| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:30 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 RTN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1764/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RTN 2.23.1 (landing page) Mauro Castro
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: RTN |
| Version: 2.23.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RTN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RTN_2.23.1.tar.gz |
| StartedAt: 2023-04-11 23:12:05 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 23:18:09 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 364.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RTN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RTN_2.23.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RTN.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘2.23.1’
* 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 ‘RTN’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
data 8.6Mb
* 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 loading without being on the library search path ... 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘RTN.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/RTN.Rcheck/00check.log’
for details.
RTN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RTN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘RTN’ ... ** using staged installation ** R ** data ** 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 (RTN)
RTN.Rcheck/tests/runTests.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> BiocGenerics:::testPackage("RTN")
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
-Preprocessing complete!
-Performing permutation analysis...
--For 5 regulons...
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-Permutation analysis complete!
-Performing bootstrap analysis...
--For 5 regulons...
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-Bootstrap analysis complete!
-Applying dpi filter...
-DPI filter complete!
-Preprocessing for input data...
--Mapping 'phenotype' to 'phenoIDs'...
--Removing genes without names or values in 'phenotype'...
--Removing duplicated genes...
--Mapping 'hits' to 'phenoIDs'...
--Removing duplicated hits...
--Mapping 'transcriptionalNetwork' annotation to 'phenotype'...
--Checking agreement between 'transcriptionalNetwork' and 'phenotype'... 99.8% !
--Removing 'hits' not listed in 'transcriptionalNetwork' universe...
--Extracting regulons...
-Preprocessing complete!
-Performing master regulatory analysis...
--For 5 regulons...
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-Master regulatory analysis complete
-Performing gene set enrichment analysis...
--For 5 regulons...
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-Gene set enrichment analysis complete
-Performing two-tailed GSEA analysis...
--For 5 regulons...
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-GSEA2 analysis complete
-Preprocessing for input data...
--Mapping 'expData' to 'rowAnnotation'...
--Checking 'regulatoryElements' in 'rowAnnotation'...
--Checking 'expData'...
-Preprocessing complete!
-Performing permutation analysis...
--For 2 regulons...
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-Permutation analysis complete!
-Performing bootstrap analysis...
--For 2 regulons...
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-Bootstrap analysis complete!
-Applying dpi filter...
-DPI filter complete!
-Preprocessing for input data...
--Checking modulators in the dataset...
--Extracting TF-targets...
--Applying modulator independence constraint...
--Applying modulator range constraint...
--Selecting subsamples...
-Estimating mutual information threshold...
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-Performing conditional mutual information analysis...
--For 2 tfs and 2 candidate modulator(s)
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-Conditional analysis complete!
RUNIT TEST PROTOCOL -- Tue Apr 11 23:16:07 2023
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
RTN RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
41.059 1.988 43.038
RTN.Rcheck/RTN-Ex.timings
| name | user | system | elapsed | |
| AVS-class | 0.000 | 0.000 | 0.001 | |
| RTN.data | 0.286 | 0.008 | 0.293 | |
| TNA-class | 0.001 | 0.000 | 0.001 | |
| TNI-class | 0 | 0 | 0 | |
| TNI.data | 0.342 | 0.004 | 0.345 | |
| avs.evse | 0.001 | 0.000 | 0.001 | |
| avs.get | 0.000 | 0.000 | 0.001 | |
| avs.pevse | 0.000 | 0.001 | 0.001 | |
| avs.plot1 | 0 | 0 | 0 | |
| avs.plot2 | 0 | 0 | 0 | |
| avs.rvse | 0.000 | 0.001 | 0.001 | |
| avs.vse | 0.000 | 0.001 | 0.001 | |
| tna.get | 0.229 | 0.018 | 0.248 | |
| tna.gsea1 | 0.309 | 0.024 | 0.333 | |
| tna.gsea2 | 0.243 | 0.004 | 0.247 | |
| tna.mra | 0.824 | 0.052 | 0.876 | |
| tna.plot.gsea1 | 0.249 | 0.003 | 0.254 | |
| tna.plot.gsea2 | 0.250 | 0.004 | 0.253 | |
| tni.alpha.adjust | 0.114 | 0.004 | 0.118 | |
| tni.annotate.regulons | 0.052 | 0.008 | 0.060 | |
| tni.annotate.samples | 0.055 | 0.004 | 0.059 | |
| tni.area3 | 0.050 | 0.008 | 0.058 | |
| tni.bootstrap | 0.061 | 0.004 | 0.065 | |
| tni.conditional | 0.055 | 0.004 | 0.058 | |
| tni.constructor | 0.167 | 0.000 | 0.167 | |
| tni.dpi.filter | 0.053 | 0.004 | 0.056 | |
| tni.get | 0.062 | 0.012 | 0.074 | |
| tni.graph | 0.055 | 0.000 | 0.055 | |
| tni.gsea2 | 0.055 | 0.000 | 0.055 | |
| tni.overlap.genesets | 0.056 | 0.000 | 0.056 | |
| tni.permutation | 0.053 | 0.004 | 0.057 | |
| tni.plot.checks | 0.059 | 0.000 | 0.059 | |
| tni.plot.sre | 0.058 | 0.000 | 0.059 | |
| tni.preprocess | 0 | 0 | 0 | |
| tni.prune | 0.065 | 0.015 | 0.081 | |
| tni.regulon.summary | 0.048 | 0.008 | 0.056 | |
| tni.replace.samples | 0 | 0 | 0 | |
| tni.sre | 0.058 | 0.000 | 0.058 | |
| tni2tna.preprocess | 0.252 | 0.004 | 0.256 | |
| upgradeTNA | 0 | 0 | 0 | |
| upgradeTNI | 0 | 0 | 0 | |