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 13:20:48 -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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RpsiXML_2.38.0.tar.gz |
| StartedAt: 2022-10-18 21:34:56 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 21:37:06 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 129.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RpsiXML.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RpsiXML_2.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (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 ‘/home/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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/home/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck/00check.log’ for details.
RpsiXML.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RpsiXML ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-pc-linux-gnu (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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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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71% ============================>
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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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58% =======================>
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65% ==========================>
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100% ========================================>
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
16.379 0.681 17.048
RpsiXML.Rcheck/RpsiXML-Ex.timings
| name | user | system | elapsed | |
| availableXrefs | 0.050 | 0.000 | 0.051 | |
| bait | 0.032 | 0.001 | 0.032 | |
| buildPCHypergraph | 1.402 | 0.115 | 1.519 | |
| complexName | 0.949 | 0.004 | 0.953 | |
| complexes | 1.171 | 0.072 | 1.242 | |
| eListHandler | 0.008 | 0.000 | 0.008 | |
| getAbstractByPMID | 0.308 | 0.009 | 1.207 | |
| graphSpeciesConverter | 1.525 | 0.056 | 1.582 | |
| interactionType | 0.059 | 0.000 | 0.058 | |
| interactions | 0.038 | 0.003 | 0.042 | |
| interactorInfo | 0.038 | 0.000 | 0.039 | |
| interactors | 1.085 | 0.120 | 1.205 | |
| null2na | 0.001 | 0.000 | 0.001 | |
| parsePsimi25Interaction | 1.945 | 0.076 | 2.021 | |
| psimi25Complex-class | 0.002 | 0.000 | 0.002 | |
| psimi25ComplexEntry-class | 0.001 | 0.000 | 0.001 | |
| psimi25Experiment-class | 0.001 | 0.000 | 0.001 | |
| psimi25Graph-class | 0.001 | 0.000 | 0.001 | |
| psimi25Hypergraph-class | 1.088 | 0.000 | 1.088 | |
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 | |
| psimi25Interaction-class | 0.002 | 0.000 | 0.002 | |
| psimi25InteractionEntry-class | 0.001 | 0.000 | 0.001 | |
| psimi25Interactor-class | 0.001 | 0.000 | 0.001 | |
| psimi25Source-class | 0.001 | 0.000 | 0.001 | |
| psimi25XML2Graph | 1.373 | 0.088 | 1.461 | |
| separateXMLDataByExpt | 0.244 | 0.004 | 0.248 | |
| translateID | 2.595 | 0.048 | 2.643 | |
| uniprot | 0 | 0 | 0 | |
| validatePSIMI25 | 0.048 | 0.002 | 0.052 | |