Dorothee Childs
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TPP |
| Branch: RELEASE_3_11 |
| Last Commit: e18f1c3 |
| Last Changed Date: 2020-10-06 01:47:24 -0400 (Tue, 06 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:56 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TPP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1817/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TPP 3.16.5 Dorothee Childs
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: TPP |
| Version: 3.16.5 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TPP_3.16.5.tar.gz |
| StartedAt: 2020-10-17 08:55:27 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 09:20:17 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1490.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TPP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TPP_3.16.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TPP.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TPP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TPP' version '3.16.5'
* 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 whether package 'TPP' can be installed ... OK
* checking installed package size ... NOTE
installed size is 13.1Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespace in Imports field not imported from: 'broom'
All declared Imports should be used.
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'.
fitSigmoidCCR: no visible global function definition for
'capture.output'
modelSelector: no visible binding for global variable 'testHypothesis'
modelSelector: no visible binding for global variable 'fitMetric'
modelSelector: no visible binding for global variable 'minMetric'
plot_fSta_distribution: no visible binding for global variable
'..density..'
plot_pVal_distribution: no visible binding for global variable
'..density..'
tpp2dCreateTPPTRreference: no visible binding for global variable
'meltcurve_plot'
tpp2dCreateTPPTRreference: no visible binding for global variable
'Protein_ID'
tpp2dExport: no visible binding for global variable 'temperature'
tpp2dImport: no visible binding for global variable 'temperature'
tpp2dNormalize: no visible binding for global variable 'temperature'
Undefined global functions or variables:
..density.. Protein_ID capture.output fitMetric meltcurve_plot
minMetric temperature testHypothesis
Consider adding
importFrom("utils", "capture.output")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tpptrSplineFitAndTest 13.60 0.03 31.59
tpp2dCreateDRplots 12.80 0.01 12.81
tppQCPlotsCorrelateExperiments 11.70 0.05 11.75
analyze2DTPP 9.45 0.07 9.55
tpp2dSplineFitAndTest 8.67 0.01 14.85
analyzeTPPTR 7.78 0.06 26.79
tppccrPlotCurves 6.59 0.01 6.62
tpp2dMerge2dRef 6.45 0.05 6.50
tpptrPlotSplines 6.06 0.00 17.43
tpp2dCurveFit 5.95 0.00 5.96
tpptrFTest 5.36 0.01 14.86
analyzeTPPCCR 5.20 0.02 5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tpptrSplineFitAndTest 15.82 0.05 38.72
tppQCPlotsCorrelateExperiments 12.64 0.08 12.72
tpp2dCreateDRplots 11.29 0.03 11.31
tpp2dSplineFitAndTest 10.28 0.03 16.76
tpp2dMerge2dRef 6.83 0.03 6.86
tpp2dCurveFit 6.79 0.03 6.83
tppccrPlotCurves 6.44 0.02 6.45
analyzeTPPTR 6.43 0.00 30.85
tpptrPlotSplines 6.39 0.02 29.53
tpptrFTest 6.08 0.00 15.62
analyze2DTPP 6.01 0.04 6.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.11-bioc/meat/TPP.Rcheck/00check.log'
for details.
TPP.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TPP_3.16.5.tar.gz && rm -rf TPP.buildbin-libdir && mkdir TPP.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TPP.buildbin-libdir TPP_3.16.5.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TPP_3.16.5.zip && rm TPP_3.16.5.tar.gz TPP_3.16.5.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
44 8056k 44 3584k 0 0 5441k 0 0:00:01 --:--:-- 0:00:01 5480k
100 8056k 100 8056k 0 0 5834k 0 0:00:01 0:00:01 --:--:-- 5859k
install for i386
* installing *source* package 'TPP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TPP'
finding HTML links ... done
TPP-defunct html
TPP-deprecated html
TPP html
TPPTR_reference_results_HepG2 html
analyze2DTPP html
finding level-2 HTML links ... done
analyzeTPPCCR html
analyzeTPPTR html
hdacCCR_config html
hdacCCR_data html
hdacCCR_smallExample html
hdacTR_config html
hdacTR_data html
hdacTR_resultsTable_smallExample html
hdacTR_smallExample html
panobinostat_2DTPP_config html
panobinostat_2DTPP_data html
panobinostat_2DTPP_smallExample html
resultTable html
tpp2dAddAdditionalInfo html
tpp2dCalcFractAbundance html
tpp2dComputeFoldChanges html
tpp2dCreateDRplots html
tpp2dCreateReport html
tpp2dCreateTPPTRreference html
tpp2dCurveFit html
tpp2dExport html
tpp2dExportPlots html
tpp2dImport html
tpp2dMerge2dRef html
tpp2dNormalize html
tpp2dPlotQChist html
tpp2dPlotQCpEC50 html
tpp2dSplineFitAndTest html
tpp2dSplinePlot html
tpp2dTRReferenceObject html
tppDefaultTheme html
tppExport html
tppQCPlotsCorrelateExperiments html
tppRefData html
tppccrCurveFit html
tppccrImport html
tppccrNormalize html
tppccrNormalizeToReference html
tppccrPlotCurves html
tppccrResultTable html
tppccrTransform html
tpptrAnalyzeMeltingCurves html
tpptrCurveFit html
tpptrDefaultNormReqs html
tpptrFTest html
tpptrFitSplines html
tpptrImport html
tpptrNormalize html
tpptrPlotSplines html
tpptrSplineFitAndTest html
tpptrTidyUpESets html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'TPP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TPP' as TPP_3.16.5.zip
* DONE (TPP)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TPP' successfully unpacked and MD5 sums checked
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TPP.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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
The following object is masked from 'package:testthat':
matches
>
> test_check("TPP")
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
== testthat results ===========================================================
[ OK: 285 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
229.32 3.82 515.62
|
TPP.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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
The following object is masked from 'package:testthat':
matches
>
> test_check("TPP")
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
[[2]]
[[3]]
[[1]]
== testthat results ===========================================================
[ OK: 285 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
222.54 3.04 445.35
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TPP.Rcheck/examples_i386/TPP-Ex.timings
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TPP.Rcheck/examples_x64/TPP-Ex.timings
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