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 15:06:50 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RpsiXML_2.34.0.tar.gz |
| StartedAt: 2021-10-14 23:23:33 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:26:35 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 182.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RpsiXML.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RpsiXML_2.34.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RpsiXML.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.34.0’
* 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 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 4.877 0.132 5.023
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RpsiXML ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 ** 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-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
>
> 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% ============>
32% =============>
35% ==============>
39% ================>
42% =================>
45% ==================>
48% ===================>
52% =====================>
55% ======================>
58% =======================>
61% ========================>
65% ==========================>
68% ===========================>
71% ============================>
74% ==============================>
77% ===============================>
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% ==============>
39% ================>
42% =================>
45% ==================>
48% ===================>
52% =====================>
55% ======================>
58% =======================>
61% ========================>
65% ==========================>
68% ===========================>
71% ============================>
74% ==============================>
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% ===========>
30% ============>
33% =============>
35% ==============>
38% ===============>
40% ================>
43% =================>
45% ==================>
48% ===================>
50% ====================>
53% =====================>
55% ======================>
58% =======================>
60% ========================>
63% =========================>
65% ==========================>
68% ===========================>
70% ============================>
73% =============================>
75% ==============================>
78% ===============================>
80% ================================>
83% =================================>
86% ==================================>
88% ===================================>
91% ====================================>
93% =====================================>
96% ======================================>
98% =======================================>
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
25.953 0.747 26.856
RpsiXML.Rcheck/RpsiXML-Ex.timings
| name | user | system | elapsed | |
| availableXrefs | 0.078 | 0.005 | 0.084 | |
| bait | 0.045 | 0.004 | 0.049 | |
| buildPCHypergraph | 2.047 | 0.098 | 2.148 | |
| complexName | 1.336 | 0.015 | 1.353 | |
| complexes | 1.583 | 0.057 | 1.641 | |
| eListHandler | 0.007 | 0.001 | 0.009 | |
| getAbstractByPMID | 0.336 | 0.013 | 1.015 | |
| graphSpeciesConverter | 2.230 | 0.061 | 2.301 | |
| interactionType | 0.052 | 0.003 | 0.054 | |
| interactions | 0.057 | 0.005 | 0.062 | |
| interactorInfo | 0.048 | 0.002 | 0.051 | |
| interactors | 1.429 | 0.102 | 1.531 | |
| null2na | 0 | 0 | 0 | |
| parsePsimi25Interaction | 1.747 | 0.022 | 1.769 | |
| psimi25Complex-class | 0.002 | 0.000 | 0.001 | |
| psimi25ComplexEntry-class | 0.001 | 0.000 | 0.001 | |
| psimi25Experiment-class | 0.000 | 0.000 | 0.001 | |
| psimi25Graph-class | 0.001 | 0.000 | 0.002 | |
| psimi25Hypergraph-class | 1.583 | 0.011 | 1.596 | |
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 | |
| psimi25Interaction-class | 0.001 | 0.001 | 0.001 | |
| psimi25InteractionEntry-class | 0.001 | 0.001 | 0.001 | |
| psimi25Interactor-class | 0.000 | 0.000 | 0.001 | |
| psimi25Source-class | 0 | 0 | 0 | |
| psimi25XML2Graph | 1.881 | 0.033 | 1.915 | |
| separateXMLDataByExpt | 0.393 | 0.011 | 0.405 | |
| translateID | 4.877 | 0.132 | 5.023 | |
| uniprot | 0 | 0 | 0 | |
| validatePSIMI25 | 0.073 | 0.017 | 0.098 | |