| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:18 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the AMARETTO package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 44/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AMARETTO 1.15.0 (landing page) Olivier Gevaert
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
| Package: AMARETTO |
| Version: 1.15.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AMARETTO.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings AMARETTO_1.15.0.tar.gz |
| StartedAt: 2022-12-28 21:30:37 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 21:34:35 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 238.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: AMARETTO.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AMARETTO.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings AMARETTO_1.15.0.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/AMARETTO.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AMARETTO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AMARETTO' version '1.15.0'
* 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 6.1Mb
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
* 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 ... WARNING
Codoc mismatches from documentation object 'get_firehoseData':
get_firehoseData
Code: function(TargetDirectory = "./", TCGA_acronym_uppercase =
"LUAD", dataType = "stddata", dataFileTag =
"mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
"tar.gz", gdacURL =
"https://gdac.broadinstitute.org/runs/", untarUngzip =
TRUE, printDisease_abbr = FALSE)
Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase =
"LUAD", dataType = "stddata", dataFileTag =
"mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
"tar.gz", gdacURL =
"http://gdac.broadinstitute.org/runs/", untarUngzip =
TRUE, printDisease_abbr = FALSE)
Mismatches in argument default values:
Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/"
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'AMARETTO-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AMARETTO_Download
> ### Title: AMARETTO_Download
> ### Aliases: AMARETTO_Download
>
> ### ** Examples
>
> TargetDirectory <- file.path(getwd(),"Downloads/");dir.create(TargetDirectory)
> CancerSite <- 'CHOL'
> DataSetDirectories <- AMARETTO_Download(CancerSite,TargetDirectory = TargetDirectory)
Downloading Gene Expression and Copy Number Variation data for: CHOL
This TCGA cancer site/type was not tested, continue at your own risk.
Searching CNV data for:CHOL
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
NOTE: the TCGA run dated NA for CHOL isn't available for download yet.
Taking the run dated just before this one.
Error in get_firehoseData(TargetDirectory = TargetDirectory, TCGA_acronym_uppercase = TCGA_acronym_uppercase, :
Not Found (HTTP 404). Failed to FALIED to download input TCGA data type.
Calls: AMARETTO_Download -> get_firehoseData -> <Anonymous>
Execution halted
* 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: 1 ERROR, 1 WARNING, 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/AMARETTO.Rcheck/00check.log'
for details.
AMARETTO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL AMARETTO ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * 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 ** 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 * DONE (AMARETTO)
AMARETTO.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 2.15.0
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 either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
The new InteractiveComplexHeatmap package can directly export static
complex heatmaps into an interactive Shiny app with zero effort. Have a try!
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
>
> 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 9.850000 seconds
Average nr of regulators per module: 9.200000
Elapsed time is 0.230000 seconds
Nr of reassignments is: 48
Elapsed time is 1.110000 seconds
Average nr of regulators per module: 9.100000
Elapsed time is 0.230000 seconds
Nr of reassignments is: 9
Elapsed time is 1.100000 seconds
Average nr of regulators per module: 9.600000
Elapsed time is 0.190000 seconds
Nr of reassignments is: 8
Elapsed time is 1.060000 seconds
Average nr of regulators per module: 9.700000
Elapsed time is 0.200000 seconds
Nr of reassignments is: 8
Elapsed time is 1.060000 seconds
Average nr of regulators per module: 9.300000
Elapsed time is 0.220000 seconds
Nr of reassignments is: 4
Elapsed time is 15.250000 seconds
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
>
> proc.time()
user system elapsed
9.42 0.85 24.60
AMARETTO.Rcheck/AMARETTO-Ex.timings
| name | user | system | elapsed | |
| AMARETTO_CreateModuleData | 1.11 | 0.02 | 11.29 | |
| AMARETTO_CreateRegulatorPrograms | 0.49 | 0.09 | 10.04 | |