Jitao David Zhang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/RpsiXML |
| git_branch: master |
| git_last_commit: 9cb6fba |
| git_last_commit_date: 2022-01-10 10:29:24 -0400 (Mon, 10 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:32 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? 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 1659/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| 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: 2.37.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RpsiXML.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RpsiXML_2.37.1.tar.gz |
| StartedAt: 2022-03-17 20:07:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:09:37 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 121.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RpsiXML.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RpsiXML.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RpsiXML_2.37.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'RpsiXML/DESCRIPTION' ... OK * this is package 'RpsiXML' version '2.37.1' * 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 'RpsiXML' can be installed ... WARNING Found the following significant warnings: Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor See 'D:/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 'D:/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck/00check.log' for details.
RpsiXML.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RpsiXML
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'RpsiXML'
finding HTML links ... done
BIOGRID.PSIMI25 html
availableXrefs-methods html
availableXrefs html
bait html
buildPCHypergraph html
complexName html
complexes html
eListHandler html
getAbstractByPMID html
graphSpeciesConverter html
interactionType html
interactions html
interactorInfo-methods html
interactorInfo html
interactors html
list2Matrix html
null2na html
numInteractions-methods html
parsePsimi25Interaction html
psimi25Attribute-class html
psimi25Complex-class html
psimi25ComplexEntry-class html
psimi25Experiment-class html
psimi25Graph-class html
psimi25Hypergraph-class html
psimi25Hypergraph2GraphNEL html
psimi25Interaction-class html
psimi25InteractionEntry-class html
psimi25Interactor-class html
psimi25Source-class html
psimi25XML2Graph html
separateXMLDataByExpt html
sourceId-methods html
taxId-methods html
translateID-methods html
translateID html
uniprot-methods html
uniprot html
validatePSIMI25 html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MGFR' is missing or broken
done
RpsiXML.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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% ============>
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
15.98 0.75 16.70
RpsiXML.Rcheck/RpsiXML-Ex.timings
| name | user | system | elapsed | |
| availableXrefs | 0.03 | 0.00 | 0.03 | |
| bait | 0.02 | 0.02 | 0.03 | |
| buildPCHypergraph | 0.99 | 0.01 | 1.00 | |
| complexName | 0.90 | 0.05 | 0.97 | |
| complexes | 1.46 | 0.06 | 1.51 | |
| eListHandler | 0 | 0 | 0 | |
| getAbstractByPMID | 0.20 | 0.02 | 1.02 | |
| graphSpeciesConverter | 1.28 | 0.02 | 1.29 | |
| interactionType | 0.03 | 0.00 | 0.03 | |
| interactions | 0.03 | 0.00 | 0.04 | |
| interactorInfo | 0.03 | 0.00 | 0.03 | |
| interactors | 0.85 | 0.07 | 0.92 | |
| null2na | 0 | 0 | 0 | |
| parsePsimi25Interaction | 1.01 | 0.08 | 1.09 | |
| psimi25Complex-class | 0 | 0 | 0 | |
| psimi25ComplexEntry-class | 0 | 0 | 0 | |
| psimi25Experiment-class | 0 | 0 | 0 | |
| psimi25Graph-class | 0 | 0 | 0 | |
| psimi25Hypergraph-class | 0.82 | 0.05 | 0.86 | |
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 | |
| psimi25Interaction-class | 0 | 0 | 0 | |
| psimi25InteractionEntry-class | 0 | 0 | 0 | |
| psimi25Interactor-class | 0 | 0 | 0 | |
| psimi25Source-class | 0 | 0 | 0 | |
| psimi25XML2Graph | 1.04 | 0.05 | 1.10 | |
| separateXMLDataByExpt | 0.17 | 0.03 | 0.20 | |
| translateID | 1.96 | 0.06 | 2.01 | |
| uniprot | 0 | 0 | 0 | |
| validatePSIMI25 | 0 | 0 | 0 | |