Olivier Gevaert
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/AMARETTO |
| Branch: RELEASE_3_10 |
| Last Commit: 8b0d34e |
| Last Changed Date: 2019-11-26 13:32:25 -0400 (Tue, 26 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:02 -0400 (Wed, 15 Apr 2020).
| Package 49/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AMARETTO 1.2.0 Olivier Gevaert
| malbec1 | Linux (Ubuntu 18.04.4 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: AMARETTO |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AMARETTO.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings AMARETTO_1.2.0.tar.gz |
| StartedAt: 2020-04-15 01:14:03 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:22:47 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 524.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AMARETTO.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AMARETTO.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings AMARETTO_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/AMARETTO.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AMARETTO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AMARETTO' version '1.2.0'
* 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 'AMARETTO' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 1.5Mb
extdata 3.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Apache License (== 2.0) + file LICENSE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'knitr'
A package should be listed in only one of these fields.
'LinkingTo' field is unused: package has no 'src' directory
* 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
AMARETTO_HTMLreport: no visible binding for global variable 'ModuleNr'
AMARETTO_HTMLreport: no visible binding for global variable 'Weights'
AMARETTO_HTMLreport: no visible binding for global variable
'RegulatorIDs'
AMARETTO_HTMLreport: no visible binding for global variable 'TargetIDs'
AMARETTO_HTMLreport: no visible binding for global variable 'moduleNr'
AMARETTO_HTMLreport: no visible binding for global variable 'Testset'
AMARETTO_HTMLreport: no visible binding for global variable 'padj'
AMARETTO_HTMLreport: no visible binding for global variable
'n_Overlapping'
AMARETTO_HTMLreport: no visible binding for global variable
'NumberGenes'
AMARETTO_HTMLreport: no visible binding for global variable
'overlap_perc'
AMARETTO_HTMLreport: no visible binding for global variable 'Geneset'
AMARETTO_HTMLreport: no visible binding for global variable
'Description'
AMARETTO_HTMLreport: no visible binding for global variable
'Geneset_length'
AMARETTO_HTMLreport: no visible binding for global variable
'Overlapping_genes'
AMARETTO_HTMLreport: no visible binding for global variable 'p_value'
AMARETTO_HTMLreport: no visible binding for global variable 'p.value'
AMARETTO_HTMLreport: no visible binding for global variable 'q.value'
AMARETTO_HTMLreport: no visible binding for global variable 'Genes'
AMARETTO_HTMLreport: no visible binding for global variable 'value'
AMARETTO_HTMLreport: no visible binding for global variable 'Type'
AMARETTO_HTMLreport: no visible binding for global variable 'Color'
AMARETTO_HTMLreport: no visible binding for global variable 'Modules'
AMARETTO_HTMLreport: no visible binding for global variable
'dt_gensesetsall'
GeneSetDescription: no visible binding for global variable
'MsigdbMapping'
GeneSetDescription : <anonymous>: no visible binding for global
variable 'MsigdbMapping'
GmtFromModules: no visible binding for global variable 'value'
GmtFromModules: no visible binding for global variable 'variable'
GmtFromModules: no visible binding for global variable 'GeneNames'
HyperGTestGeneEnrichment: no visible binding for global variable 'i'
HyperGTestGeneEnrichment: no visible binding for global variable 'j'
read_gct: no visible binding for global variable 'Description'
Undefined global functions or variables:
Color Description GeneNames Genes Geneset Geneset_length ModuleNr
Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs
TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr
n_Overlapping overlap_perc p.value p_value padj q.value 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 ... NOTE
Note: found 152 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
AMARETTO_Download 11.88 1.57 23.20
AMARETTO_VisualizeModule 2.45 0.06 14.83
plot_run_history 1.60 0.05 12.16
AMARETTO_CreateRegulatorPrograms 1.08 0.03 12.08
AMARETTO_EvaluateTestSet 0.97 0.06 11.85
AMARETTO_ExportResults 0.89 0.06 10.18
AMARETTO_CreateModuleData 0.77 0.09 11.56
AMARETTO_Run 0.64 0.00 9.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
AMARETTO_Download 13.94 1.24 18.35
AMARETTO_VisualizeModule 2.98 0.03 14.96
AMARETTO_CreateModuleData 1.64 0.05 12.23
plot_run_history 1.21 0.04 11.15
AMARETTO_Run 1.11 0.00 12.22
AMARETTO_EvaluateTestSet 1.06 0.04 10.72
AMARETTO_ExportResults 1.02 0.02 12.19
AMARETTO_CreateRegulatorPrograms 0.87 0.06 13.74
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/AMARETTO.Rcheck/00check.log'
for details.
AMARETTO.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/AMARETTO_1.2.0.tar.gz && rm -rf AMARETTO.buildbin-libdir && mkdir AMARETTO.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AMARETTO.buildbin-libdir AMARETTO_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL AMARETTO_1.2.0.zip && rm AMARETTO_1.2.0.tar.gz AMARETTO_1.2.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 5472k 100 5472k 0 0 9446k 0 --:--:-- --:--:-- --:--:-- 9501k
install for i386
* installing *source* package 'AMARETTO' ...
