| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-16 11:07:23 -0400 (Wed, 16 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4060 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4081 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4133 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 577/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ELMER 2.19.0 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: ELMER |
| Version: 2.19.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ELMER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ELMER_2.19.0.tar.gz |
| StartedAt: 2022-03-15 18:52:37 -0400 (Tue, 15 Mar 2022) |
| EndedAt: 2022-03-15 19:00:43 -0400 (Tue, 15 Mar 2022) |
| EllapsedTime: 485.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ELMER.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ELMER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ELMER_2.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ELMER/DESCRIPTION' ... OK
* this is package 'ELMER' version '2.19.0'
* 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 '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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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.enriched.motif: no visible global function definition for 'ranges'
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 ranges 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 ... OK
* 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: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo
Recording analysis information into: D:/biocbuild/bbs-3.15-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: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo
ooooooooooooooooo
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Saving results
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
File saved: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo/hypo.probes_nearGenes.rda
Identify putative probe-gene pair for hypomethylated probes
Using pre-defined groups. U (unmethylated): Primary solid Tumor, M (methylated): Solid Tissue Normal
-------------------
* Filtering probes
-------------------
For more information see function preAssociationProbeFiltering
Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3.
Removing 47 probes out of 101
Calculating Pp (probe - gene) for all nearby genes
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File created: D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/Result/LUSC/definition_Primary solid Tumor_vs_Solid Tissue Normal/hypo/getPair.hypo.all.pairs.statistic.csv
---------------
* Motif search
---------------
Identify enriched motif for hypomethylated probes
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|====================================================|100% Completed after 1 s
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
------------------------------------
** Filtering motifs based on quality
------------------------------------
Number of enriched motifs with quality:
-----------
=> A: 220
=> B: 98
=> C: 141
=> D: 269
=> S: 0
-----------
Considering only motifs with quality from A up to DS: 728 motifs are enriched.
---------------------------------------------------
* Adding enriched motifs to significant pairs file
---------------------------------------------------
Adding coordinates for probes and genes from the provided data
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': could not find function "ranges"
Calls: TCGA.pipe ... <Anonymous> -> as.data.frame -> .handleSimpleError -> h
Execution halted
* 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:
== Failed tests ================================================================
-- Error (test-pipe.R:5:3): TCGA.pipe is working -------------------------------
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': could not find function "ranges"
Backtrace:
x
1. +-ELMER::TCGA.pipe(...) at test-pipe.R:5:2
2. | +-base::do.call(...)
3. | \-ELMER `<fn>`(...)
4. | \-BiocGenerics::as.data.frame(ranges(getMet(data)))
5. \-base::.handleSimpleError(...)
6. \-base h(simpleError(msg, call))
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted
* 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 ERRORs, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/00check.log'
for details.
ELMER.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ELMER
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ELMER' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ELMER'
finding HTML links ... done
ELMER html
Get.Pvalue.p html
GetNearGenes html
Stat.diff.meth html
Stat.nonpara html
Stat.nonpara.permu html
TCGA.pipe html
TF.rank.plot html
TFsurvival.plot html
addDistNearestTSS html
addMutCol html
calcDistNearestTSS html
calculateEnrichement html
createBigWigDNAmetArray html
createIGVtrack html
createMAE html
createMotifRelevantTfs html
createSummaryDocument html
createTSVTemplates html
findMotifRegion html
get.TFs html
get.diff.meth html
get.enriched.motif html
get.feature.probe html
get.pair html
get.permu html
get.tab html
get.tabs html
get450K html
getClinic html
getExp html
getExpSamples html
getGeneID html
getMet html
getMetSamples html
getRNAseq html
getRandomPairs html
getRegionNearGenes html
getSymbol html
getTCGA html
getTF html
getTFBindingSites html
getTFtargets html
getTSS html
heatmapGene html
heatmapPairs html
lm_eqn html
metBoxPlot html
motif.enrichment.plot html
preAssociationProbeFiltering html
promoterMeth html
render_report html
scatter html
scatter.plot html
schematic.plot html
summarizeTF 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
* DONE (ELMER)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RNAmodR' is missing or broken
done
ELMER.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(ELMER)
Loading required package: ELMER.data
>
> test_check("ELMER")
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[ FAIL 1 | WARN 5 | SKIP 0 | PASS 112 ]
== Failed tests ================================================================
-- Error (test-pipe.R:5:3): TCGA.pipe is working -------------------------------
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': could not find function "ranges"
Backtrace:
x
1. +-ELMER::TCGA.pipe(...) at test-pipe.R:5:2
2. | +-base::do.call(...)
3. | \-ELMER `<fn>`(...)
4. | \-BiocGenerics::as.data.frame(ranges(getMet(data)))
5. \-base::.handleSimpleError(...)
6. \-base h(simpleError(msg, call))
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted
ELMER.Rcheck/ELMER-Ex.timings
| name | user | system | elapsed | |
| GetNearGenes | 6.86 | 0.51 | 7.47 | |