Claudia Cava
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/SpidermiR |
| Branch: RELEASE_3_6 |
| Last Commit: 58ab31b |
| Last Changed Date: 2018-01-20 06:58:27 -0400 (Sat, 20 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:27:43 -0400 (Thu, 12 Apr 2018).
| Package 1330/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SpidermiR 1.8.2 Claudia Cava
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SpidermiR |
| Version: 1.8.2 |
| Command: rm -rf SpidermiR.buildbin-libdir SpidermiR.Rcheck && mkdir SpidermiR.buildbin-libdir SpidermiR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpidermiR.buildbin-libdir SpidermiR_1.8.2.tar.gz >SpidermiR.Rcheck\00install.out 2>&1 && cp SpidermiR.Rcheck\00install.out SpidermiR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SpidermiR.buildbin-libdir --install="check:SpidermiR-install.out" --force-multiarch --no-vignettes --timings SpidermiR_1.8.2.tar.gz |
| StartedAt: 2018-04-12 03:21:22 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:30:25 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 543.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpidermiR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf SpidermiR.buildbin-libdir SpidermiR.Rcheck && mkdir SpidermiR.buildbin-libdir SpidermiR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpidermiR.buildbin-libdir SpidermiR_1.8.2.tar.gz >SpidermiR.Rcheck\00install.out 2>&1 && cp SpidermiR.Rcheck\00install.out SpidermiR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SpidermiR.buildbin-libdir --install="check:SpidermiR-install.out" --force-multiarch --no-vignettes --timings SpidermiR_1.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SpidermiR.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 'SpidermiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpidermiR' version '1.8.2'
* 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 'SpidermiR' 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
.SpidermiRvisualize_gene: possible error in simpleNetwork(NetworkData,
linkColour = "gray", textColour = "black", zoom = TRUE): unused
argument (textColour = "black")
Case_Study1_loading_3_network: no visible global function definition
for 'SpidermiRanalyze_DEnetworkTCGA'
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:
SpidermiRanalyze_DEnetworkTCGA 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
SpidermiRprepare_NET 12.56 3.69 16.54
SpidermiRdownload_net 7.25 2.04 9.61
SpidermiRdownload_miRNAprediction 6.55 0.36 6.91
SpidermiRdownload_miRNAextra_cir 5.14 1.47 6.89
SpidermiRanalyze_mirna_gene_complnet 5.87 0.59 7.33
SpidermiRanalyze_mirna_network 5.14 0.64 6.49
SpidermiRdownload_miRNAvalidate 3.25 0.31 11.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpidermiRprepare_NET 6.79 2.47 9.50
SpidermiRanalyze_mirna_gene_complnet 6.81 0.67 8.22
SpidermiRdownload_miRNAprediction 5.28 0.39 5.67
SpidermiRdownload_net 3.77 1.45 5.53
SpidermiRanalyze_mirna_network 4.51 0.56 5.83
SpidermiRdownload_miRNAvalidate 3.12 0.27 9.87
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.
SpidermiR.Rcheck/00install.out
install for i386
* installing *source* package 'SpidermiR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'SpidermiR'
finding HTML links ... done
Case_Study1_loading_1_network html
Case_Study1_loading_2_network html
Case_Study1_loading_3_network html
Case_Study1_loading_4_network html
Case_Study2_loading_1_network html
Case_Study2_loading_2_network html
Case_Study2_loading_3_network html
Data_CANCER_normUQ_filt html
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_mirna_gene_complnet html
SpidermiRanalyze_mirna_network 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
dataClin 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_1.8.2.zip
* DONE (SpidermiR)
In R CMD INSTALL
In R CMD INSTALL
|
SpidermiR.Rcheck/tests_i386/testthat.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.
> 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, cbind, colMeans, colSums, colnames, 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
>
> 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
17.28 2.00 19.81
|
SpidermiR.Rcheck/tests_x64/testthat.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.
> 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, cbind, colMeans, colSums, colnames, 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
>
> 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
16.73 2.12 19.39
|
|
SpidermiR.Rcheck/examples_i386/SpidermiR-Ex.timings
|
SpidermiR.Rcheck/examples_x64/SpidermiR-Ex.timings
|