Jitao David Zhang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/RpsiXML |
| git_branch: RELEASE_3_13 |
| git_last_commit: 94db0a3 |
| git_last_commit_date: 2021-05-19 11:41:31 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1626/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RpsiXML 2.34.0 (landing page) Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RpsiXML |
| Version: 2.34.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RpsiXML_2.34.0.tar.gz |
| StartedAt: 2021-10-14 11:24:47 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:26:48 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 121.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RpsiXML.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RpsiXML_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RpsiXML.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘2.34.0’ * 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 ... 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 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: OK
RpsiXML.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RpsiXML ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RpsiXML)
RpsiXML.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
>
> 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% ===============>
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62% =========================>
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81% ================================>
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100% ========================================>
Parsing interactions:
.................
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
3% =>
6% ==>
10% ====>
13% =====>
16% ======>
19% ========>
23% =========>
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81% ================================>
84% ==================================>
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94% ======================================>
97% =======================================>
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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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% ==========>
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Parsing interactions:
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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
15.979 0.699 16.666
RpsiXML.Rcheck/RpsiXML-Ex.timings
| name | user | system | elapsed | |
| availableXrefs | 0.043 | 0.004 | 0.048 | |
| bait | 0.026 | 0.004 | 0.030 | |
| buildPCHypergraph | 1.502 | 0.091 | 1.596 | |
| complexName | 0.939 | 0.016 | 0.955 | |
| complexes | 1.074 | 0.060 | 1.134 | |
| eListHandler | 0.006 | 0.000 | 0.007 | |
| getAbstractByPMID | 0.278 | 0.009 | 1.954 | |
| graphSpeciesConverter | 1.543 | 0.052 | 1.596 | |
| interactionType | 0.046 | 0.005 | 0.049 | |
| interactions | 0.041 | 0.008 | 0.049 | |
| interactorInfo | 0.031 | 0.004 | 0.035 | |
| interactors | 1.030 | 0.124 | 1.155 | |
| null2na | 0 | 0 | 0 | |
| parsePsimi25Interaction | 1.211 | 0.040 | 1.252 | |
| psimi25Complex-class | 0.000 | 0.002 | 0.001 | |
| psimi25ComplexEntry-class | 0.000 | 0.001 | 0.001 | |
| psimi25Experiment-class | 0.001 | 0.000 | 0.001 | |
| psimi25Graph-class | 0.000 | 0.001 | 0.001 | |
| psimi25Hypergraph-class | 0.984 | 0.012 | 0.996 | |
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 | |
| psimi25Interaction-class | 0.000 | 0.001 | 0.001 | |
| psimi25InteractionEntry-class | 0.000 | 0.001 | 0.001 | |
| psimi25Interactor-class | 0.000 | 0.001 | 0.001 | |
| psimi25Source-class | 0.000 | 0.000 | 0.001 | |
| psimi25XML2Graph | 1.450 | 0.078 | 1.532 | |
| separateXMLDataByExpt | 0.249 | 0.032 | 0.281 | |
| translateID | 3.602 | 0.564 | 4.165 | |
| uniprot | 0 | 0 | 0 | |
| validatePSIMI25 | 0.039 | 0.010 | 0.050 | |