.069 11.378
analyze2DTPP 7.968 0.107 8.218
tpp2dMerge2dRef 7.188 0.108 7.408
tppccrPlotCurves 6.538 0.039 6.656
tpp2dCurveFit 6.428 0.078 6.600
analyzeTPPCCR 5.145 0.032 5.250
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/TPP.Rcheck/00check.log’
for details.
TPP.Rcheck/00install.out
* installing *source* package ‘TPP’ ... ** 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 (TPP)
TPP.Rcheck/tests/testthat.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-apple-darwin15.6.0 (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(testthat)
> library(TPP)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
>
> test_check("TPP")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 38 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.052 0.175 4.264
TPP.Rcheck/TPP-Ex.timings
| name | user | system | elapsed | |
| analyze2DTPP | 7.968 | 0.107 | 8.218 | |
| analyzeTPPCCR | 5.145 | 0.032 | 5.250 | |
| analyzeTPPTR | 28.235 | 0.201 | 28.730 | |
| tpp2dAddAdditionalInfo | 0.022 | 0.001 | 0.023 | |
| tpp2dCalcFractAbundance | 2.999 | 0.064 | 3.103 | |
| tpp2dComputeFoldChanges | 0.492 | 0.009 | 0.506 | |
| tpp2dCreateDRplots | 11.162 | 0.069 | 11.378 | |
| tpp2dCurveFit | 6.428 | 0.078 | 6.600 | |
| tpp2dExport | 0.041 | 0.007 | 0.052 | |
| tpp2dImport | 0.346 | 0.009 | 0.356 | |
| tpp2dMerge2dRef | 7.188 | 0.108 | 7.408 | |
| tpp2dNormalize | 0.607 | 0.019 | 0.632 | |
| tpp2dSplineFitAndTest | 14.341 | 0.082 | 14.651 | |
| tpp2dSplinePlot | 0.007 | 0.000 | 0.008 | |
| tpp2dTRReferenceObject | 0.018 | 0.000 | 0.021 | |
| tppDefaultTheme | 0.560 | 0.007 | 0.572 | |
| tppExport | 0.268 | 0.025 | 0.299 | |
| tppQCPlotsCorrelateExperiments | 15.339 | 0.109 | 15.692 | |
| tppccrCurveFit | 4.163 | 0.022 | 4.258 | |
| tppccrImport | 0.104 | 0.002 | 0.109 | |
| tppccrNormalize | 0.124 | 0.004 | 0.133 | |
| tppccrNormalizeToReference | 0.180 | 0.004 | 0.189 | |
| tppccrPlotCurves | 6.538 | 0.039 | 6.656 | |
| tppccrResultTable | 4.179 | 0.026 | 4.246 | |
| tppccrTransform | 0.184 | 0.005 | 0.188 | |
| tpptrAnalyzeMeltingCurves | 0.396 | 0.004 | 0.418 | |
| tpptrCurveFit | 0.991 | 0.017 | 1.032 | |
| tpptrDefaultNormReqs | 0.402 | 0.005 | 0.407 | |
| tpptrFTest | 14.999 | 0.304 | 14.836 | |
| tpptrFitSplines | 1.431 | 0.067 | 1.331 | |
| tpptrImport | 0.203 | 0.004 | 0.219 | |
| tpptrNormalize | 0.453 | 0.005 | 0.464 | |
| tpptrPlotSplines | 15.106 | 0.107 | 15.239 | |
| tpptrSplineFitAndTest | 24.833 | 0.160 | 25.182 | |
| tpptrTidyUpESets | 0.601 | 0.052 | 0.501 | |