Jitao David Zhang
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/RpsiXML |
| git_branch: RELEASE_3_15 |
| git_last_commit: c2e1b0f |
| git_last_commit_date: 2022-04-26 11:01:44 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:38 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 RpsiXML package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RpsiXML.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 1698/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: RpsiXML |
| Version: 2.38.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RpsiXML_2.38.0.tar.gz |
| StartedAt: 2022-10-19 07:21:37 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 07:25:51 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 254.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RpsiXML.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RpsiXML_2.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.38.0’
* 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 ‘RpsiXML’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck/00install.out’ for details.
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
translateID 6.368 0.074 6.462
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 WARNING
See
‘/Users/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.
RpsiXML.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RpsiXML ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘RpsiXML’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor version 3.16 ** testing if installed package can be loaded from final location Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor version 3.16 ** testing if installed package keeps a record of temporary installation path * DONE (RpsiXML)
RpsiXML.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(RpsiXML)
Loading required package: XML
Warning message:
Package 'RpsiXML' is deprecated and will be removed from Bioconductor
version 3.16
>
> test_check("RpsiXML")
1 Entries found
Parsing entry 1
Parsing experiments: .........
Parsing interactors:
14% ======>
29% ============>
43% =================>
57% =======================>
71% ============================>
86% ==================================>
100% ========================================>
Parsing interactions:
......
1 Entries found
Parsing entry 1
Parsing experiments: ...
Parsing interactors:
14% ======>
29% ============>
43% =================>
57% =======================>
71% ============================>
86% ==================================>
100% ========================================>
Parsing interactions:
.....
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
6% ==>
12% =====>
19% ========>
25% ==========>
31% ============>
38% ===============>
44% ==================>
50% ====================>
56% ======================>
62% =========================>
69% ============================>
75% ==============================>
81% ================================>
88% ===================================>
94% ======================================>
100% ========================================>
Parsing interactions:
.................
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
3% =>
6% ==>
10% ====>
13% =====>
16% ======>
19% ========>
23% =========>
26% ==========>
29% ============>
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65% ==========================>
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81% ================================>
84% ==================================>
87% ===================================>
90% ====================================>
94% ======================================>
97% =======================================>
100% ========================================>
Parsing interactions:
.............................................................................................
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
3% =>
6% ==>
10% ====>
13% =====>
16% ======>
19% ========>
23% =========>
26% ==========>
29% ============>
32% =============>
35% ==============>
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65% ==========================>
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77% ===============================>
81% ================================>
84% ==================================>
87% ===================================>
90% ====================================>
94% ======================================>
97% =======================================>
100% ========================================>
Parsing interactions:
.............................................................................................
1 Entries found
Parsing entry 1
Parsing experiments:
Parsing interactors:
3% =>
5% ==>
8% ===>
10% ====>
13% =====>
15% ======>
18% =======>
20% ========>
23% =========>
25% ==========>
28% ===========>
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Parsing interactions:
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
141 Entries found
Parsing entry 1
Parsing experiments:
Parsing interactors:
50% ====================>
100% ========================================>
Parsing interactions:
.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
34.809 0.765 35.930
RpsiXML.Rcheck/RpsiXML-Ex.timings
| name | user | system | elapsed | |
| availableXrefs | 0.103 | 0.003 | 0.107 | |
| bait | 0.075 | 0.007 | 0.082 | |
| buildPCHypergraph | 3.007 | 0.147 | 3.163 | |
| complexName | 2.318 | 0.025 | 2.347 | |
| complexes | 2.654 | 0.052 | 2.711 | |
| eListHandler | 0.013 | 0.000 | 0.013 | |
| getAbstractByPMID | 0.561 | 0.018 | 1.169 | |
| graphSpeciesConverter | 3.478 | 0.071 | 3.557 | |
| interactionType | 0.079 | 0.002 | 0.080 | |
| interactions | 0.071 | 0.003 | 0.075 | |
| interactorInfo | 0.082 | 0.002 | 0.084 | |
| interactors | 2.476 | 0.081 | 2.559 | |
| null2na | 0 | 0 | 0 | |
| parsePsimi25Interaction | 3.445 | 0.079 | 3.534 | |
| psimi25Complex-class | 0.002 | 0.001 | 0.003 | |
| psimi25ComplexEntry-class | 0.001 | 0.001 | 0.001 | |
| psimi25Experiment-class | 0.000 | 0.000 | 0.001 | |
| psimi25Graph-class | 0.001 | 0.000 | 0.001 | |
| psimi25Hypergraph-class | 2.560 | 0.010 | 2.583 | |
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 | |
| psimi25Interaction-class | 0.001 | 0.001 | 0.002 | |
| psimi25InteractionEntry-class | 0.001 | 0.000 | 0.002 | |
| psimi25Interactor-class | 0.001 | 0.000 | 0.001 | |
| psimi25Source-class | 0.001 | 0.000 | 0.001 | |
| psimi25XML2Graph | 3.325 | 0.020 | 3.369 | |
| separateXMLDataByExpt | 0.603 | 0.008 | 0.614 | |
| translateID | 6.368 | 0.074 | 6.462 | |
| uniprot | 0 | 0 | 0 | |
| validatePSIMI25 | 0.082 | 0.015 | 0.101 | |