Dongmin Jung
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) |
| URL: https://git.bioconductor.org/packages/PPInfer |
| Branch: RELEASE_3_5 |
| Last Commit: 8afb8be |
| Last Changed Date: 2017-10-12 23:27:22 -0400 (Thu, 12 Oct 2017) |
| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O [P] Q R S T U V W X Y Z |
This page was generated on 2017-10-18 14:35:38 -0400 (Wed, 18 Oct 2017).
| Package 1000/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PPInfer 1.2.4 Dongmin Jung
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: PPInfer |
| Version: 1.2.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PPInfer_1.2.4.tar.gz |
| StartedAt: 2017-10-18 07:25:11 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 07:38:32 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 800.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PPInfer.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PPInfer_1.2.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PPInfer.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PPInfer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PPInfer’ version ‘1.2.4’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘biomaRt’ ‘fgsea’ ‘kernlab’ ‘ggplot2’ ‘igraph’ ‘STRINGdb’
‘yeastExpData’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PPInfer’ 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
* 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 loading without being on the library search path ... 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
ORA: no visible global function definition for ‘txtProgressBar’
ORA: no visible global function definition for ‘fisher.test’
ORA: no visible global function definition for ‘setTxtProgressBar’
ORA: no visible global function definition for ‘p.adjust’
ORA.dotplot: no visible global function definition for ‘p.adjust’
enrich.net: no visible global function definition for ‘stack’
enrich.net: no visible global function definition for ‘adjustcolor’
enrich.net : <anonymous>: no visible global function definition for
‘adjustcolor’
enrich.net: no visible binding for global variable ‘legend’
net.infer: no visible global function definition for ‘na.omit’
net.infer.ST: no visible global function definition for ‘na.omit’
ppi.infer.human: no visible global function definition for ‘na.omit’
ppi.infer.mouse: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar
stack txtProgressBar
Consider adding
importFrom("grDevices", "adjustcolor")
importFrom("graphics", "legend")
importFrom("stats", "fisher.test", "na.omit", "p.adjust")
importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ppi.infer.human 68.663 2.494 86.530
ppi.infer.mouse 63.118 2.424 83.664
ORA.dotplot 2.305 0.039 19.375
ORA 1.362 0.075 18.578
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1: expect_is(ppi.infer.mouse(target[1:100], K.10090, classifier = net.infer.ST, input = "ensembl_peptide_id"),
"list") at testthat/test_ppi.infer.mouse.R:21
2: klass(object)
3: paste(class(x), collapse = "/")
4: ppi.infer.mouse(target[1:100], K.10090, classifier = net.infer.ST, input = "ensembl_peptide_id")
5: useDataset("mmusculus_gene_ensembl", mart = ensembl)
6: checkDataset(dataset = dataset, mart = mart)
7: stop(paste("The given dataset: ", dataset, ", is not valid. Correct dataset names can be obtained with the listDatasets() function."))
testthat results ================================================================
OK: 62 SKIPPED: 0 FAILED: 1
1. Error: ppi.infer.mouse() gives correct errors (@test_ppi.infer.mouse.R#21)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘httr’
* 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 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/PPInfer.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("PPInfer")
Loading required package: biomaRt
Loading required package: fgsea
Loading required package: Rcpp
Loading required package: kernlab
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following object is masked from 'package:kernlab':
alpha
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: STRINGdb
Loading required package: yeastExpData
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:igraph':
normalize, union
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
Attaching package: 'graph'
The following objects are masked from 'package:igraph':
degree, edges, intersection
> test_check("PPInfer")
pathway NES pval
887 5991851_Mitotic_Prometaphase 2.994157 0.001529052
