Mauro Castro
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RTN |
| Branch: RELEASE_3_8 |
| Last Commit: ccc7d72 |
| Last Changed Date: 2019-03-25 22:20:20 -0400 (Mon, 25 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:05 -0400 (Sat, 13 Apr 2019).
| Package 1362/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTN 2.6.3 Mauro Castro
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RTN |
| Version: 2.6.3 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RTN_2.6.3.tar.gz |
| StartedAt: 2019-04-13 05:14:22 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:19:55 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 332.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RTN_2.6.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTN.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTN' version '2.6.3'
* 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 whether package 'RTN' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
data 8.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTN.Rcheck/00check.log'
for details.
RTN.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RTN_2.6.3.tar.gz && rm -rf RTN.buildbin-libdir && mkdir RTN.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTN.buildbin-libdir RTN_2.6.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RTN_2.6.3.zip && rm RTN_2.6.3.tar.gz RTN_2.6.3.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 8543k 100 8543k 0 0 58.6M 0 --:--:-- --:--:-- --:--:-- 60.0M
install for i386
* installing *source* package 'RTN' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RTN'
finding HTML links ... done
AVS-class html
RTN-package html
RTN.data html
TNA-class html
TNI-class html
TNI.data html
avs.evse html
avs.get html
avs.pevse html
avs.plot1 html
avs.plot2 html
avs.vse html
tna.get html
tna.graph html
tna.gsea1 html
tna.gsea2 html
tna.mra html
tna.overlap html
tna.plot.gsea1 html
tna.plot.gsea2 html
tna.shadow html
tna.synergy html
tni.area3 html
finding level-2 HTML links ... done
tni.bootstrap html
tni.conditional html
tni.constructor html
tni.dpi.filter html
tni.get html
tni.graph html
tni.gsea2 html
tni.permutation html
tni.preprocess html
tni.prune html
tni.regulon.summary html
tni2tna.preprocess html
upgradeTNA html
upgradeTNI html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'RTN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTN' as RTN_2.6.3.zip
* DONE (RTN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RTN' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
RTN.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking 'regulatoryElements' in 'gexp'...
-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 overlap analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Overlap 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
-Performing synergy analysis...
--For 10 regulon pairs...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Synergy analysis complete
-Performing shadow analysis...
--For 3 regulon pairs...
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
-Shadow analysis complete
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking 'regulatoryElements' in 'gexp'...
-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 -- Sat Apr 13 05:19:26 2019
***********************************************
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
26.59 0.81 27.42
|
RTN.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("RTN")
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking 'regulatoryElements' in 'gexp'...
-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 overlap analysis...
--For 5 regulons...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
-Overlap 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
-Performing synergy analysis...
--For 10 regulon pairs...
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
-Synergy analysis complete
-Performing shadow analysis...
--For 4 regulon pairs...
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
-Shadow analysis complete
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking 'regulatoryElements' in 'gexp'...
-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 -- Sat Apr 13 05:19:50 2019
***********************************************
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
23.20 0.46 23.67
|
|
RTN.Rcheck/examples_i386/RTN-Ex.timings
|
RTN.Rcheck/examples_x64/RTN-Ex.timings
|