Ana Galhoz
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_16 |
| git_last_commit: cd4b58e |
| git_last_commit_date: 2022-11-01 11:24:35 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 wppi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.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 2165/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.6.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: wppi |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings wppi_1.6.0.tar.gz |
| StartedAt: 2023-04-11 00:51:32 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:55:54 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 261.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings wppi_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/wppi.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ 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
[2023-04-11 00:52:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 00:52:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 00:52:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 00:52:08] [TRACE] [OmnipathR] Contains 1 files.
[2023-04-11 00:52:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-11 00:52:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 00:52:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 00:52:08] [TRACE] [OmnipathR] Cache locked: FALSE
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
wppi 30.506 0.320 30.826
random_walk 15.431 0.211 15.641
prioritization_genes 15.103 0.369 15.473
score_candidate_genes_from_PPI 14.846 0.056 14.902
weighted_adj 11.149 0.119 11.268
count_genes 8.273 0.643 8.025
wppi_data 6.295 0.076 6.370
filter_annot_with_network 5.923 0.160 6.082
common_neighbors 5.450 0.498 24.474
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘wppi_workflow.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.16-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2023-04-10 15:24:16] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:24:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:16] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:24:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:24:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:24:16] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2023-04-10 15:24:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:24:19] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:19] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:24:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:24:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:24:19] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-10 15:24:22] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:24:22] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:22] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:24:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:24:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-10 15:24:22] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:24:22] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi)
wppi.Rcheck/wppi-Ex.timings
| name | user | system | elapsed | |
| common_neighbors | 5.450 | 0.498 | 24.474 | |
| count_genes | 8.273 | 0.643 | 8.025 | |
| filter_annot_with_network | 5.923 | 0.160 | 6.082 | |
| functional_annot | 1.266 | 0.092 | 2.015 | |
| graph_from_op | 3.021 | 0.112 | 3.133 | |
| in_omnipath | 3.014 | 0.085 | 3.099 | |
| prioritization_genes | 15.103 | 0.369 | 15.473 | |
| process_annot | 0.554 | 0.000 | 0.554 | |
| random_walk | 15.431 | 0.211 | 15.641 | |
| score_candidate_genes_from_PPI | 14.846 | 0.056 | 14.902 | |
| subgraph_op | 3.086 | 0.000 | 3.086 | |
| weighted_adj | 11.149 | 0.119 | 11.268 | |
| wppi | 30.506 | 0.320 | 30.826 | |
| wppi_data | 6.295 | 0.076 | 6.370 | |
| wppi_go_data | 2.94 | 0.08 | 3.02 | |
| wppi_hpo_data | 0.41 | 0.00 | 0.41 | |
| wppi_omnipath_data | 2.802 | 0.000 | 2.802 | |