Mauro Castro
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/RTN |
| git_branch: devel |
| git_last_commit: 84b09ed |
| git_last_commit_date: 2024-10-29 09:47:19 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 | ||||
| Package 1798/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RTN 2.31.0 (landing page) Mauro Castro
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RTN |
| Version: 2.31.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTN_2.31.0.tar.gz |
| StartedAt: 2024-11-28 01:49:47 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 01:56:57 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 430.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTN_2.31.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RTN.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘2.31.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... INFO
installed size is 9.8Mb
sub-directories of 1Mb or more:
R 1.0Mb
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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) TNI.data.Rd:14-15: Lost braces
14 | \code{stni}{A TNI-class with a subset of samples and genes from
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
tni.area3.Rd: aREA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/RTN.Rcheck/00check.log’
for details.
RTN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RTN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Permutation analysis complete!
-Performing bootstrap analysis...
--For 5 regulons...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-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...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Master regulatory analysis complete
-Performing gene set enrichment analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Gene set enrichment analysis complete
-Performing two-tailed GSEA analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-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...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Permutation analysis complete!
-Performing bootstrap analysis...
--For 2 regulons...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-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...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Performing conditional mutual information analysis...
--For 2 tfs and 2 candidate modulator(s)
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
-Conditional analysis complete!
RUNIT TEST PROTOCOL -- Thu Nov 28 01:56:49 2024
***********************************************
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
30.575 3.338 34.069
RTN.Rcheck/RTN-Ex.timings
| name | user | system | elapsed | |
| AVS-class | 0.000 | 0.000 | 0.001 | |
| RTN.data | 0.205 | 0.009 | 0.216 | |
| TNA-class | 0.001 | 0.000 | 0.001 | |
| TNI-class | 0.000 | 0.000 | 0.001 | |
| TNI.data | 0.279 | 0.005 | 0.285 | |
| avs.evse | 0 | 0 | 0 | |
| avs.get | 0 | 0 | 0 | |
| avs.pevse | 0.000 | 0.000 | 0.001 | |
| avs.plot1 | 0.001 | 0.000 | 0.001 | |
| avs.plot2 | 0 | 0 | 0 | |
| avs.rvse | 0.000 | 0.001 | 0.000 | |
| avs.vse | 0.000 | 0.001 | 0.001 | |
| tna.get | 0.186 | 0.004 | 0.190 | |
| tna.gsea1 | 0.191 | 0.006 | 0.197 | |
| tna.gsea2 | 0.251 | 0.008 | 0.258 | |
| tna.mra | 0.195 | 0.004 | 0.198 | |
| tna.plot.gsea1 | 0.193 | 0.005 | 0.198 | |
| tna.plot.gsea2 | 0.624 | 0.008 | 0.633 | |
| tni.alpha.adjust | 0.083 | 0.001 | 0.084 | |
| tni.annotate.regulons | 0.042 | 0.004 | 0.047 | |
| tni.annotate.samples | 0.042 | 0.002 | 0.044 | |
| tni.area3 | 0.043 | 0.004 | 0.047 | |
| tni.bootstrap | 0.042 | 0.003 | 0.046 | |
| tni.conditional | 0.042 | 0.004 | 0.047 | |
| tni.constructor | 0.129 | 0.017 | 0.147 | |
| tni.dpi.filter | 0.044 | 0.004 | 0.048 | |
| tni.get | 0.039 | 0.002 | 0.042 | |
| tni.graph | 0 | 0 | 0 | |
| tni.gsea2 | 0.049 | 0.009 | 0.058 | |
| tni.overlap.genesets | 0.040 | 0.004 | 0.044 | |
| tni.permutation | 0.039 | 0.003 | 0.041 | |
| tni.plot.checks | 0.039 | 0.004 | 0.044 | |
| tni.plot.sre | 0.040 | 0.004 | 0.044 | |
| tni.preprocess | 0.001 | 0.000 | 0.000 | |
| tni.prune | 0.039 | 0.004 | 0.042 | |
| tni.regulon.summary | 0.046 | 0.007 | 0.053 | |
| tni.replace.samples | 0 | 0 | 0 | |
| tni.sre | 0.040 | 0.002 | 0.042 | |
| tni2tna.preprocess | 0.186 | 0.003 | 0.190 | |
| upgradeTNA | 0 | 0 | 0 | |
| upgradeTNI | 0 | 0 | 0 | |