Ana Galhoz
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1ad2e46 |
| git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 | ||||
| Package 2282/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.12.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the wppi package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: wppi |
| Version: 1.12.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings wppi_1.12.0.tar.gz |
| StartedAt: 2024-06-27 07:23:10 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 07:27:51 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 280.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings wppi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.12.0'
* 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 whether package 'wppi' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... NOTE
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 07:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:23:45] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Contains 1 files.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 07:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:23:45] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-27 07:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-27 07:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-27 07:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-27 07:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:23:45] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
[2024-06-27 07:24:05] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 07:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:24:05] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-27 07:24:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-06-27 07:24:05] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-27 07:24:05] [TRACE] [OmnipathR] Contains 1 files.
[2024-06-27 07:24:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-06-27 07:24:05] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 07:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:24:05] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-27 07:24:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-27 07:24:06] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-27 07:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:24:06] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-27 07:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:24:06] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-27 07:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:24:06] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-27 07:24:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-06-27 07:24:06] [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 36.70 0.92 37.62
score_candidate_genes_from_PPI 18.74 0.36 19.11
random_walk 18.43 0.39 18.83
prioritization_genes 17.80 0.40 18.20
weighted_adj 14.14 0.49 16.19
count_genes 12.45 0.88 12.28
wppi_data 8.88 0.11 8.99
common_neighbors 7.96 0.48 19.30
filter_annot_with_network 7.85 0.22 8.06
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log'
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'wppi' ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-06-26 16:23:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-06-26 16:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:02] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-26 16:23:02] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:02] [TRACE] [OmnipathR] Contains 1 files. [2024-06-26 16:23:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-26 16:23:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-06-26 16:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:02] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-26 16:23:03] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-26 16:23:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:03] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-26 16:23:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:03] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-26 16:23:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:03] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-26 16:23:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:03] [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 [2024-06-26 16:23:08] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-06-26 16:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:08] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Contains 1 files. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-06-26 16:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:08] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-26 16:23:08] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-26 16:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:08] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-26 16:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:09] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-26 16:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:09] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-26 16:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:09] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-06-26 16:23:12] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-06-26 16:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:12] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Contains 1 files. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-06-26 16:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:12] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-26 16:23:12] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-26 16:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:12] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-26 16:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:12] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-26 16:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:13] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-26 16:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-26 16:23:13] [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 | 7.96 | 0.48 | 19.30 | |
| count_genes | 12.45 | 0.88 | 12.28 | |
| filter_annot_with_network | 7.85 | 0.22 | 8.06 | |
| functional_annot | 2.47 | 0.23 | 3.02 | |
| graph_from_op | 4.50 | 0.12 | 4.64 | |
| in_omnipath | 3.93 | 0.07 | 4.00 | |
| prioritization_genes | 17.8 | 0.4 | 18.2 | |
| process_annot | 0.88 | 0.05 | 0.92 | |
| random_walk | 18.43 | 0.39 | 18.83 | |
| score_candidate_genes_from_PPI | 18.74 | 0.36 | 19.11 | |
| subgraph_op | 3.56 | 0.06 | 3.64 | |
| weighted_adj | 14.14 | 0.49 | 16.19 | |
| wppi | 36.70 | 0.92 | 37.62 | |
| wppi_data | 8.88 | 0.11 | 8.99 | |
| wppi_go_data | 3.56 | 0.05 | 3.61 | |
| wppi_hpo_data | 0.86 | 0.04 | 0.89 | |
| wppi_omnipath_data | 3.89 | 0.05 | 3.94 | |