** 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 'AMARETTO'
finding HTML links ... done
AMARETTO_CreateModuleData html
AMARETTO_CreateRegulatorPrograms html
AMARETTO_Download html
AMARETTO_EvaluateTestSet html
AMARETTO_ExportResults html
AMARETTO_HTMLreport html
AMARETTO_Initialize html
AMARETTO_LarsenBased html
AMARETTO_LearnRegulatoryProgramsLarsen
html
AMARETTO_Preprocess html
AMARETTO_ReassignGenesToClusters html
AMARETTO_Run html
AMARETTO_VisualizeModule html
BatchData html
Beta.NA html
ComBat_NoFiles html
CreateRegulatorData html
Driver_Genes html
FindTranscriptionallyPredictive_CNV html
GeneSetDescription html
GmtFromModules html
HyperGTestGeneEnrichment html
L html
Lambda_Sequence html
MsigdbMapping html
Preprocess_MAdata html
ProcessedDataLIHC html
Save_CancerSite html
TCGA_BatchCorrection_MolecularData html
TCGA_GENERIC_BatchCorrection html
TCGA_GENERIC_CheckBatchEffect html
TCGA_GENERIC_CleanUpSampleNames html
TCGA_GENERIC_GetSampleGroups html
TCGA_GENERIC_MergeData html
TCGA_Load_GISTICdata html
TCGA_Load_MolecularData html
aprior html
bprior html
build.design html
cacheResource html
computeGisticURL html
design.mat html
filter.absent html
geneFiltering html
get_firehoseData html
int.eprior html
it.sol html
list.batch html
plot_run_history html
postmean html
postvar html
printf html
readGMT html
read_gct html
trim.dat html
write_gct 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 'AMARETTO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AMARETTO' as AMARETTO_1.2.0.zip
* DONE (AMARETTO)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'AMARETTO' successfully unpacked and MD5 sums checked
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AMARETTO.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(AMARETTO)
Loading required package: impute
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: dplyr
Attaching package: 'dplyr'
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: ComplexHeatmap
Loading required package: grid
========================================
ComplexHeatmap version 2.2.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
========================================
>
> test_check("AMARETTO")
Found 10 CNV driver genes.
Found 89 MethylMix driver genes.
Found a total of 96 unique drivers with your selected method.
Running AMARETTO on 402 genes and 45 samples.
Stopping if less then 4.02 genes reassigned.
Autoregulation is turned ON.
Elapsed time is 10.340000 seconds
Average nr of regulators per module: 9.200000
Elapsed time is 0.380000 seconds
Nr of reassignments is: 48
Elapsed time is 1.690000 seconds
Average nr of regulators per module: 9.100000
Elapsed time is 0.340000 seconds
Nr of reassignments is: 9
Elapsed time is 1.670000 seconds
Average nr of regulators per module: 9.600000
Elapsed time is 0.370000 seconds
Nr of reassignments is: 8
Elapsed time is 1.740000 seconds
Average nr of regulators per module: 9.700000
Elapsed time is 0.370000 seconds
Nr of reassignments is: 8
Elapsed time is 1.750000 seconds
Average nr of regulators per module: 9.300000
Elapsed time is 0.350000 seconds
Nr of reassignments is: 4
Elapsed time is 19.020000 seconds
== testthat results ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.73 1.18 29.21
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AMARETTO.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(AMARETTO)
Loading required package: impute
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: dplyr
Attaching package: 'dplyr'
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: ComplexHeatmap
Loading required package: grid
========================================
ComplexHeatmap version 2.2.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
========================================
>
> test_check("AMARETTO")
Found 10 CNV driver genes.
Found 89 MethylMix driver genes.
Found a total of 96 unique drivers with your selected method.
Running AMARETTO on 402 genes and 45 samples.
Stopping if less then 4.02 genes reassigned.
Autoregulation is turned ON.
Elapsed time is 12.500000 seconds
Average nr of regulators per module: 9.200000
Elapsed time is 0.250000 seconds
Nr of reassignments is: 48
Elapsed time is 1.690000 seconds
Average nr of regulators per module: 9.100000
Elapsed time is 0.330000 seconds
Nr of reassignments is: 9
Elapsed time is 2.000000 seconds
Average nr of regulators per module: 9.600000
Elapsed time is 0.310000 seconds
Nr of reassignments is: 8
Elapsed time is 2.030000 seconds
Average nr of regulators per module: 9.700000
Elapsed time is 0.280000 seconds
Nr of reassignments is: 8
Elapsed time is 1.780000 seconds
Average nr of regulators per module: 9.300000
Elapsed time is 0.330000 seconds
Nr of reassignments is: 4
Elapsed time is 21.520000 seconds
== testthat results ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.82 0.67 33.78
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AMARETTO.Rcheck/examples_i386/AMARETTO-Ex.timings
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AMARETTO.Rcheck/examples_x64/AMARETTO-Ex.timings
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