1231 5992217_Resolution_of_Sister_Chromatid_Cohesion 2.976027 0.001533742
795 5991757_RHO_GTPases_Activate_Formins 2.729367 0.001540832
24 5990979_Cell_Cycle,_Mitotic 2.720314 0.001257862
640 5991599_Separation_of_Sister_Chromatids 2.697155 0.001428571
36 5990991_Mitotic_G1-G1_S_phases 2.678130 0.001479290
25 5990980_Cell_Cycle 2.665177 0.001216545
543 5991502_Mitotic_Metaphase_and_Anaphase 2.663071 0.001434720
26 5990981_DNA_Replication 2.658441 0.001529052
641 5991600_Mitotic_Anaphase 2.640638 0.001443001
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Category
5991441_PAOs_oxidise_polyamines_to_amines 5991441_PAOs_oxidise_polyamines_to_amines
5991267_Beta_oxidation_of_myristoyl-CoA_to_lauroyl-CoA 5991267_Beta_oxidation_of_myristoyl-CoA_to_lauroyl-CoA
5991442_Interconversion_of_polyamines 5991442_Interconversion_of_polyamines
5991860_Glycoprotein_hormones 5991860_Glycoprotein_hormones
5991195_SHC_activation 5991195_SHC_activation
5991437_Amine_Oxidase_reactions 5991437_Amine_Oxidase_reactions
5991265_Beta_oxidation_of_lauroyl-CoA_to_decanoyl-CoA-CoA 5991265_Beta_oxidation_of_lauroyl-CoA_to_decanoyl-CoA-CoA
5991808_Peptide_hormone_biosynthesis 5991808_Peptide_hormone_biosynthesis
5992315_RMTs_methylate_histone_arginines 5992315_RMTs_methylate_histone_arginines
5991184_IRS_activation 5991184_IRS_activation
Size Count Pvalue
5991441_PAOs_oxidise_polyamines_to_amines 2 1 0.02792963
5991267_Beta_oxidation_of_myristoyl-CoA_to_lauroyl-CoA 3 1 0.04160343
5991442_Interconversion_of_polyamines 3 1 0.04160343
5991860_Glycoprotein_hormones 3 1 0.04160343
5991195_SHC_activation 4 1 0.05508678
5991437_Amine_Oxidase_reactions 4 1 0.05508678
5991265_Beta_oxidation_of_lauroyl-CoA_to_decanoyl-CoA-CoA 5 1 0.06838231
5991808_Peptide_hormone_biosynthesis 5 1 0.06838231
5992315_RMTs_methylate_histone_arginines 32 2 0.07394618
5991184_IRS_activation 6 1 0.08149260
GeneRatio
5991441_PAOs_oxidise_polyamines_to_amines 0.5000000
5991267_Beta_oxidation_of_myristoyl-CoA_to_lauroyl-CoA 0.3333333
5991442_Interconversion_of_polyamines 0.3333333
5991860_Glycoprotein_hormones 0.3333333
5991195_SHC_activation 0.2500000
5991437_Amine_Oxidase_reactions 0.2500000
5991265_Beta_oxidation_of_lauroyl-CoA_to_decanoyl-CoA-CoA 0.2000000
5991808_Peptide_hormone_biosynthesis 0.2000000
5992315_RMTs_methylate_histone_arginines 0.0625000
5991184_IRS_activation 0.1666667
trying URL 'http://string.uzh.ch/permanent/string/10/protein_links/9606__protein_links.tsv.gz'
Content type 'application/x-gzip' length 36637376 bytes (34.9 MB)
==================================================
downloaded 34.9 MB
trying URL 'http://string.uzh.ch/permanent/string/10/protein_links/10090__protein_links.tsv.gz'
Content type 'application/x-gzip' length 44320148 bytes (42.3 MB)
==================================================
downloaded 42.3 MB
1. Error: ppi.infer.mouse() gives correct errors (@test_ppi.infer.mouse.R#21) --
The given dataset: mmusculus_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.
1: expect_is(ppi.infer.mouse(target[1:100], K.10090, classifier = net.infer.ST, input = "ensembl_peptide_id"),
"list") at testthat/test_ppi.infer.mouse.R:21
2: klass(object)
3: paste(class(x), collapse = "/")
4: ppi.infer.mouse(target[1:100], K.10090, classifier = net.infer.ST, input = "ensembl_peptide_id")
5: useDataset("mmusculus_gene_ensembl", mart = ensembl)
6: checkDataset(dataset = dataset, mart = mart)
7: stop(paste("The given dataset: ", dataset, ", is not valid. Correct dataset names can be obtained with the listDatasets() function."))
testthat results ================================================================
OK: 62 SKIPPED: 0 FAILED: 1
1. Error: ppi.infer.mouse() gives correct errors (@test_ppi.infer.mouse.R#21)
Error: testthat unit tests failed
Execution halted
PPInfer.Rcheck/00install.out:
* installing *source* package ‘PPInfer’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (PPInfer)
PPInfer.Rcheck/PPInfer-Ex.timings:
| name | user | system | elapsed | |
| GSEA.barplot | 3.928 | 0.096 | 3.955 | |
| ORA | 1.362 | 0.075 | 18.578 | |
| ORA.dotplot | 2.305 | 0.039 | 19.375 | |
| enrich.net | 2.904 | 0.057 | 2.912 | |
| net.infer | 3.772 | 0.058 | 3.941 | |
| net.infer.ST | 0.247 | 0.003 | 0.255 | |
| net.kernel | 0.036 | 0.002 | 0.041 | |
| ppi.infer.human | 68.663 | 2.494 | 86.530 | |
| ppi.infer.mouse | 63.118 | 2.424 | 83.664 | |
| self.train.kernel | 0.250 | 0.143 | 0.399 | |