Diana Diaz
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/mirIntegrator |
| git_branch: RELEASE_3_13 |
| git_last_commit: 7ce3bbd |
| git_last_commit_date: 2021-05-19 12:14:07 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the mirIntegrator package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mirIntegrator.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 1148/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mirIntegrator 1.22.0 (landing page) Diana Diaz
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mirIntegrator |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mirIntegrator.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mirIntegrator_1.22.0.tar.gz |
| StartedAt: 2021-10-15 02:01:56 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:05:28 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 212.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mirIntegrator.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mirIntegrator.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mirIntegrator_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mirIntegrator.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 'mirIntegrator/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mirIntegrator' version '1.22.0'
* 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 'mirIntegrator' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
integrate_mir : isGraphNEL: no visible global function definition for
'is'
pathways2pdf: no visible global function definition for 'pdf'
pathways2pdf: no visible global function definition for 'par'
pathways2pdf: no visible global function definition for 'graphics.off'
plotLines: no visible binding for global variable 'x'
plotLines: no visible binding for global variable 'y'
plotLines: no visible binding for global variable 'pathways_set'
plotPathway2Colors: no visible global function definition for 'legend'
plot_change: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
complete.cases graphics.off is legend par pathways_set pdf x y
Consider adding
importFrom("grDevices", "graphics.off", "pdf")
importFrom("graphics", "legend", "par")
importFrom("methods", "is")
importFrom("stats", "complete.cases")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
pathways2pdf 5.67 0.14 5.82
** 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-3.13-bioc/meat/mirIntegrator.Rcheck/00check.log'
for details.
mirIntegrator.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/mirIntegrator_1.22.0.tar.gz && rm -rf mirIntegrator.buildbin-libdir && mkdir mirIntegrator.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mirIntegrator.buildbin-libdir mirIntegrator_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL mirIntegrator_1.22.0.zip && rm mirIntegrator_1.22.0.tar.gz mirIntegrator_1.22.0.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
4 1592k 4 72687 0 0 461k 0 0:00:03 --:--:-- 0:00:03 460k
84 1592k 84 1345k 0 0 1166k 0 0:00:01 0:00:01 --:--:-- 1166k
100 1592k 100 1592k 0 0 1224k 0 0:00:01 0:00:01 --:--:-- 1223k
install for i386
* installing *source* package 'mirIntegrator' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mirIntegrator'
finding HTML links ... done
GSE43592_mRNA html
GSE43592_miRNA html
augmented_pathways html
integrate_mir html
kegg_pathways html
mirTarBase html
names_pathways html
pathways2pdf html
plot_augmented_pathway html
plot_change html
smallest_pathway 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 'mirIntegrator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mirIntegrator' as mirIntegrator_1.22.0.zip
* DONE (mirIntegrator)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'mirIntegrator' successfully unpacked and MD5 sums checked
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mirIntegrator.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.
> BiocGenerics:::testPackage("mirIntegrator")
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
RUNIT TEST PROTOCOL -- Fri Oct 15 02:05:11 2021
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
mirIntegrator 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
7.71 0.50 8.20
|
mirIntegrator.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.
> BiocGenerics:::testPackage("mirIntegrator")
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
RUNIT TEST PROTOCOL -- Fri Oct 15 02:05:20 2021
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
mirIntegrator 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
8.45 0.40 8.86
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mirIntegrator.Rcheck/examples_i386/mirIntegrator-Ex.timings
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mirIntegrator.Rcheck/examples_x64/mirIntegrator-Ex.timings
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