Vinicius Chagas
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/RTNduals |
| Branch: RELEASE_3_6 |
| Last Commit: 4948437 |
| Last Changed Date: 2017-10-30 12:41:25 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:20 -0400 (Thu, 12 Apr 2018).
| Package 1226/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTNduals 1.2.0 Vinicius Chagas
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RTNduals |
| Version: 1.2.0 |
| Command: rm -rf RTNduals.buildbin-libdir RTNduals.Rcheck && mkdir RTNduals.buildbin-libdir RTNduals.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTNduals.buildbin-libdir RTNduals_1.2.0.tar.gz >RTNduals.Rcheck\00install.out 2>&1 && cp RTNduals.Rcheck\00install.out RTNduals-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RTNduals.buildbin-libdir --install="check:RTNduals-install.out" --force-multiarch --no-vignettes --timings RTNduals_1.2.0.tar.gz |
| StartedAt: 2018-04-12 02:54:09 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:58:02 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 233.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RTNduals.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf RTNduals.buildbin-libdir RTNduals.Rcheck && mkdir RTNduals.buildbin-libdir RTNduals.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTNduals.buildbin-libdir RTNduals_1.2.0.tar.gz >RTNduals.Rcheck\00install.out 2>&1 && cp RTNduals.Rcheck\00install.out RTNduals-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RTNduals.buildbin-libdir --install="check:RTNduals-install.out" --force-multiarch --no-vignettes --timings RTNduals_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTNduals.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTNduals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTNduals' version '1.2.0'
* 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 'RTNduals' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/MBR-class.Rd:30: missing file link 'mbrAssociation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/MBR-class.Rd:46: missing file link 'mbrPreprocess'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/MBR-class.Rd:47: missing file link 'tni2mbrPreprocess'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:32: missing file link 'mbrPreprocess'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:34: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:36: missing file link 'mbrBootstrap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:38: missing file link 'mbrDpiFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:40: missing file link 'mbrAssociation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:42: missing file link 'mbrDuals'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:44: missing file link 'tni2mbrPreprocess'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrAssociation-methods.Rd:15: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrAssociation-methods.Rd:16: missing file link 'mbrBootstrap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrAssociation-methods.Rd:17: missing file link 'mbrDpiFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrBootstrap-methods.Rd:13: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrDpiFilter-methods.Rd:14: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrDpiFilter-methods.Rd:15: missing file link 'mbrBootstrap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrDuals-methods.Rd:14: missing file link 'mbrAssociation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrPlotDuals.Rd:12: missing file link 'mbrAssociation'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTNduals.Rcheck/00install.out' for details.
* 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
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mbrAssociation-methods 9.30 0.44 9.94
mbrPlotDuals 8.83 0.41 9.24
mbrDuals-methods 8.30 0.60 8.89
mbrDpiFilter-methods 7.78 0.64 8.42
mbrBootstrap-methods 7.73 0.51 8.25
mbrPermutation-methods 7.18 0.32 7.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mbrPlotDuals 10.97 0.74 11.71
mbrAssociation-methods 9.82 0.58 10.39
mbrDpiFilter-methods 7.77 0.47 8.23
mbrDuals-methods 7.54 0.51 8.07
mbrPermutation-methods 6.66 0.47 7.12
mbrBootstrap-methods 6.58 0.39 6.97
* 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 WARNING
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTNduals.Rcheck/00check.log'
for details.
RTNduals.Rcheck/00install.out
install for i386
* installing *source* package 'RTNduals' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'RTNduals'
finding HTML links ... done
MBR-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/MBR-class.Rd:30: missing file link 'mbrAssociation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/MBR-class.Rd:46: missing file link 'mbrPreprocess'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/MBR-class.Rd:47: missing file link 'tni2mbrPreprocess'
RTNduals-package html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:32: missing file link 'mbrPreprocess'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:34: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:36: missing file link 'mbrBootstrap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:38: missing file link 'mbrDpiFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:40: missing file link 'mbrAssociation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:42: missing file link 'mbrDuals'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/RTNduals-package.Rd:44: missing file link 'tni2mbrPreprocess'
mbrAssociation-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrAssociation-methods.Rd:15: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrAssociation-methods.Rd:16: missing file link 'mbrBootstrap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrAssociation-methods.Rd:17: missing file link 'mbrDpiFilter'
mbrBootstrap-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrBootstrap-methods.Rd:13: missing file link 'mbrPermutation'
mbrDpiFilter-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrDpiFilter-methods.Rd:14: missing file link 'mbrPermutation'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrDpiFilter-methods.Rd:15: missing file link 'mbrBootstrap'
mbrDuals-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrDuals-methods.Rd:14: missing file link 'mbrAssociation'
mbrGet-methods html
mbrPermutation-methods html
mbrPlotDuals html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEvJoIR/R.INSTALL3a9029316da7/RTNduals/man/mbrPlotDuals.Rd:12: missing file link 'mbrAssociation'
mbrPreprocess-methods html
tni2mbrPreprocess-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'RTNduals' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTNduals' as RTNduals_1.2.0.zip
* DONE (RTNduals)
In R CMD INSTALL
In R CMD INSTALL
|
RTNduals.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("RTNduals")
-Preprocessing TNI objects...
