Remy Nicolle
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CoRegNet |
| git_branch: RELEASE_3_13 |
| git_last_commit: 340f25d |
| git_last_commit_date: 2021-05-19 12:09:00 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the CoRegNet package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoRegNet.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 392/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoRegNet 1.30.0 (landing page) Remy Nicolle
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CoRegNet |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CoRegNet_1.30.0.tar.gz |
| StartedAt: 2021-10-14 21:37:41 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:40:37 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 175.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CoRegNet.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CoRegNet_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegNet.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoRegNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoRegNet' version '1.30.0'
* 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 'CoRegNet' 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
* 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 ... NOTE
'library' or 'require' calls in package code:
'RColorBrewer' 'gplots'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.descriptionUpdate: no visible global function definition for 'vcount'
.descriptionUpdate: no visible global function definition for
'fisher.test'
.distfun: no visible global function definition for 'as.dist'
.distfun: no visible global function definition for 'cor'
.fitGRN : <anonymous>: no visible global function definition for 'lm'
.fitGRN : <anonymous>: no visible global function definition for 'coef'
.fitGRN: no visible global function definition for 'cor'
.fitGRN: no visible global function definition for 'lm'
.fitGRN: no visible global function definition for 'coef'
.hclustfun: no visible global function definition for 'hclust'
.heatplot: no visible global function definition for 'rainbow'
.heatplot : distf: no visible global function definition for 'as.dist'
.heatplot : distf: no visible global function definition for 'cor'
.heatplot : hclustf: no visible global function definition for 'hclust'
.heatplot: no visible global function definition for 'colorRampPalette'
.heatplot: no visible global function definition for 'heatmap.2'
.heatplot: no visible global function definition for 'quantile'
.tfPlot: no visible global function definition for 'colorRampPalette'
.tfPlot: no visible global function definition for 'rainbow'
.tfPlot: no visible global function definition for 'par'
.tfPlot: no visible global function definition for 'mtext'
.tfPlot: no visible global function definition for 'quantile'
.traits : <anonymous>: no visible global function definition for
'lines'
.traits: no visible global function definition for 'abline'
automaticParameters: no visible global function definition for
'quantile'
automaticParameters : <anonymous>: no visible global function
definition for 'pnorm'
automaticParameters: no visible global function definition for 'abline'
automaticParameters: no visible global function definition for 'sd'
coregnet : <anonymous>: no visible global function definition for 'cor'
coregnet: no visible global function definition for 'cor'
directedNetworkEnrichment: no visible global function definition for
'fisher.test'
discretizeExpressionData: no visible global function definition for
'sd'
fishersMethod: no visible global function definition for 'pchisq'
legendPlot: no visible global function definition for 'par'
legendPlot: no visible global function definition for
'colorRampPalette'
legendPlot: no visible global function definition for 'axis'
legendPlot: no visible global function definition for 'rainbow'
list.enriched: no visible global function definition for 'wilcox.test'
networkLegendPlot: no visible global function definition for 'par'
networkLegendPlot: no visible global function definition for 'symbols'
networkLegendPlot: no visible global function definition for 'text'
networkLegendPlot: no visible global function definition for 'rainbow'
networkLegendPlot: no visible global function definition for 'segments'
networkLegendPlot: no visible global function definition for 'arrows'
reactiveAdjacencyMatrix : <anonymous>: no visible global function
definition for 'rainbow'
set.overlap: no visible global function definition for 'fisher.test'
undirectedNetworkEnrichment: no visible global function definition for
'fisher.test'
updateData : <anonymous> : <anonymous>: no visible global function
definition for 't.test'
activators,coregnet: no visible global function definition for
'na.omit'
coregulators,coregnet: no visible global function definition for
'p.adjust'
coregulators,coregnet : <anonymous>: no visible global function
definition for 'fisher.test'
refine,coregnet: no visible global function definition for 'glm'
refine,coregnet: no visible global function definition for 'abline'
regulatorInfluence,coregnet : <anonymous> : <anonymous>: no visible
global function definition for 't.test'
regulators,coregnet: no visible global function definition for
'na.omit'
repressors,coregnet: no visible global function definition for
'na.omit'
targets,coregnet: no visible global function definition for 'na.omit'
Undefined global functions or variables:
abline arrows as.dist axis coef colorRampPalette cor fisher.test glm
hclust heatmap.2 lines lm mtext na.omit p.adjust par pchisq pnorm
quantile rainbow sd segments symbols t.test text vcount wilcox.test
Consider adding
importFrom("grDevices", "colorRampPalette", "rainbow")
importFrom("graphics", "abline", "arrows", "axis", "lines", "mtext",
"par", "segments", "symbols", "text")
importFrom("stats", "as.dist", "coef", "cor", "fisher.test", "glm",
"hclust", "lm", "na.omit", "p.adjust", "pchisq", "pnorm",
"quantile", "sd", "t.test", "wilcox.test")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CoRegNet/libs/i386/CoRegNet.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CoRegNet/libs/x64/CoRegNet.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
hLICORN 22.72 0.04 22.75
masterRegulator 9.05 0.00 9.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
hLICORN 26.31 0.03 26.34
masterRegulator 11.33 0.00 11.33
* checking for unstated dependencies in 'tests' ... WARNING
'::' or ':::' import not declared from: 'BiocGenerics'
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegNet.Rcheck/00check.log'
for details.
