Marta R. Hidalgo
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/hipathia |
| Branch: RELEASE_3_10 |
| Last Commit: 4e96525 |
| Last Changed Date: 2019-12-02 12:37:33 -0400 (Mon, 02 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:21 -0400 (Wed, 15 Apr 2020).
| Package 792/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hipathia 2.2.1 Marta R. Hidalgo
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: hipathia |
| Version: 2.2.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings hipathia_2.2.1.tar.gz |
| StartedAt: 2020-04-15 03:54:01 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:25:18 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1877.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: hipathia.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings hipathia_2.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/hipathia.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hipathia/DESCRIPTION' ... OK
* this is package 'hipathia' version '2.2.1'
* package encoding: UTF-8
* 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 'hipathia' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.8Mb
sub-directories of 1Mb or more:
data 4.9Mb
extdata 4.3Mb
* 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 ... OK
* 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 or elapsed time > 5s
user system elapsed
quantify_terms 41.18 1.36 43.41
create_report 31.30 3.33 43.25
visualize_report 27.17 0.53 27.89
get_pathways_annotations 25.25 0.59 26.81
save_results 24.56 0.38 25.05
get_path_names 24.29 0.52 25.08
hipathia 23.30 0.59 24.06
load_pathways 23.17 0.34 24.36
pathway_comparison_plot 23.17 0.28 23.61
get_node_names 22.83 0.50 23.44
get_pathways_list 22.85 0.34 23.33
node_color_per_de 22.12 0.30 22.59
get_pathways_summary 22.10 0.29 22.56
normalize_paths 21.77 0.31 22.27
node_color 20.60 0.24 21.07
translate_data 11.34 0.69 12.22
normalize_data 11.25 0.34 12.06
get_go_names 5.26 0.55 7.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
quantify_terms 45.27 1.57 47.66
get_pathways_annotations 36.09 0.95 37.81
get_pathways_summary 31.01 0.47 31.77
load_pathways 28.12 0.45 29.48
get_pathways_list 27.88 0.41 28.45
get_path_names 27.56 0.38 28.20
pathway_comparison_plot 27.00 0.46 27.69
node_color 27.00 0.44 27.73
node_color_per_de 27.01 0.42 28.59
visualize_report 26.52 0.40 27.65
hipathia 26.27 0.41 26.99
normalize_paths 25.69 0.44 26.33
get_node_names 24.77 0.73 28.39
save_results 24.59 0.30 25.03
create_report 23.49 1.33 35.55
normalize_data 19.61 0.54 20.74
translate_data 14.36 0.39 14.99
get_go_names 5.03 0.52 5.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
8. AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
9. base::tryCatch(...)
10. base:::tryCatchList(expr, classes, parentenv, handlers)
11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. value[[3L]](cond)
translated ids = 3184 (1)
untranslated ids = 3 (0.00094)
multihit ids = 0 (0)
== testthat results ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
1. Error: (unknown) (@test-path-annots.R#9)
Error: testthat unit tests failed
Execution halted
** 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 ERROR, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/hipathia.Rcheck/00check.log'
for details.
hipathia.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/hipathia_2.2.1.tar.gz && rm -rf hipathia.buildbin-libdir && mkdir hipathia.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hipathia.buildbin-libdir hipathia_2.2.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL hipathia_2.2.1.zip && rm hipathia_2.2.1.tar.gz hipathia_2.2.1.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
0 5168k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 5168k 100 5168k 0 0 20.9M 0 --:--:-- --:--:-- --:--:-- 21.2M
install for i386
* installing *source* package 'hipathia' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'hipathia'
finding HTML links ... done
annotate_paths html
brca html
brca_data html
brca_design html
comp html
create_report html
do_pca html
do_wilcoxon html
exp_data html
get_go_names html
get_highest_sig_ancestor html
get_node_names html
get_nodes_data html
get_path_names html
get_paths_data html
get_pathway_functions html
get_pathways_annotations html
get_pathways_list html
get_pathways_summary html
go_vals html
heatmap_plot html
hhead html
hipathia html
igraphs_upgrade html
is_accepted_species html
load_annofuns html
load_annots html
load_entrez_hgnc html
load_gobp_frame html
load_gobp_net html
load_mgi html
load_pathways html
load_pseudo_mgi html
load_xref html
mgi_from_sif html
multiple_pca_plot html
node_color html
node_color_per_de html
normalize_data html
normalize_paths html
path_vals html
paths_to_go_ancestor html
pathway_comparison_plot html
pca_plot html
quantify_terms html
results html
save_results html
top_pathways html
translate_data html
translate_matrix html
visualize_report 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 'hipathia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hipathia' as hipathia_2.2.1.zip
* DONE (hipathia)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'hipathia' successfully unpacked and MD5 sums checked
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hipathia.Rcheck/tests_i386/testthat.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(hipathia)
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: AnnotationHub
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, path, 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, 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, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:AnnotationHub':
cache
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:igraph':
simplify
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("hipathia")
HiPathia processing...
hsa03320 - PPAR signaling pathway
hsa04012 - ErbB signaling pathway
HiPathia processing...
hsa03320 - PPAR signaling pathway
hsa04012 - ErbB signaling pathway
-- 1. Error: (unknown) (@test-path-annots.R#9) --------------------------------
failed to load resource
name: AH69097
title: annofuns_uniprot_hsa_v2.rda
reason: 1 resources failed to download
Backtrace:
1. hipathia::get_pathways_annotations(rownames(comp), mgi, "uniprot")
2. hipathia:::load_annofuns(dbannot, metaginfo$species)
6. hp[[names(hp)[hp$title == file]]]
7. AnnotationHub:::.local(x, i, j, ...)
8. AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
9. base::tryCatch(...)
10. base:::tryCatchList(expr, classes, parentenv, handlers)
11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. value[[3L]](cond)
translated ids = 3184 (1)
untranslated ids = 3 (0.00094)
multihit ids = 0 (0)
== testthat results ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
1. Error: (unknown) (@test-path-annots.R#9)
Error: testthat unit tests failed
Execution halted
|
hipathia.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(hipathia)
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: AnnotationHub
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, path, 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, 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, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:AnnotationHub':
cache
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:igraph':
simplify
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("hipathia")
HiPathia processing...
hsa03320 - PPAR signaling pathway
hsa04012 - ErbB signaling pathway
HiPathia processing...
hsa03320 - PPAR signaling pathway
hsa04012 - ErbB signaling pathway
translated ids = 3184 (1)
untranslated ids = 3 (0.00094)
multihit ids = 0 (0)
== testthat results ===========================================================
[ OK: 119 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
310.96 8.06 331.65
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hipathia.Rcheck/examples_i386/hipathia-Ex.timings
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hipathia.Rcheck/examples_x64/hipathia-Ex.timings
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