Mattia Chiesa
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DaMiRseq |
| Branch: RELEASE_3_8 |
| Last Commit: f5f6030 |
| Last Changed Date: 2019-01-16 09:41:14 -0400 (Wed, 16 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:39 -0400 (Sat, 13 Apr 2019).
| Package 368/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DaMiRseq 1.6.2 Mattia Chiesa
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DaMiRseq |
| Version: 1.6.2 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DaMiRseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DaMiRseq_1.6.2.tar.gz |
| StartedAt: 2019-04-13 01:37:37 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:46:40 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 542.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DaMiRseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DaMiRseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DaMiRseq_1.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DaMiRseq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.6.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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.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.EnsembleLearning2cl_Training: no visible binding for global
variable 'Classifiers'
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
variable 'Accuracy'
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
variable 'MCC'
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
variable 'Sensitivity'
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
variable 'Specificity'
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
variable 'PPV'
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
variable 'NPV'
DaMiR.EnsembleLearning2cl_Training: 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'
Undefined global functions or variables:
Accuracy Classifiers MCC NPV PPV Sensitivity Specificity X1 X2 colSds
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DaMiRseq_1.6.2.tar.gz && rm -rf DaMiRseq.buildbin-libdir && mkdir DaMiRseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DaMiRseq.buildbin-libdir DaMiRseq_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DaMiRseq_1.6.2.zip && rm DaMiRseq_1.6.2.tar.gz DaMiRseq_1.6.2.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
0 2847k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2847k 100 2847k 0 0 28.2M 0 --:--:-- --:--:-- --:--:-- 28.9M
install for i386
* installing *source* package 'DaMiRseq' ...
** 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.EnsembleLearning html
DaMiR.EnsembleLearning2cl html
DaMiR.EnsembleLearning2cl_Predict html
DaMiR.EnsembleLearning2cl_Test html
DaMiR.EnsembleLearning2cl_Training 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.SV html
DaMiR.SVadjust html
DaMiR.corrplot html
DaMiR.goldenDice 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
'DaMiRseq.Rnw' using 'UTF-8'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DaMiRseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DaMiRseq' as DaMiRseq_1.6.2.zip
* DONE (DaMiRseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DaMiRseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
DaMiRseq.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, 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: 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
Loading required package: BiocParallel
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
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.
15 Genes have been discarded for classification 985 Genes remained.
All the genes have been discarded!!!
th.VIP argument is too high. Please choose a lower level of th.VIPPlease wait. This operation will take about 21 seconds (i.e. about 0 minutes).Your dataset has:
100 Features;
11 Samples, divided in: 5 A 6 B
3 variables: a b class ;
'class' included.
Your dataset has:
100 Features;
11 Samples, divided in: 5 A 6 B
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: 292 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
26.90 2.46 29.26
|
DaMiRseq.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, 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: 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
Loading required package: BiocParallel
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
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.
15 Genes have been discarded for classification 985 Genes remained.
All the genes have been discarded!!!
th.VIP argument is too high. Please choose a lower level of th.VIPPlease wait. This operation will take about 21 seconds (i.e. about 0 minutes).Your dataset has:
100 Features;
11 Samples, divided in: 5 A 6 B
3 variables: a b class ;
'class' included.
Your dataset has:
100 Features;
11 Samples, divided in: 5 A 6 B
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: 292 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
27.03 1.28 27.31
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DaMiRseq.Rcheck/examples_i386/DaMiRseq-Ex.timings
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DaMiRseq.Rcheck/examples_x64/DaMiRseq-Ex.timings
|