| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:01 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 ELMER package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ELMER.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 594/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ELMER 2.23.0 (landing page) Tiago Chedraoui Silva
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: ELMER |
| Version: 2.23.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ELMER_2.23.0.tar.gz |
| StartedAt: 2023-02-07 00:44:20 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 01:24:21 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 2400.9 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: ELMER.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ELMER_2.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.23.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ELMER’ can be installed ... OK
* checking installed package size ... OK
* 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
* 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 ... WARNING
Missing or unexported object: 'TCGAbiolinks::GDCquery_Maf'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TCGA.pipe: warning in render_report(genome = genome, mode = mode, title
= paste0(disease, " report"), minSubgroupFrac = ifelse(mode ==
"supervised", 1, 0.2), mae = mae.path, direction = direction,
group.col = group.col, group1 = group1, group2 = group2, dir.out =
results.path, out_file = file.path(results.path, paste0(disease,
"_report.html"))): partial argument match of 'mae' to 'mae.file'
Stat.nonpara: no visible global function definition for 'head'
Stat.nonpara: no visible global function definition for 'tail'
Stat.nonpara.permu: no visible global function definition for 'head'
Stat.nonpara.permu: no visible global function definition for 'tail'
TFsurvival.plot: no visible global function definition for 'head'
TFsurvival.plot: no visible global function definition for 'tail'
addMutCol: no visible binding for global variable 'Hugo_Symbol'
calcDistNearestTSS: no visible binding for global variable
'DistanceTSS'
get.top.tf.by.pval: no visible global function definition for 'head'
getRegionNearGenes : f: no visible binding for global variable 'Side'
getRegionNearGenes: no visible binding for global variable 'ID'
getTFtargets: no visible binding for global variable 'TF'
Undefined global functions or variables:
DistanceTSS Hugo_Symbol ID Side TF head tail
Consider adding
importFrom("utils", "head", "tail")
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 ... WARNING
Codoc mismatches from documentation object 'render_report':
render_report
Code: function(title = "Report", mae.file, group.col, group1, group2,
direction, dir.out, genome = "hg38", mode =
"supervised", minSubgroupFrac = 0.2, minMetdiff = 0.3,
metfdr = 0.01, permu = 10000, rawpval = 0.01, pe =
0.01, nprobes = 10, lower.OR = 1.1, out_file =
file.path(getwd(), "report.html"), funcivar = FALSE)
Docs: function(title = "Report", mae.file, group.col, group1, group2,
direction, dir.out, genome = "hg38", mode =
"supervised", minSubgroupFrac = "20%", minMetdiff =
"0.3", metfdr = "0.01", permu = "10000", rawpval =
"0.01", pe = "0.01", nprobes = "10", lower.OR = "1.1",
out_file = file.path(getwd(), "report.html"), funcivar
= FALSE)
Mismatches in argument default values:
Name: 'minSubgroupFrac' Code: 0.2 Docs: "20%"
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ELMER-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TCGA.pipe
> ### Title: ELMER analysis pipeline for TCGA data.
> ### Aliases: TCGA.pipe
>
> ### ** Examples
>
> data <- ELMER:::getdata("elmer.data.example")
> TCGA.pipe(
+ disease = "LUSC",
+ data = data,
+ analysis = c("diffMeth","pair", "motif","TF.search"),
+ mode = "supervised",
+ group.col = "definition",
+ group1 = "Primary solid Tumor",
+ group2 = "Solid Tissue Normal",
+ diff.dir = c("hypo"),
+ dir.out = "pipe",
+ sig.dif = 0.0001,
+ pvalue = 1.0,
+ min.incidence = 0,
+ lower.OR = 0.0
+ )
=> supervised was selected: using all samples
=> Analysis results wil be save in: /home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo
Recording analysis information into: /home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo/TCGA.pipe_records.txt
----------------------------------------
* Get differential DNA methylation loci
----------------------------------------
ELMER will search for probes hypomethylated in group Primary solid Tumor (n:226) compared to Solid Tissue Normal (n:8)
ooo Arguments ooo
o Number of probes: 101
o Beta value difference cut-off: 1e-04
o FDR cut-off: 1
o Mode: unsupervised
o % of samples per group in each comparison: 1
o Min number of samples per group in each comparison: 5
o Nb of samples group1 in each comparison: 226
o Nb of samples group2 in each comparison: 8
Output direction: /home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo
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Saving results
Saving file as: /home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo/volcanoPlot.probes.hypo.png
Number of relevant probes found: 76
----------------
* Predict pairs
----------------
Rows: 76 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (1): probe
dbl (3): pvalue, Primary.solid.Tumor_Minus_Solid.Tissue.Normal, adjust.p
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Get nearby genes
Searching for the 20 near genes
Identifying gene position for each probe
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘analysis_data_input.Rmd’ using ‘UTF-8’... OK
‘analysis_diff_meth.Rmd’ using ‘UTF-8’... OK
‘analysis_get_pair.Rmd’ using ‘UTF-8’... OK
‘analysis_gui.Rmd’ using ‘UTF-8’... OK
‘analysis_motif_enrichment.Rmd’ using ‘UTF-8’... OK
‘analysis_regulatory_tf.Rmd’ using ‘UTF-8’... OK
‘index.Rmd’ using ‘UTF-8’... OK
‘input.Rmd’ using ‘UTF-8’... OK
‘pipe.Rmd’ using ‘UTF-8’... OK
‘plots_TF.Rmd’ using ‘UTF-8’... OK
‘plots_heatmap.Rmd’ using ‘UTF-8’... OK
‘plots_motif_enrichment.Rmd’ using ‘UTF-8’... OK
‘plots_scatter.Rmd’ using ‘UTF-8’... OK
‘plots_schematic.Rmd’ using ‘UTF-8’... OK
‘usecase.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ...
ELMER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ELMER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ELMER’ ... ** using staged installation ** R ** 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 (ELMER)
ELMER.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(ELMER)
Loading required package: ELMER.data
>
> test_check("ELMER")
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Killed
ELMER.Rcheck/ELMER-Ex.timings
| name | user | system | elapsed | |
| GetNearGenes | 11.193 | 0.108 | 11.319 | |