Claudia Cava
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SpidermiR |
| Branch: RELEASE_3_8 |
| Last Commit: c728d83 |
| Last Changed Date: 2019-02-04 04:53:47 -0400 (Mon, 04 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:28 -0400 (Sat, 13 Apr 2019).
| Package 1488/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SpidermiR 1.12.1 Claudia Cava
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SpidermiR |
| Version: 1.12.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SpidermiR_1.12.1.tar.gz |
| StartedAt: 2019-04-13 05:41:59 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:47:30 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 331.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SpidermiR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SpidermiR_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SpidermiR.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 'SpidermiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpidermiR' version '1.12.1'
* 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 'SpidermiR' can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black")
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SpidermiR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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
Namespace in Imports field not imported from: 'TCGAbiolinks'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.SpidermiRvisualize_gene: possible error in simpleNetwork(NetworkData,
linkColour = "gray", textColour = "black", zoom = TRUE): unused
argument (textColour = "black")
SpidermiRvisualize_plot_target: no visible binding for global variable
'miRNAs'
SpidermiRvisualize_plot_target: no visible binding for global variable
'mRNA_target'
Undefined global functions or variables:
mRNA_target miRNAs
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpidermiRquery_disease 22.79 7.44 34.78
SpidermiRprepare_NET 11.36 3.42 15.06
SpidermiRdownload_net 5.92 1.61 7.88
SpidermiRdownload_miRNAextra_cir 3.75 1.15 5.36
SpidermiRdownload_miRNAvalidate 1.62 0.04 9.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpidermiRquery_disease 16.64 7.58 26.87
SpidermiRprepare_NET 6.67 2.80 9.75
SpidermiRdownload_net 3.39 1.78 5.53
SpidermiRdownload_miRNAvalidate 1.85 0.09 8.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.
SpidermiR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SpidermiR_1.12.1.tar.gz && rm -rf SpidermiR.buildbin-libdir && mkdir SpidermiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpidermiR.buildbin-libdir SpidermiR_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SpidermiR_1.12.1.zip && rm SpidermiR_1.12.1.tar.gz SpidermiR_1.12.1.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
100 22257 100 22257 0 0 561k 0 --:--:-- --:--:-- --:--:-- 621k
install for i386
* installing *source* package 'SpidermiR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black")
** help
*** installing help indices
converting help for package 'SpidermiR'
finding HTML links ... done
SpidermiR html
SpidermiRanalyze_Community_detection html
SpidermiRanalyze_Community_detection_bi
html
SpidermiRanalyze_Community_detection_net
html
SpidermiRanalyze_degree_centrality html
SpidermiRanalyze_direct_net html
SpidermiRanalyze_direct_subnetwork html
SpidermiRanalyze_mirnanet_pharm html
SpidermiRanalyze_subnetwork_neigh html
SpidermiRdownload_miRNAextra_cir html
SpidermiRdownload_miRNAprediction html
SpidermiRdownload_miRNAvalidate html
SpidermiRdownload_net html
SpidermiRdownload_pharmacomir html
SpidermiRprepare_NET html
SpidermiRquery_disease html
SpidermiRquery_networks_type html
SpidermiRquery_spec_networks html
SpidermiRquery_species html
SpidermiRvisualize_3Dbarplot html
SpidermiRvisualize_BI html
SpidermiRvisualize_adj_matrix html
SpidermiRvisualize_degree_dist html
SpidermiRvisualize_direction html
SpidermiRvisualize_mirnanet html
SpidermiRvisualize_plot_target html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SpidermiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpidermiR' as SpidermiR_1.12.1.zip
* DONE (SpidermiR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SpidermiR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
SpidermiR.Rcheck/tests_i386/testthat.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.
> library(testthat)
> library(SpidermiR)
Loading required package: miRNAtap
Loading required package: AnnotationDbi
Loading required package: stats4
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
>
> test_check("SpidermiR")
[1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.INTERPRO.txt ... reference n. 1 of 2"
[1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.PFAM.txt ... reference n. 2 of 2"
== testthat results ===========================================================
OK: 4 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.31 2.07 13.95
|
SpidermiR.Rcheck/tests_x64/testthat.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.
> library(testthat)
> library(SpidermiR)
Loading required package: miRNAtap
Loading required package: AnnotationDbi
Loading required package: stats4
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
>
> test_check("SpidermiR")
[1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.INTERPRO.txt ... reference n. 1 of 2"
[1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.PFAM.txt ... reference n. 2 of 2"
== testthat results ===========================================================
OK: 4 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
8.32 1.78 10.73
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SpidermiR.Rcheck/examples_i386/SpidermiR-Ex.timings
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SpidermiR.Rcheck/examples_x64/SpidermiR-Ex.timings
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