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-Preprocessing complete!
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-Preprocessing complete!
-Performing permutation analysis for two TNI objects...
-Performing permutation analysis...
--For 2 regulons...
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-Permutation analysis complete!
-Performing permutation analysis...
--For 2 regulons...
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-Permutation analysis complete!
-Performing bootstrap analysis for two TNI
objects...
-Performing bootstrap analysis...
--For 2 regulons...
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-Bootstrap analysis complete!
-Performing bootstrap analysis...
--For 2 regulons...
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-Bootstrap analysis complete!
-Applying dpi filter for two TNI objects...
-Applying dpi filter...
-DPI filter complete!
-Applying dpi filter...
-DPI filter complete!
-Checking expression matrix consistency...
-Checking parameter consistency...
-Checking if all TNI methods are completed...
-Selecting regulatory elements from TNI1 object...
-Selecting regulatory elements from TNI2 object...
-Extrating inferred regulatory associations...
-Computing correlation statistics between regulators and targets...
-Computing correlation statistics between regulon pairs...
-Computing quantile statistics...
-Computing Mutual Information...
-Computing Jaccard similarity...
-Running hypergeometric analysis...
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-Sorting by the R value...
RUNIT TEST PROTOCOL -- Thu Apr 12 02:57:47 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
RTNduals RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning messages:
1: In tni.preprocess(TNI1, verbose = verbose, ... = ...) :
'gexpIDs' argument is deprected!
please use 'rowAnnotation' instead.'
2: In tni.preprocess(TNI2, verbose = verbose, ... = ...) :
'gexpIDs' argument is deprected!
please use 'rowAnnotation' instead.'
3: Only 4 regulon pair(s) is(are) being tested!
Ideally, the search space should represent all possible
combinations of a given class of regulators! For example,
all nuclear receptors annotated for a given species.
>
> proc.time()
user system elapsed
11.73 0.68 12.40
|
RTNduals.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("RTNduals")
-Preprocessing TNI objects...
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-Preprocessing complete!
-Preprocessing for input data...
--Mapping 'gexp' to 'rowAnnotation'...
--Removing duplicated genes (keep max coefficient of variation!)...
--Checking TFs in the dataset...
-Preprocessing complete!
-Performing permutation analysis for two TNI objects...
-Performing permutation analysis...
--For 2 regulons...
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-Permutation analysis complete!
-Performing permutation analysis...
--For 2 regulons...
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-Permutation analysis complete!
-Performing bootstrap analysis for two TNI
objects...
-Performing bootstrap analysis...
--For 2 regulons...
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-Bootstrap analysis complete!
-Performing bootstrap analysis...
--For 2 regulons...
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-Bootstrap analysis complete!
-Applying dpi filter for two TNI objects...
-Applying dpi filter...
-DPI filter complete!
-Applying dpi filter...
-DPI filter complete!
-Checking expression matrix consistency...
-Checking parameter consistency...
-Checking if all TNI methods are completed...
-Selecting regulatory elements from TNI1 object...
-Selecting regulatory elements from TNI2 object...
-Extrating inferred regulatory associations...
-Computing correlation statistics between regulators and targets...
-Computing correlation statistics between regulon pairs...
-Computing quantile statistics...
-Computing Mutual Information...
-Computing Jaccard similarity...
-Running hypergeometric analysis...
|
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|=================================== | 50%
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|======================================================================| 100%
-Sorting by the R value...
RUNIT TEST PROTOCOL -- Thu Apr 12 02:57:58 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
RTNduals RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning messages:
1: In tni.preprocess(TNI1, verbose = verbose, ... = ...) :
'gexpIDs' argument is deprected!
please use 'rowAnnotation' instead.'
2: In tni.preprocess(TNI2, verbose = verbose, ... = ...) :
'gexpIDs' argument is deprected!
please use 'rowAnnotation' instead.'
3: Only 4 regulon pair(s) is(are) being tested!
Ideally, the search space should represent all possible
combinations of a given class of regulators! For example,
all nuclear receptors annotated for a given species.
>
> proc.time()
user system elapsed
10.32 0.64 10.96
|
|
RTNduals.Rcheck/examples_i386/RTNduals-Ex.timings
|
RTNduals.Rcheck/examples_x64/RTNduals-Ex.timings
|