CoRegNet.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CoRegNet_1.30.0.tar.gz && rm -rf CoRegNet.buildbin-libdir && mkdir CoRegNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegNet.buildbin-libdir CoRegNet_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CoRegNet_1.30.0.zip && rm CoRegNet_1.30.0.tar.gz CoRegNet_1.30.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
16 4983k 16 805k 0 0 1665k 0 0:00:02 --:--:-- 0:00:02 1664k
79 4983k 79 3982k 0 0 2696k 0 0:00:01 0:00:01 --:--:-- 2696k
100 4983k 100 4983k 0 0 2782k 0 0:00:01 0:00:01 --:--:-- 2782k
install for i386
* installing *source* package 'CoRegNet' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c comblicorn.c -o comblicorn.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CoRegNet.dll tmp.def comblicorn.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegNet.buildbin-libdir/00LOCK-CoRegNet/00new/CoRegNet/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CoRegNet'
finding HTML links ... done
CoRegNet-class html
HumanDataExamples html
HumanTF html
addEvidences html
coRegnet-package html
coregnet html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegNet.buildbin-libdir/00LOCK-CoRegNet/00new/CoRegNet/help/coregnet.html
coregulators html
discretizeExpressionData html
display html
hLICORN html
masterRegulator html
refine html
regulatorInfluence html
regulators html
summary html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegNet.buildbin-libdir/00LOCK-CoRegNet/00new/CoRegNet/help/coregnetToList.coregnet.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
install for x64
* installing *source* package 'CoRegNet' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c comblicorn.c -o comblicorn.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CoRegNet.dll tmp.def comblicorn.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegNet.buildbin-libdir/CoRegNet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoRegNet' as CoRegNet_1.30.0.zip
* DONE (CoRegNet)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CoRegNet' successfully unpacked and MD5 sums checked
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CoRegNet.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> require(CoRegNet) || stop("unable to load CoRegNet package")
Loading required package: CoRegNet
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: shiny
Loading required package: arules
Loading required package: Matrix
Attaching package: 'arules'
The following objects are masked from 'package:base':
abbreviate, write
[1] TRUE
> BiocGenerics:::testPackage('CoRegNet')
Attaching package: 'RUnit'
The following object is masked from 'package:arules':
inspect
evidence1 was integrated into the network.
[1] "coregevidence1"
[1] "coregevidence1 was integrated into the network."
evidence1 was integrated into the network.
[1] "coregevidence1"
[1] "coregevidence1 was integrated into the network."
RUNIT TEST PROTOCOL -- Thu Oct 14 21:40:24 2021
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
CoRegNet RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
4.67 0.26 4.93
|
CoRegNet.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
> require(CoRegNet) || stop("unable to load CoRegNet package")
Loading required package: CoRegNet
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: shiny
Loading required package: arules
Loading required package: Matrix
Attaching package: 'arules'
The following objects are masked from 'package:base':
abbreviate, write
[1] TRUE
> BiocGenerics:::testPackage('CoRegNet')
Attaching package: 'RUnit'
The following object is masked from 'package:arules':
inspect
evidence1 was integrated into the network.
[1] "coregevidence1"
[1] "coregevidence1 was integrated into the network."
evidence1 was integrated into the network.
[1] "coregevidence1"
[1] "coregevidence1 was integrated into the network."
RUNIT TEST PROTOCOL -- Thu Oct 14 21:40:30 2021
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
CoRegNet RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
5.12 0.21 5.32
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CoRegNet.Rcheck/examples_i386/CoRegNet-Ex.timings
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CoRegNet.Rcheck/examples_x64/CoRegNet-Ex.timings
|