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This page was generated on 2022-01-18 11:06:22 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

CHECK results for RpsiXML on nebbiolo1


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.

raw results

Package 1645/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RpsiXML 2.37.1  (landing page)
Jitao David Zhang
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 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 -0500 (Mon, 10 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'annotate' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RpsiXML
Version: 2.37.1
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_2.37.1.tar.gz
StartedAt: 2022-01-17 20:47:23 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 20:49:23 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 119.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RpsiXML.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RpsiXML.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘2.37.1’
* 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 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.



Installation output

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)

Tests output

RpsiXML.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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% ============>
  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 
 15.802   0.821  16.617 

Example timings

RpsiXML.Rcheck/RpsiXML-Ex.timings

nameusersystemelapsed
availableXrefs0.0410.0040.046
bait0.0300.0000.031
buildPCHypergraph1.4260.0911.520
complexName0.8820.0160.898
complexes1.0890.0591.148
eListHandler0.0030.0040.007
getAbstractByPMID0.2470.0080.833
graphSpeciesConverter1.5670.0281.598
interactionType0.0290.0080.036
interactions0.0320.0080.039
interactorInfo0.0330.0040.036
interactors1.0010.1091.111
null2na000
parsePsimi25Interaction1.4320.0341.466
psimi25Complex-class0.0000.0020.002
psimi25ComplexEntry-class0.0000.0010.000
psimi25Experiment-class0.0000.0010.001
psimi25Graph-class0.0000.0010.001
psimi25Hypergraph-class1.1460.0141.162
psimi25Hypergraph2GraphNEL000
psimi25Interaction-class0.0010.0000.001
psimi25InteractionEntry-class0.0000.0010.001
psimi25Interactor-class0.0000.0000.001
psimi25Source-class0.0000.0000.001
psimi25XML2Graph1.4750.0201.495
separateXMLDataByExpt0.2280.0080.236
translateID2.8310.0872.918
uniprot0.0000.0010.000
validatePSIMI250.0340.0150.050