Mattia Chiesa
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DaMiRseq |
| Branch: RELEASE_3_11 |
| Last Commit: 43c49ad |
| Last Changed Date: 2020-04-27 15:06:15 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:24 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE DaMiRseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 420/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DaMiRseq 2.0.0 Mattia Chiesa
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DaMiRseq |
| Version: 2.0.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DaMiRseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DaMiRseq_2.0.0.tar.gz |
| StartedAt: 2020-10-17 03:09:06 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:21:41 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 755.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DaMiRseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DaMiRseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DaMiRseq_2.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DaMiRseq.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 'DaMiRseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DaMiRseq' version '2.0.0'
* 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 whether package 'DaMiRseq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 5.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DaMiR.Allplot: warning in pheatmap(sampleDistMatrix,
clustering_distance_rows = mydist, clustering_distance_cols = mydist,
col = colors, breaks = seque, annotation_col = df): partial argument
match of 'col' to 'color'
DaMiR.Clustplot: warning in pheatmap(count_data,
clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale
= "row", col = colors, annotation_col = df): partial argument match
of 'col' to 'color'
DaMiR.Allplot: no visible binding for global variable 'X1'
DaMiR.Allplot: no visible binding for global variable 'X2'
DaMiR.Allplot: no visible binding for global variable 'value'
DaMiR.Allplot: no visible binding for global variable 'variable'
DaMiR.EnsembleLearning2cl: no visible binding for global variable
'Classifiers'
DaMiR.EnsembleLearning2cl: no visible binding for global variable
'Accuracy'
DaMiR.EnsembleLearning2cl: no visible binding for global variable 'MCC'
DaMiR.EnsembleLearning2cl: no visible binding for global variable
'Specificity'
DaMiR.EnsembleLearning2cl: no visible binding for global variable
'Sensitivity'
DaMiR.EnsembleLearning2cl: no visible binding for global variable 'PPV'
DaMiR.EnsembleLearning2cl: no visible binding for global variable 'NPV'
DaMiR.EnsembleLearning2cl: no visible global function definition for
'colSds'
DaMiR.EnsembleLearningNcl: no visible binding for global variable
'Classifiers'
DaMiR.EnsembleLearningNcl: no visible binding for global variable
'Accuracy'
DaMiR.EnsembleLearningNcl: no visible global function definition for
'colSds'
DaMiR.MDSplot: no visible binding for global variable 'X1'
DaMiR.MDSplot: no visible binding for global variable 'X2'
DaMiR.ModelSelect: no visible binding for global variable 'Accuracy'
DaMiR.ModelSelect: no visible binding for global variable
'N.predictors'
DaMiR.ModelSelect: no visible binding for global variable 'counts'
DaMiR.iTSadjust: no visible binding for global variable 'value'
DaMiR.iTSadjust: no visible binding for global variable 'variable'
DaMiR.iTSnorm: no visible binding for global variable 'value'
DaMiR.iTSnorm: no visible binding for global variable 'variable'
Undefined global functions or variables:
Accuracy Classifiers MCC N.predictors NPV PPV Sensitivity Specificity
X1 X2 colSds counts value variable
* 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
DaMiR.Allplot 4.81 0.57 5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DaMiR.Allplot 5 0.23 5.24
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/DaMiRseq.Rcheck/00check.log'
for details.
DaMiRseq.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/DaMiRseq_2.0.0.tar.gz && rm -rf DaMiRseq.buildbin-libdir && mkdir DaMiRseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DaMiRseq.buildbin-libdir DaMiRseq_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DaMiRseq_2.0.0.zip && rm DaMiRseq_2.0.0.tar.gz DaMiRseq_2.0.0.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
100 3401k 100 3401k 0 0 24.9M 0 --:--:-- --:--:-- --:--:-- 26.3M
install for i386
* installing *source* package 'DaMiRseq' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DaMiRseq'
finding HTML links ... done
DaMiR.Allplot html
DaMiR.Clustplot html
DaMiR.EnsL_Predict html
DaMiR.EnsL_Test html
DaMiR.EnsL_Train html
DaMiR.EnsembleLearning html
DaMiR.EnsembleLearning2cl html
DaMiR.EnsembleLearningNcl html
DaMiR.FBest html
DaMiR.FReduct html
finding level-2 HTML links ... done
DaMiR.FSelect html
DaMiR.FSort html
DaMiR.MDSplot html
DaMiR.ModelSelect html
DaMiR.SV html
DaMiR.SVadjust html
DaMiR.corrplot html
DaMiR.goldenDice html
DaMiR.iTSadjust html
DaMiR.iTSnorm html
DaMiR.makeSE html
DaMiR.normalization html
DaMiR.sampleFilt html
DaMiR.transpose html
SE html
SEtest_norm html
data_min html
data_norm html
data_reduced html
data_relief html
df html
selected_features html
sv 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 'DaMiRseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DaMiRseq' as DaMiRseq_2.0.0.zip
* DONE (DaMiRseq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DaMiRseq' successfully unpacked and MD5 sums checked
|
DaMiRseq.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(DaMiRseq)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: ggplot2
>
> test_check("DaMiRseq")
10 Predictors have been selected for classification
3 Predictors have been selected for classification
100 Highly correlated features have been discarded for classification.
0 Features remained.
100 Highly correlated features have been discarded for classification.
0 Features remained.
Your dataset has:
100 Features;
11 Samples, divided in:
3 variables: a b class ;
'class' included.
Your dataset has:
100 Features;
11 Samples, divided in:
3 variables: a b class ;
'class' included.
0 Features have been filtered out by espression. 100 Features remained.
0 'Hypervariant' Features have been filtered out. 100 Features remained.
Performing Normalization by 'vst' with dispersion parameter: parametric
0 Samples have been excluded by averaged Sample-per-Sample correlation.
40 Samples remained.
The number of SVs identified, which explain 95 % of Variance, is: 4
All the sv have been used to adjust the dataAll the sv have been used to adjust the data== testthat results ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
25.71 2.35 31.14
|
DaMiRseq.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(DaMiRseq)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: ggplot2
>
> test_check("DaMiRseq")
10 Predictors have been selected for classification
3 Predictors have been selected for classification
100 Highly correlated features have been discarded for classification.
0 Features remained.
100 Highly correlated features have been discarded for classification.
0 Features remained.
Your dataset has:
100 Features;
11 Samples, divided in:
3 variables: a b class ;
'class' included.
Your dataset has:
100 Features;
11 Samples, divided in:
3 variables: a b class ;
'class' included.
0 Features have been filtered out by espression. 100 Features remained.
0 'Hypervariant' Features have been filtered out. 100 Features remained.
Performing Normalization by 'vst' with dispersion parameter: parametric
0 Samples have been excluded by averaged Sample-per-Sample correlation.
40 Samples remained.
The number of SVs identified, which explain 95 % of Variance, is: 4
All the sv have been used to adjust the dataAll the sv have been used to adjust the data== testthat results ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
27.50 1.67 31.29
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DaMiRseq.Rcheck/examples_i386/DaMiRseq-Ex.timings
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DaMiRseq.Rcheck/examples_x64/DaMiRseq-Ex.timings
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