Federico Marini
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_14 |
| git_last_commit: c9ee95b |
| git_last_commit_date: 2022-03-24 08:30:47 -0400 (Thu, 24 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:37 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the GeneTonic package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneTonic.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 739/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 1.6.4 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeneTonic |
| Version: 1.6.4 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneTonic_1.6.4.tar.gz |
| StartedAt: 2022-04-12 20:12:05 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:31:43 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1177.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeneTonic.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneTonic_1.6.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneTonic/DESCRIPTION' ... OK
* this is package 'GeneTonic' version '1.6.4'
* 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 'GeneTonic' 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 ... 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 (user + system) or elapsed time > 5s
user system elapsed
ggs_backbone 8.05 0.23 8.50
gs_mds 7.94 0.16 8.10
ggs_graph 7.72 0.16 7.87
GeneTonic 7.48 0.29 8.00
summarize_ggs_hubgenes 7.63 0.09 7.72
gs_heatmap 7.28 0.28 7.57
gs_scores 6.71 0.11 6.81
gs_scoresheat 6.25 0.12 6.38
signature_volcano 6.26 0.08 6.34
gs_dendro 5.86 0.16 6.02
export_for_iSEE 5.75 0.11 5.86
checkup_gtl 5.48 0.24 5.72
checkup_GeneTonic 5.31 0.37 5.69
gs_horizon 5.52 0.09 5.60
distill_enrichment 5.46 0.12 5.58
gene_plot 5.38 0.11 5.49
gs_alluvial 5.12 0.28 6.08
gs_volcano 5.23 0.17 5.40
gs_radar 5.04 0.25 5.36
enhance_table 5.11 0.11 5.22
GeneTonic_list 4.74 0.35 5.08
gs_summary_overview_pair 4.95 0.11 5.06
happy_hour 4.97 0.08 5.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
summarize_ggs_hubgenes 8.36 0.33 9.57
gs_mds 7.96 0.19 8.19
ggs_backbone 7.87 0.25 8.30
gs_heatmap 7.13 0.16 7.29
ggs_graph 7.00 0.22 7.21
gs_scores 6.88 0.28 7.15
GeneTonic 6.64 0.15 6.80
gs_scoresheat 6.07 0.17 6.25
gs_dendro 6.02 0.15 6.17
signature_volcano 5.62 0.09 5.72
export_for_iSEE 4.91 0.21 5.11
gs_summary_overview 4.84 0.17 5.02
* 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:
|
|======================================================================| 99%
|
|======================================================================| 100%
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 242 ]
== Failed tests ================================================================
-- Failure (test-ggs_graph.R:121:3): Backbone functionality up and running -----
vcount(bbg4) not equal to 0.
1/1 mismatches
[1] 2 - 0 == 2
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 242 ]
Error: Test failures
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
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck/00check.log'
for details.
GeneTonic.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GeneTonic_1.6.4.tar.gz && rm -rf GeneTonic.buildbin-libdir && mkdir GeneTonic.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneTonic.buildbin-libdir GeneTonic_1.6.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeneTonic_1.6.4.zip && rm GeneTonic_1.6.4.tar.gz GeneTonic_1.6.4.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
25 1835k 25 461k 0 0 728k 0 0:00:02 --:--:-- 0:00:02 728k
100 1835k 100 1835k 0 0 1205k 0 0:00:01 0:00:01 --:--:-- 1206k
install for i386
* installing *source* package 'GeneTonic' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneTonic'
finding HTML links ... done
GeneTonic-pkg html
GeneTonic html
GeneTonic_list html
check_colors html
checkup_GeneTonic html
checkup_gtl html
cluster_markov html
create_jaccard_matrix html
create_kappa_matrix html
describe_gtl html
deseqresult2df html
distill_enrichment html
dot-check_pandoc html
enhance_table html
enrichment_map html
enrichr_output_macrophage html
export_for_iSEE html
finding level-2 HTML links ... done
export_to_sif html
fgseaRes html
gene_plot html
geneinfo_2_html html
get_aggrscores html
get_expression_values html
ggs_backbone html
ggs_graph html
go_2_html html
gostres_macrophage html
gs_alluvial html
gs_dendro html
gs_fuzzyclustering html
gs_heatmap html
gs_horizon html
gs_mds html
gs_radar html
gs_scores html
gs_scoresheat html
gs_simplify html
gs_summary_heat html
gs_summary_overview html
gs_summary_overview_pair html
gs_volcano html
happy_hour html
map2color html
overlap_coefficient html
overlap_jaccard_index html
res_macrophage_IFNg_vs_naive html
shake_davidResult html
shake_enrichResult html
shake_enrichrResult html
shake_fgseaResult html
shake_gprofilerResult html
shake_gsenrichResult html
shake_topGOtableResult html
signature_volcano html
styleColorBar_divergent html
summarize_ggs_hubgenes html
topgoDE_macrophage_IFNg_vs_naive 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 'GeneTonic' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneTonic' as GeneTonic_1.6.4.zip
* DONE (GeneTonic)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GeneTonic' successfully unpacked and MD5 sums checked
|
GeneTonic.Rcheck/tests_i386/testthat.Rout.fail
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(GeneTonic)
>
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
--- Running gseGO...
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
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[ FAIL 1 | WARN 2 | SKIP 0 | PASS 242 ]
== Failed tests ================================================================
-- Failure (test-ggs_graph.R:121:3): Backbone functionality up and running -----
vcount(bbg4) not equal to 0.
1/1 mismatches
[1] 2 - 0 == 2
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 242 ]
Error: Test failures
Execution halted
|
GeneTonic.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(GeneTonic)
>
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
--- Running gseGO...
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
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|================================================================= | 93%
|
|================================================================= | 94%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 99%
|
|======================================================================| 100%
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 243 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 243 ]
>
> proc.time()
user system elapsed
148.89 4.95 280.95
|
|
GeneTonic.Rcheck/examples_i386/GeneTonic-Ex.timings
|
GeneTonic.Rcheck/examples_x64/GeneTonic-Ex.timings
|